| Next changeset 1:58a5249e47cb (2020-12-29) |
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Commit message:
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e" |
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added:
PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.py PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out1.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out2.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out3.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out4.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsvOLD PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out6.tsv PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/test.fasta PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out1.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out2.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out3.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out4.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out5.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out6.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out7.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out8.fasta PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out9.fasta PDAUG_AddClassLabel/PDAUG_AddClassLabel.py PDAUG_AddClassLabel/test-data/new.tsv PDAUG_AddClassLabel/test-data/out.tsv PDAUG_Basic_Plots/PDAUG_Basic_Plots.py PDAUG_Basic_Plots/PDAUG_Basic_Plots.xml PDAUG_Basic_Plots/test-data/positive.fasta PDAUG_Basic_Plots/test-data/test1.tsv PDAUG_Basic_Plots/test-data/test1/report_dir/report.html PDAUG_Basic_Plots/test-data/test1/report_dir/report.html.re PDAUG_Basic_Plots/test-data/test2.tsv PDAUG_Basic_Plots/test-data/test2/report_dir/.re PDAUG_Basic_Plots/test-data/test2/report_dir/report.html PDAUG_Basic_Plots/test-data/test2/report_dir/report.html.re PDAUG_Basic_Plots/test-data/test3/report_dir/report.html PDAUG_Basic_Plots/test-data/test3/report_dir/report.html.re PDAUG_Basic_Plots/test-data/test4/report_dir/report.html.re PDAUG_Basic_Plots/test-data/test5/out.png PDAUG_Basic_Plots/test-data/test5/report_dir/Out.png PDAUG_Basic_Plots/test-data/test5/report_dir/report.html PDAUG_Fishers_Plot/PDAUG_Fishers_Plot.py PDAUG_Fishers_Plot/test-data/negative.fasta PDAUG_Fishers_Plot/test-data/out.png PDAUG_Fishers_Plot/test-data/positive.fasta PDAUG_ML_Models/PDAUG_ML_Models.py PDAUG_ML_Models/test-data/test.tsv PDAUG_ML_Models/test-data/test1/SVMC.tsv PDAUG_ML_Models/test-data/test1/report_dir/SVMC.html PDAUG_ML_Models/test-data/test1/report_dir/SVMC.tsv PDAUG_ML_Models/test-data/test2/.zip PDAUG_ML_Models/test-data/test2/GNBC.tsv PDAUG_ML_Models/test-data/test2/report_dir/GNBC.html PDAUG_ML_Models/test-data/test2/report_dir/GNBC.tsv PDAUG_ML_Models/test-data/test3/SGDC.tsv PDAUG_ML_Models/test-data/test3/report_dir/SGDC.html PDAUG_ML_Models/test-data/test4/DTC.tsv PDAUG_ML_Models/test-data/test4/report_dir/DTC.html PDAUG_ML_Models/test-data/test5/GBC.tsv PDAUG_ML_Models/test-data/test5/report_dir/GBC.html PDAUG_ML_Models/test-data/test6/RFC.tsv PDAUG_ML_Models/test-data/test6/report_dir/RFC.html PDAUG_ML_Models/test-data/test7/LRC.tsv PDAUG_ML_Models/test-data/test7/report_dir/LRC.html PDAUG_ML_Models/test-data/test8/KNC.tsv PDAUG_ML_Models/test-data/test8/report_dir/KNC.html PDAUG_ML_Models/test-data/test9/MLP.tsv PDAUG_ML_Models/test-data/test9/report_dir/MLP.html PDAUG_Merge_Dataframes/PDAUG_Merge_Dataframes.py PDAUG_Merge_Dataframes/test-data/.RData PDAUG_Merge_Dataframes/test-data/.Rhistory PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Blast_baseline_bacteriocin_paper-checkpoint.ipynb PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled-checkpoint.ipynb PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled1-checkpoint.ipynb PDAUG_Merge_Dataframes/test-data/1.tsv PDAUG_Merge_Dataframes/test-data/2.tsv PDAUG_Merge_Dataframes/test-data/3.tsv PDAUG_Merge_Dataframes/test-data/4.tsv PDAUG_Merge_Dataframes/test-data/5.tsv PDAUG_Merge_Dataframes/test-data/6.tsv PDAUG_Merge_Dataframes/test-data/out.tsv PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/0.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/1.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/0.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/1.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/0.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/1.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Halicity.tsv PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF1/0.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF1/1.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF1/1_M.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF2/0.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF2/1.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF2/1_M.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF3/0.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF3/1.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/PDF3/1_M.pdf PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide1_T.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide2_W.csv PDAUG_Peptide_CD_Spectral_Analysis/test-data/calc_meanres_ellipticity.tsv PDAUG_Peptide_CD_Spectral_Analysis/test-data/calc_molar_ellipticity.tsv PDAUG_Peptide_CD_Spectral_Analysis/test-data/helicity.tsv PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py PDAUG_Peptide_Core_Descriptors/test-data/Out.tsv PDAUG_Peptide_Core_Descriptors/test-data/test.fasta PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py PDAUG_Peptide_Core_Functions/test-data/out1.fasta PDAUG_Peptide_Core_Functions/test-data/out2.fasta PDAUG_Peptide_Core_Functions/test-data/out3.fasta PDAUG_Peptide_Core_Functions/test-data/out4.fasta PDAUG_Peptide_Core_Functions/test-data/test1.fasta PDAUG_Peptide_Core_Functions/test-data/test2.fasta PDAUG_Peptide_Core_Functions/test-data/test3.fasta PDAUG_Peptide_Core_Functions/test-data/test4.fasta PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py PDAUG_Peptide_Data_Access/test-data/apd.tsv PDAUG_Peptide_Data_Access/test-data/camp.tsv PDAUG_Peptide_Data_Access/test-data/out.tsv PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py PDAUG_Peptide_Data_Plotting/test-data/out1.png PDAUG_Peptide_Data_Plotting/test-data/out2.png PDAUG_Peptide_Data_Plotting/test-data/out3.png PDAUG_Peptide_Data_Plotting/test-data/out4.png PDAUG_Peptide_Data_Plotting/test-data/test1.tsv PDAUG_Peptide_Data_Plotting/test-data/test2.fasta PDAUG_Peptide_Data_Plotting/test-data/test3.tsv PDAUG_Peptide_Data_Plotting/test-data/test4.fasta PDAUG_Peptide_Global_Descriptors/.tsv PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py PDAUG_Peptide_Global_Descriptors/test-data/out.tsv PDAUG_Peptide_Global_Descriptors/test-data/test.fasta PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py PDAUG_Peptide_Length_Distribution/test-data/out.png PDAUG_Peptide_Length_Distribution/test-data/positive.fasta PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.py PDAUG_Peptide_Ngrams/test-data/out.png PDAUG_Peptide_Ngrams/test-data/test1.fasta PDAUG_Peptide_Ngrams/test-data/test2.fasta PDAUG_Peptide_Sequence_Analysis/PDAUG_Peptide_Sequence_Analysis.py PDAUG_Peptide_Sequence_Analysis/test-data/ACPs.fasta PDAUG_Peptide_Sequence_Analysis/test-data/non_ACPs.fasta PDAUG_Peptide_Sequence_Analysis/test-data/out1.tsv PDAUG_Peptide_Sequence_Analysis/test-data/test1.fasta PDAUG_Peptide_Sequence_Analysis/test-data/test1/out.tsv PDAUG_Peptide_Sequence_Analysis/test-data/test2.fasta PDAUG_Peptide_Sequence_Analysis/test-data/test2/out2.tsv PDAUG_Peptide_Sequence_Analysis/test-data/test3/out3.tsv PDAUG_Peptide_Sequence_Analysis/test-data/test4/report_dir/report.html.re PDAUG_Peptide_Sequence_Analysis/test-data/test5/out5.tsv PDAUG_Peptide_Sequence_Analysis/test-data/test6/out.tsv PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py PDAUG_Peptide_Structure_Builder/test-data/DataFile/GLF.pdb PDAUG_Peptide_Structure_Builder/test-data/test.fasta PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py PDAUG_Sequence_Based_Peptide_Generation/test-data/out1.fasta PDAUG_Sequence_Based_Peptide_Generation/test-data/out2.fasta PDAUG_Sequence_Based_Peptide_Generation/test-data/out3.fasta PDAUG_Sequence_Based_Peptide_Generation/test-data/test1.fasta PDAUG_Sequence_Network/PDAUG_Sequence_Network.py PDAUG_Sequence_Network/test-data/out.png PDAUG_Sequence_Network/test-data/positive.fasta PDAUG_Sequence_Property_Based_Descriptors/Out.tsv PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py PDAUG_Sequence_Property_Based_Descriptors/test-data/Out.tsv PDAUG_Sequence_Property_Based_Descriptors/test-data/Out1.tsv PDAUG_Sequence_Property_Based_Descriptors/test-data/positive.fasta PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py PDAUG_TSVtoFASTA/test-data/test1.tsv PDAUG_TSVtoFASTA/test-data/test1/Negative.fasta PDAUG_TSVtoFASTA/test-data/test1/Positive.fasta PDAUG_TSVtoFASTA/test-data/test2.tsv PDAUG_TSVtoFASTA/test-data/test2/Out.fasta PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py PDAUG_Uversky_Plot/test-data/out.png PDAUG_Uversky_Plot/test-data/test1.fasta PDAUG_Uversky_Plot/test-data/test2.fasta PDAUG_Word_Vector_Descriptor/PDAUG_Word_Vector_Descriptor.py PDAUG_Word_Vector_Descriptor/test-data/Out.tsv PDAUG_Word_Vector_Descriptor/test-data/model.txt PDAUG_Word_Vector_Descriptor/test-data/test.fasta PDAUG_Word_Vector_Model/PDAUG_Word_Vector_Model.py PDAUG_Word_Vector_Model/test-data/model.txt PDAUG_Word_Vector_Model/test-data/test.fasta license.txt readme.txt |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.py Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,154 @@ +from modlamp.descriptors import * +import pandas as pd +import os + + + +def PepFasta(InFile): + file = open(InFile) + lines = file.readlines() + + Index = [] + Peptides = [] + + for line in lines: + if '>' in line: + Index.append(line.strip('\n')) + else: + Peptides.append(line.strip('\n')) + + return Peptides, Index + + +def AutoCorrCal(InFile, window, ScaleName, OutFile): + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, ScaleName) + AMP.calculate_autocorr(int(window)) + df = AMP.descriptor + + columns = ["CroAut_"+str(i) for i in range(len(df[0]))] + df = pd.DataFrame(df, columns=columns) + df.to_csv(OutFile, index=False,sep='\t') + +def CrossCorrCal(InFile, window, ScaleName, OutFile): + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, ScaleName) + AMP.calculate_crosscorr(int(window)) + df = AMP.descriptor + + columns = ["CroCor_"+str(i) for i in range(len(df[0]))] + df = pd.DataFrame(df, columns=columns) + df.to_csv(OutFile, index=False,sep='\t') + +def CalculateMovementCal(InFile, window, angle, modality, ScaleName, OutFile): + + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, ScaleName) + AMP.calculate_moment(int(window), int(angle), modality) + df = AMP.descriptor + + df = pd.DataFrame(df, columns=['Movement']) + df.to_csv(OutFile, index=False,sep='\t') + +def CalculateGlobalCal(InFile, WindowSize, modality, ScaleName, OutFile): + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, ScaleName) + AMP.calculate_global(int(WindowSize), modality) + df = AMP.descriptor + + df = pd.DataFrame(df, columns=['Global']) + df.to_csv(OutFile, index=False, sep='\t') + +def CalculateProfileCal(InFile, prof_type, WindowSize, ScaleName, OutFile): + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, ScaleName) + AMP.calculate_profile(prof_type, int(WindowSize)) + df = AMP.descriptor + + df = pd.DataFrame(df, columns=['hyPhoPro','hyPhoMov']) + df.to_csv(OutFile, index=False, sep='\t') + +def CalculateArcCal(InFile, modality, OutFile): + + list_pep_name,_ = PepFasta(InFile) + + AMP = PeptideDescriptor(list_pep_name, scalename="peparc") + AMP.calculate_arc(modality) + df = AMP.descriptor + + columns = ["Arc_"+str(i) for i in range(len(df[0]))] + df = pd.DataFrame(df, columns=columns) + df.to_csv(OutFile, index=False, sep='\t') + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser(description='Deployment tool') + subparsers = parser.add_subparsers() + + Aut = subparsers.add_parser('AutoCorrCal') + Aut.add_argument("-i","--InFile", required=True, default=None, help="") + Aut.add_argument("-w","--WindowSize", required=False, default=7, help="") + Aut.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="") + Aut.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + Cro = subparsers.add_parser('CrossCorrCal') + Cro.add_argument("-i","--InFile", required=True, default=None, help="") + Cro.add_argument("-w","--WindowSize", required=False, default=7, help="") + Cro.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="") + Cro.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + Mov = subparsers.add_parser('CalculateMovement') + Mov.add_argument("-i","--InFile", required=True, default=None, help="") + Mov.add_argument("-w","--WindowSize", required=False, default=1000, help="") + Mov.add_argument("-a","--Angle", required=False, default=100, help="") + Mov.add_argument("-m","--Modality", required=False, default="max", help="") + Mov.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="") + Mov.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + Glo = subparsers.add_parser('GlobalCal') + Glo.add_argument("-i","--InFile", required="", default="", help="") + Glo.add_argument("-w","--WindowSize", required=False, default=1000, help="") + Glo.add_argument("-m","--Modality", required=False, default="max", help="") + Glo.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="") + Glo.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + Pro = subparsers.add_parser('ProfileCal') + Pro.add_argument("-i","--InFile", required=True, default=None, help="") + Pro.add_argument("-p","--ProfType", required=False, default="text", help="") + Pro.add_argument("-w","--WindowSize", required=False, default=7, help="") + Pro.add_argument("-s","--ScaleName", required=False, default="Eisenberg", help="") + Pro.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + Arc = subparsers.add_parser('ArcCal') + Arc.add_argument("-i","--InFile", required=True, default=None, help="") + Arc.add_argument("-m","--Modality", required=False, default="max", help="") + Arc.add_argument("-o","--OutFile", required=False, default="Descriptor.tsv", help="") + + args = parser.parse_args() + + if sys.argv[1] == 'AutoCorrCal': + AutoCorrCal(args.InFile, args.WindowSize, args.ScaleName, args.OutFile) + elif sys.argv[1] == 'CrossCorrCal': + CrossCorrCal(args.InFile, args.WindowSize, args.ScaleName, args.OutFile) + elif sys.argv[1] == 'CalculateMovement': + CalculateMovementCal(args.InFile, args.WindowSize, args.Angle, args.Modality, args.ScaleName, args.OutFile) + elif sys.argv[1] == 'GlobalCal': + CalculateGlobalCal(args.InFile, args.WindowSize, args.Modality, args.ScaleName, args.OutFile) + elif sys.argv[1] == 'ProfileCal': + CalculateProfileCal(args.InFile, args.ProfType, args.WindowSize, args.ScaleName, args.OutFile) + elif sys.argv[1] == 'ArcCal': + CalculateArcCal(args.InFile, args.Modality, args.OutFile) + else: + print ("You entered Wrong Values: ") \ No newline at end of file |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,139 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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out2.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,139 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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out3.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +Movement +0.2774594853118652 +0.6893304784278844 +0.4942223886681905 +0.4879022569098747 +0.44928748941321683 +0.48806178738858674 +0.4669403105902714 +0.5036883970558701 +0.2154087258482626 +0.23979843502296416 +0.4148659428820385 +0.1336752433612987 +0.42050172623243376 +0.31929548629945326 +0.30940024725427256 +0.21702306187227818 +0.3299344419094044 +0.21076749332479502 +0.6823332724963809 +0.33227495617039615 +0.374280171875485 +0.27694439596355835 +0.19214123548230658 +0.4586310607350617 +0.3589698816442937 +0.3104846462036025 +0.07829845874025636 +0.22946874484220134 +0.431889304227059 +0.18795022241574336 +0.09334995188252893 +0.28651765021427744 +0.3123171568411732 +0.30020346522496427 +0.2306046045936626 +0.30742761594480517 +0.22580297575660496 +0.5160770736050732 +0.42418087568398827 +0.4662320267678134 +0.30510565290499236 +0.5153089915263588 +0.5066586478523495 +0.4348299376955373 +0.6294167809882232 +0.07341767238855738 +0.42048493885819194 +0.05979736465312132 +0.3011279514921717 +0.6697596118193816 +0.697249179019688 +0.32738385361185923 +0.4740530027406926 +0.2722451852258311 +0.377225347089546 +0.2663531832793621 +0.3328298763654114 +0.11146951283410829 +0.3101492391947477 +0.40528228849020076 +0.3007123184344794 +0.37876923909573884 +0.303340210193212 +0.07790563558928469 +0.1268522709352264 +0.05098768578867241 +0.05744793631087191 +0.04257177643688409 +0.01724636454950971 +0.21601775041714222 +0.02259044319726739 +0.41001485302954344 +0.13836717232597007 +0.16432649038670458 +0.15718388681304243 +0.08149375918061791 +0.16302510827881284 +0.3333834963264693 +0.3866785757046207 +0.33171565184196383 +0.33002512021176883 +0.3039772546746435 +0.36382522468683326 +0.21470872654453724 +0.5295796291832363 +0.539270061747465 +0.4415705665227539 +0.15827403805653534 +0.476096626614862 +0.1905601809470215 +0.06471272433607658 +0.10338737520665338 +0.16748789482560633 +0.15336689741837634 +0.4402545159172683 +0.0969067762942479 +0.079697967495238 +0.03889702720030025 +0.09073602009751042 +0.08878762429509186 +0.576351142919988 +0.5626876474168332 +0.5587627844989237 +0.2929055437237022 +0.041928757622971206 +0.03612895077373906 +0.1010583141843274 +0.19580711052239802 +0.09225114957906165 +0.016111803974935734 +0.08811374694676156 +0.18980623621727705 +0.029912035360840795 +0.48935076569394603 +0.7128266034647883 +0.4006561814688358 +0.4271052740293019 +0.10939133470727964 +0.4139307319247934 +0.1231691382233704 +0.0032321159995884778 +0.18851321484398556 +0.06017560056957848 +0.5624413407035735 +0.3690812500176626 +0.7088747699407729 +0.5636335289669467 +0.04743626398192347 +0.17977818302206242 +0.575438682276335 +0.16305715459762246 +0.10431035909837237 +0.10135202807902083 +0.16959375298472332 +0.11347169126959285 +0.10918994422833458 +0.10336817474245052 +0.24920727895691838 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out4.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +Global +0.1475757575757576 +0.3215384615384615 +0.44875 +0.44875 +0.45687500000000003 +0.48624999999999996 +0.4235294117647058 +0.4129411764705882 +-0.10278350515463919 +0.15153846153846157 +-0.296 +-0.14411764705882354 +-0.0019230769230769162 +0.20703703703703702 +0.2162962962962963 +0.28814814814814815 +0.24777777777777776 +0.4795833333333333 +0.35076923076923083 +0.03171428571428572 +-0.035128205128205144 +0.04405405405405406 +-0.1698809523809524 +0.17913043478260865 +0.11269230769230772 +0.28448275862068967 +0.07433333333333328 +-0.6266666666666666 +0.14071428571428576 +-0.43117647058823527 +-0.19765957446808508 +0.4856 +0.5168 +0.3433333333333333 +0.4583333333333333 +0.5745454545454545 +0.3282608695652174 +0.3733333333333333 +0.17192307692307696 +-0.3457142857142857 +0.1076 +0.4675 +0.4675 +-0.16962962962962963 +0.08749999999999998 +-0.3174358974358975 +0.4411111111111112 +-0.050120481927710826 +-0.025555555555555557 +0.24727272727272726 +-0.15142857142857138 +-0.066 +0.07142857142857142 +0.34882352941176475 +0.6842857142857143 +0.6666666666666666 +0.5438095238095239 +0.18681818181818183 +-0.231 +0.5955 +0.35541666666666666 +0.08687500000000001 +0.5977777777777777 +0.15000000000000002 +0.19517241379310335 +0.1663333333333333 +0.33566666666666667 +0.19225806451612903 +0.21999999999999997 +-0.2715662650602409 +0.28916666666666674 +0.2563157894736842 +-0.10543478260869568 +-0.12173913043478261 +-0.15695652173913047 +-0.43962962962962954 +-0.21695652173913044 +0.12199999999999997 +0.38833333333333336 +0.4166666666666667 +0.4054166666666666 +0.4258333333333333 +0.35625 +0.14285714285714288 +0.055333333333333366 +0.07533333333333335 +0.6094117647058823 +-0.21846153846153846 +-0.058333333333333334 +-0.2692857142857143 +0.20566666666666658 +0.00366666666666667 +0.1886206896551724 +0.13266666666666665 +0.24470588235294113 +0.2412903225806451 +0.23933333333333323 +0.264516129032258 +0.27419354838709675 +0.12766666666666668 +0.23583333333333334 +0.12916666666666668 +0.3400000000000001 +-0.16058823529411767 +0.33214285714285713 +0.19161290322580643 +0.0384 +0.12482758620689656 +0.2403125 +0.2882142857142857 +0.24965517241379304 +0.06206896551724138 +0.26321428571428573 +0.37636363636363634 +0.07636363636363636 +-0.034615384615384596 +0.0023076923076923396 +0.026500000000000013 +0.16733333333333336 +0.3899999999999999 +0.2585 +-0.24882352941176467 +-0.053333333333333316 +-0.29405405405405405 +0.23041666666666671 +-0.05090909090909091 +0.2141666666666667 +-0.11818181818181818 +-0.18722222222222226 +0.2615384615384615 +0.03583333333333333 +0.03583333333333331 +0.06166666666666661 +0.31583333333333335 +-0.031666666666666655 +0.3292307692307693 +0.02470588235294122 +-0.005333333333333309 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +hyPhoPro hyPhoMov +0.02715157858015001 -0.35193848479562767 +-0.07581632653061224 0.5953061224489795 +0.052727272727272734 -0.062025974025973984 +0.04883116883116884 -0.03423376623376628 +0.04601731601731602 -0.03612987012987007 +0.08088311688311688 -0.2343376623376623 +0.03348051948051948 0.022285714285714298 +0.03192207792207792 0.033974025974025934 +0.0021599663276681918 -0.22623725342980006 +-0.018112244897959186 0.19642857142857145 +0.05679949874686715 -0.9542255639097741 +0.02180519480519481 -0.241974025974026 +-0.02841568206229861 0.38283888292158974 +-0.01838589981447124 0.439764996907854 +-0.01668274582560297 0.38687569573283864 +-0.03239332096474954 0.719208410636982 +-0.020578849721706864 0.5204502164502165 +-0.03832375055285272 0.958421544056219 +-0.03591836734693877 0.4099999999999999 +0.03777551020408164 -0.5975531315974667 +0.025872326203208548 -0.5578945441813087 +0.02878110599078341 -0.42363594470046084 +-0.010531891255218561 0.2716888717069549 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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsvOLD --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out5.tsvOLD Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +hyPhoPro hyPhoMov +-0.013702404641270547 0.7064878431790197 +0.011176386988407512 0.7188181164692683 +-0.05198602998311481 0.958225299300909 +-0.053837767007292314 0.9662204912145689 +-0.05616965069062795 0.983986112997491 +-0.03902944742005332 0.8444062256781733 +-0.048881292947782075 0.9583602008889918 +-0.03523035187287894 0.8840454410506315 +-0.003617546518307171 0.5479566813670605 +0.028016156772162043 0.07907123740827723 +0.00866973523534085 0.3177509480189954 +-0.015519225514018015 0.694091781811162 +0.04022481558910061 0.004249979051905495 +0.0006666962157398361 0.4741011872601403 +-0.004377350380195698 0.5529088324260703 +0.01381262946263429 0.24931117708632017 +0.0006958428080390826 0.5001936029534315 +0.02144508246949223 0.13332279610071324 +0.03397529507672755 0.5100807184433006 +-0.029884538521139 1.0733153506851596 +-0.01983959429041692 0.8950337931033574 +-0.01982033242168219 0.8777620498117886 +0.002254114186276635 0.2722987349308763 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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out6.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/out6.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +Arc_0 Arc_1 Arc_2 Arc_3 Arc_4 +200 140 20 20 0 +190 130 40 60 0 +200 60 30 20 0 +200 60 30 20 0 +200 30 30 20 0 +200 60 30 20 0 +160 30 30 20 0 +160 60 30 20 0 +60 160 60 40 40 +30 100 40 0 0 +60 60 40 0 20 +50 40 40 0 0 +100 140 40 0 0 +160 60 20 20 0 +160 100 20 20 0 +100 60 20 20 0 +160 60 20 20 0 +220 40 20 0 40 +200 100 70 0 0 +100 140 40 20 20 +80 200 80 20 0 +100 140 40 20 20 +60 220 60 40 0 +100 40 40 20 0 +140 80 20 0 20 +180 60 40 0 0 +60 80 20 20 20 +40 120 40 20 0 +150 90 60 0 0 +60 100 20 0 0 +60 180 60 40 20 +160 60 20 20 20 +160 60 20 20 20 +160 60 40 20 20 +160 60 20 20 20 +260 60 20 20 20 +80 60 20 20 20 +200 60 20 20 0 +120 140 40 20 0 +80 80 40 0 20 +120 60 60 0 0 +200 80 30 20 0 +200 80 30 20 0 +140 120 100 0 20 +180 80 60 0 20 +20 40 40 0 120 +140 40 20 0 20 +120 160 60 40 20 +60 140 60 20 20 +120 140 120 0 0 +200 160 160 0 0 +20 60 20 20 20 +150 90 60 30 0 +60 80 20 0 0 +190 30 20 0 20 +200 20 20 0 20 +200 60 20 0 20 +20 100 20 0 20 +20 140 40 0 0 +180 40 20 0 20 +140 100 60 0 40 +160 120 20 20 20 +200 40 20 0 20 +20 100 20 20 40 +60 100 20 20 20 +40 120 20 20 20 +40 80 20 20 20 +40 120 20 20 20 +40 120 20 20 20 +100 260 60 40 20 +140 120 20 20 40 +120 60 20 20 0 +40 120 40 20 20 +60 120 40 20 20 +40 140 40 20 20 +60 120 40 20 20 +40 120 40 20 20 +120 60 40 0 0 +220 80 60 0 40 +220 80 60 0 40 +220 80 60 0 40 +220 80 40 0 40 +220 80 60 0 20 +160 100 40 20 0 +180 100 80 0 0 +180 100 80 0 0 +200 70 20 0 20 +80 60 60 0 80 +100 100 100 0 20 +40 160 60 20 40 +40 80 20 20 20 +40 100 20 20 40 +60 100 20 40 40 +20 100 20 20 20 +160 60 40 20 0 +80 120 20 20 20 +40 120 20 20 20 +60 80 20 20 20 +60 80 20 20 20 +40 120 20 20 20 +200 80 80 0 0 +200 110 60 0 0 +150 70 70 0 0 +40 60 40 20 20 +60 60 20 20 20 +40 120 20 20 20 +40 100 20 20 40 +80 80 20 20 20 +80 80 20 20 20 +60 80 20 20 20 +40 120 20 20 20 +60 80 20 20 20 +40 80 20 20 20 +230 70 70 0 0 +230 130 130 0 0 +100 200 100 0 0 +100 200 100 0 0 +100 120 20 20 20 +90 50 50 0 0 +70 60 30 30 0 +20 80 0 0 0 +20 100 50 20 20 +40 60 40 0 20 +160 220 100 40 20 +180 100 40 0 20 +120 140 140 0 0 +140 80 80 0 0 +60 100 30 30 40 +20 100 40 20 20 +240 70 40 0 0 +100 60 30 30 0 +130 70 60 20 0 +130 60 60 20 0 +70 70 30 40 0 +60 130 70 0 0 +100 50 20 0 0 +60 90 30 20 0 +50 70 30 0 30 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Descriptor/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| b'@@ -0,0 +1,216 @@\n+from modlamp.sequences import *\n+import argparse, sys\n+import pandas as pd \n+import os\n+\n+def Random_seq(seq_num, lenmin_s, lenmax_s, S_proba, OutFasta):\n+\n+ b = Random(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ b.generate_sequences(proba=float(S_proba))\n+\n+ OutPep = b.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+def Helices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ h = Helices(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ h.generate_sequences()\n+\n+ OutPep = h.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+ \n+def Kinked_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ k = Kinked(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ k.generate_sequences()\n+\n+ OutPep = k.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+\n+def Oblique_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ o = Oblique(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ o.generate_sequences()\n+ o.sequences\n+\n+ OutPep = o.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+\n+def Centrosymmetric_seq(seq_num, lenmin_s, lenmax_s, symmetry_s, OutFasta):\n+\n+ s = Centrosymmetric(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ s.generate_sequences(symmetry=symmetry_s)\n+\n+ OutPep = s.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+\n+def HelicesACP_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ helACP = HelicesACP(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ helACP.generate_sequences()\n+\n+ OutPep = helACP.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+\n+def Hepahelices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ h = Hepahelices(int(seq_num), int(lenmin_s),int(lenmax_s)) \n+ h.generate_sequences()\n+\n+ OutPep = h.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+\n+def AMPngrams_seq(seq_num, lenmin_s, lenmax_s, OutFasta):\n+\n+ s = AMPngrams(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ s.generate_sequences()\n+\n+ OutPep = s.sequences\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+def AmphipathicArc_seq(seq_num, lenmin_s, lenmax_s, gen_seq, hyd_gra, OutFasta):\n+\n+ amphi_hel = AmphipathicArc(int(seq_num), int(lenmin_s),int(lenmax_s))\n+ amphi_hel.generate_sequences(int(gen_seq))\n+ OutFasta = open(OutFasta, \'w\')\n+\n+ if hyd_gra == \'true\':\n+\n+ amphi_hel.make_H_gradient()\n+ OutPep = amphi_hel.sequences\n+ \n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+ elif hyd_gra == \'false\':\n+\n+ OutPep = amphi_hel.sequences\n+ \n+ for i,O in enumerate(OutPep):\n+ OutFasta.write(">sequence_"+str(i)+\'\\n\')\n+ OutFasta.write(O+\'\\n\')\n+\n+if __name__==\'__main__\':\n+\n+ parser = argparse.ArgumentParser(description=\'Deployment tool\')\n+ subparsers = parser.add_subparsers()\n+\n+ Ran = subparsers.add_parser(\'Random\')\n+ Ran.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ Ran.add_argument("-m","--lenmin_s", required=False, default=7, help="")\n+ Ran.add_ar'..b'Obl.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+\n+ Cen = subparsers.add_parser(\'Centrosymmetric\')\n+ Cen.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ Cen.add_argument("-m","--lenmin_s", required=False, default=7, help="")\n+ Cen.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")\n+ Cen.add_argument("-S","--symmetry_s", required=False, default="asymmetric", help="symmetric,asymmetric")\n+ Cen.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+\n+ Hel = subparsers.add_parser(\'HelicesACP\')\n+ Hel.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ Hel.add_argument("-m","--lenmin_s", required=False, default=7, help="")\n+ Hel.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")\n+ Hel.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+\n+ Hep = subparsers.add_parser(\'Hepahelices\')\n+ Hep.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ Hep.add_argument("-m","--lenmin_s", required=False, default=7, help="")\n+ Hep.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")\n+ Hep.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+\n+ AMP = subparsers.add_parser(\'AMPngrams\')\n+ AMP.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ AMP.add_argument("-m","--n_min", required=False, default=3, help="minimum number of ngrams to take for sequence assembly")\n+ AMP.add_argument("-M","--n_max", required=False, default=1, help="maximum number of ngrams to take for sequence assembly")\n+ AMP.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+ \n+ Arc = subparsers.add_parser(\'AmphipathicArc\')\n+ Arc.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")\n+ Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="")\n+ Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")\n+ Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture")\n+ Arc.add_argument("-y","--hyd_gra", default=\'False\', help="Method to mutate the generated sequences to have a hydrophobic gradient by substituting the last third of the sequence amino acids to hydrophobic.")\n+ Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")\n+\n+ args = parser.parse_args()\n+\n+ if sys.argv[1] == \'Random\':\n+ Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta)\n+ elif sys.argv[1] == \'Helices\':\n+ Helices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)\n+ elif sys.argv[1] == \'Kinked\':\n+ Kinked_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)\n+ elif sys.argv[1] == \'Oblique\':\n+ Oblique_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)\n+ elif sys.argv[1] == \'Centrosymmetric\':\n+ Centrosymmetric_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.symmetry_s, args.OutFasta)\n+ elif sys.argv[1] == \'HelicesACP\':\n+ HelicesACP_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)\n+ elif sys.argv[1] == \'Hepahelices\':\n+ Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)\n+ elif sys.argv[1] == \'AMPngrams\':\n+ AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)\n+ elif sys.argv[1] == \'AmphipathicArc\':\n+ AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)\n+ else:\n+ print("You entered Wrong Values: ")\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,6 @@ +sequence_0 +HVLNSPPTMWRCCMDVYCY +sequence_1 +MYHLHEHQKNQKHPKF +sequence_2 +AEAFADKGELKRNQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +AGGKAGKLALKGGRLLAKI +sequence_1 +IIAKGIRGALK +sequence_2 +LVKAGRIL +sequence_3 +AVKGVKIGAKAI +sequence_4 +VGVKIVRIAVRLARA |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out3.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +AIRGGPG +sequence_1 +KGVKVAIRILPLVVRLGRGGA +sequence_2 +KAIPGAVKG +sequence_3 +IGRGIPI +sequence_4 +AIARIAPLIAK |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out4.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +GRGAKVVI +sequence_1 +ALRVLKAAGRLARLAVI +sequence_2 +LIRVGKLAVRALLAIA +sequence_3 +ALIRVLRVAAKIAI +sequence_4 +VIIKGGKLLVRGARAAIVV |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out5.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out5.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +VKIWIKVARVYVRAIKLYLKI +sequence_1 +VKIWIKVAKVWVKAGRVFVRG +sequence_2 +LRVWVRLVRAWARV +sequence_3 +LRGFGRLVRAFARV +sequence_4 +GRAWARGLKVYVKL |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out6.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out6.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +FIGDIAKKAAAVAGKLWC +sequence_1 +GLFDVIKKIAKVLPASFVGL +sequence_2 +VLPQIIGVAAGHMVKIIL +sequence_3 +GLFKIALFVAKHVASTAAGLP +sequence_4 +GLPSTILG |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out7.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out7.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +TARKKITRAL +sequence_1 +GAKLIKTAKKKLSRALR +sequence_2 +GRGLRTIKKKIQRIVK +sequence_3 +AKIAKSAKKRANKLGRSGAK +sequence_4 +IGRILKAARKRLTRVIR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out8.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out8.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +PRP +sequence_1 +KAAGESC +sequence_2 +GKAAGGLG +sequence_3 +GGYYGGG +sequence_4 +CGEIG |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out9.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AA_Property_Based_Peptide_Generation/test-data/Out9.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,10 @@ +sequence_0 +KVIRPIK +sequence_1 +ALFRKLKRWVRSY +sequence_2 +RWYKGYA +sequence_3 +RLLQDVTAFLEHWWK +sequence_4 +NLIKAFDK |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AddClassLabel/PDAUG_AddClassLabel.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AddClassLabel/PDAUG_AddClassLabel.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,17 @@ +import pandas as pd +import argparse + +parser = argparse.ArgumentParser() + +parser.add_argument("-I", "--InFile", required=True, default=None, help="Input data file") +parser.add_argument("-C", "--ClassLabel", required=False, default=0, help="Class Label 0 or 1") +parser.add_argument("-t", "--ClassLabelTitle", required=False, default='Class_label', help="Title to use for class label column (Class_label)") +parser.add_argument("-O", "--OutFile", required=False, default='OutFile.tsv', help="Output file name") + +args = parser.parse_args() + +df1 = pd.read_csv(args.InFile, sep="\t") +df2 = pd.DataFrame([args.ClassLabel]*df1.shape[0], columns=[args.ClassLabelTitle]) + +df = pd.concat([df1, df2], axis=1) +df.to_csv(args.OutFile, sep="\t", index=False) \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AddClassLabel/test-data/new.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AddClassLabel/test-data/new.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,13 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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_AddClassLabel/test-data/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_AddClassLabel/test-data/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,13 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0.0\t8.333\t8.333\t58.333\t66.667\t100.0\t16.667\t16.667\t41.667\t50.0\t91.667\t0.0\t0.0\t0.0\t0.0\t0.0\t0.545\t0.0\t0.0\t0.5\t0.0\t0.5\t8.333\t8.333\t58.333\t66.667\t100.0\t0.0\t0.0\t0.0\t0.0\t0.0\t16.667\t16.667\t41.667\t50.0\t91.667\t0.0\t0.545\t0.0\t0.0\t0.5\t0.5\t0.0\t0.0\t0.0\t0.0\t0.0\t16.667\t16.667\t41.667\t50.0\t91.667\t8.333\t8.333\t58.333\t66.667\t100.0\t0.0\t0.0\t0.545\t0.5\t0.0\t0.5\t16.667\t16.667\t41.667\t50.0\t91.667\t0\t0\t0\t0\t0\t8.333\t8.333\t58.333\t66.667\t100.0\t0.0\t0.545\t0.0\t0.0\t0.5\t0.5\t0.0\t0.0\t0.0\t0.0\t0.0\t16.667\t16.667\t41.667\t50.0\t91.667\t8.333\t8.333\t58.333\t66.667\t100.0\t0.0\t0.0\t0.545\t1.0\t0.0\t0.0\t8.333\t25.0\t50.0\t75.0\t100.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.5\t0.5\t0.0\t16.667\t16.667\t41.667\t50.0\t91.667\t8.333\t8.333\t58.333\t66.667\t100.0\t0\t0\t0\t0\t0\t0.545\t0.0\t0.0\t0\n+0.33299999999999996\t0.667\t0.0\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t0.0\t0.0\t0.0\t0.0\t0.0\t0.5\t0.0\t0.0\t0.33299999999999996\t0.0\t0.667\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t0.0\t0.0\t0.0\t0.0\t0.0\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t0.0\t0.5\t0.0\t0.0\t0.667\t0.33299999999999996\t0.0\t0.0\t0.0\t0.0\t0.0\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t0.0\t0.0\t0.5\t0.667\t0.0\t0.33299999999999996\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t0\t0\t0\t0\t0\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t0.0\t0.5\t0.0\t0.0\t0.667\t0.33299999999999996\t0.0\t0.0\t0.0\t0.0\t0.0\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t0.0\t0.0\t0.5\t1.0\t0.0\t0.0\t11.110999999999999\t22.221999999999998\t44.443999999999996\t66.667\t100.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.667\t0.33299999999999996\t0.0\t22.221999999999998\t22.221999999999998\t44.443999999999996\t55.556000000000004\t88.889\t11.110999999999999\t100.0\t11.110999999999999\t66.667\t100.0\t0\t0\t0\t0\t0\t0.5\t0.0\t0.0\t0\n+0.14300000000000002\t0.7859999999999999\t0.071\t50.0\t57.143\t50.0\t50.0\t57.143\t7.143\t14.286\t42.857\t78.571\t100.0\t28.570999999999998\t28.570999999999998\t28.570999999999998\t28.570999999999998\t28.570999999999998\t0.154\t0.0\t0.154\t0.214\t0.28600000000000003\t0.5\t28.570999999999998\t57.143\t28.570999999999998\t50.0\t57.143\t7.143\t7.143\t78.571\t85.714\t100.0\t14.286\t14.286\t35.714\t64.286\t92.85700000000001\t0.0\t0.308\t0.308\t0.35700000000000004\t0.429\t0.214\t7.143\t7.143\t28.570999999999998\t78.571\t100.0\t14.286\t14.286\t42.857\t64.286\t92.85700000000001\t21.429000000000002\t57.143\t21.429000000000002\t50.0\t57.143\t0.385\t0.077\t0.231\t0.5\t0.0\t0.14300000000000002\t14.286\t14.286\t35.714\t64.286\t92.85700000000001\t0\t0\t0\t0\t0\t50.0\t57.143\t50.0\t50.0\t57.143\t0.0\t0.154\t0.0\t0.35700000000000004\t0.429\t0.214\t7.143\t7.143\t28.570999999999998\t78.571\t100.0\t14.286\t14.286\t42.857\t64.286\t92.85700000000001\t21.429000000000002\t57.143\t21.429000000000002\t50.0\t57.143\t0.385\t0.077\t0.231\t0.35700000000000004\t0.35700000000000004\t0.28600000000000003\t14.286\t14.286\t50.0\t57.143\t92.85700000000001\t21.429000000000002\t21.429000000000002\t35.714\t42.857\t71.429\t7.143\t7.143\t28.570999999999998\t78.571\t100.0\t0.231\t0.231\t0.231\t0.7859999999999999\t0.214\t0.0\t7.143\t14.286\t42.857\t78.571\t100.0\t28.570999999999998\t57.143\t28.570999999999998\t50.0\t57.143\t0\t0\t0\t0\t0\t0.308\t0.0\t0.0\t0\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/PDAUG_Basic_Plots.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/PDAUG_Basic_Plots.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,185 @@ +from wordcloud import WordCloud, STOPWORDS +import matplotlib.pyplot as plt +import glob, os, sys +import pandas as pd +import plotly.express as px +################################### +from wordcloud import WordCloud, STOPWORDS +import matplotlib.pyplot as plt + + +def ReturnPeptide(Infile): + + file = open(Infile) + lines = file.readlines() + + Index = [] + Pep = [] + + for line in lines: + if '>' in line: + line = line.strip('\n') + line = line.strip('\r') + Index.append(line.strip('\n')) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + return Pep, Index + + +def FragReturn(Seq, d): + + tokens = [] + for seq in Seq: + + for l in range(d): + if l < d: + for x in range(int(len(seq)/d)): + s = (x*d)+l + e = s+d + if len(seq[s:e]) == d: + tokens.append(seq[s:e]) + + else: + pass + else: + pass + return tokens + +def PlotWordCloud(TokenList, OutFile): + + comment_words = '' + stopwords = set(STOPWORDS) + comment_words += " ".join(TokenList)+" " + + wordcloud = WordCloud(width = 800, height = 800, + background_color ='white', + stopwords = stopwords, + min_font_size = 10).generate(comment_words) + + plt.figure(figsize = (8, 8), facecolor = None) + plt.imshow(wordcloud) + plt.axis("off") + plt.tight_layout(pad = 0) + plt.savefig(OutFile,dpi=600) + + +def HeatMapPlot(Infile, IndexColumn, x_label, y_label, Workdirpath, htmlOutDir, htmlFname): + + if not os.path.exists(htmlOutDir): + os.makedirs(htmlOutDir) + + df = pd.read_csv(Infile, sep="\t") + y_ticks = list(df[IndexColumn]) + + fig = px.imshow(df[df.columns.tolist()[1:]], labels=dict(x=x_label, y=y_label), y=y_ticks) + fig.update_xaxes(side="top") + + fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) + + +def BoxPlot(InFile, Feature, label, Workdirpath, htmlOutDir, htmlFname): + + Workdirpath = os.path.join(os.getcwd(),'report_dir') + + if not os.path.exists(htmlOutDir): + os.makedirs(htmlOutDir) + + df = pd.read_csv(InFile, sep="\t") + fig = px.box(df, y=Feature, color=label, notched=True, title="Box plot of "+Feature ) + fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) + + +def ScatterPlot(InFile, Feature1, Feature2, Feature3, Label, PlotType, Workdirpath, htmlOutDir, htmlFname): + + Workdirpath = os.path.join(os.getcwd(),'report_dir') + + if not os.path.exists(htmlOutDir): + os.makedirs(htmlOutDir) + + df = pd.read_csv(InFile, sep="\t") + + + if PlotType == "3D": + fig = px.scatter_3d(df, x=Feature1, y=Feature2, z=Feature3, color=Label) + fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) + + elif PlotType == "2D": + fig = px.scatter(df, x=Feature1, y=Feature2, color=Label) + fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname)) + + +def WordCloudPlot(InFile, d, Workdirpath, htmlOutDir, htmlFname): + + Workdirpath = os.path.join(os.getcwd(),'report_dir') + if not os.path.exists(htmlOutDir): + os.makedirs(htmlOutDir) + + Peps,_ = ReturnPeptide(InFile) + Frags = FragReturn(Peps, int(d)) + + PlotWordCloud(Frags, "out.png") + #HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname)) + + +if __name__=="__main__": + + + import argparse + + parser = argparse.ArgumentParser(description='Deployment tool') + subparsers = parser.add_subparsers() + + HM = subparsers.add_parser('HeatMap') + HM.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") + HM.add_argument("-C", "--IndexColumn", required=True, help="") + HM.add_argument("-x", "--x_label", required=True, help="") + HM.add_argument("-y","--y_label", required=True, help="") + HM.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html directory") + HM.add_argument("--htmlFname", required=False, help="HTML out file", default="report.html") + HM.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Path to working directory") + + BP = subparsers.add_parser('BoxPlot') + BP.add_argument("-I", "--InFile", required=True, default=None, help="Input file") + BP.add_argument("-F", "--Feature", required=True, default=None, help="Feature list") + BP.add_argument("-O", "--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="Path to html dir") + BP.add_argument("-Hf", "--htmlFname", required=False, help="HTML out file", default="report.html") + BP.add_argument("-Wp", "--Workdirpath", required=False, default=os.getcwd(), help="Path to Working Directory") + BP.add_argument("-L", "--Label", required=False, default=False, help="Working Directory Path") + + SP = subparsers.add_parser('ScatterPlot') + SP.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") + SP.add_argument("-F1", "--Feature1", required=True, default=True, help="Path to target tsv file") + SP.add_argument("-F2", "--Feature2", required=True, default=True, help="Roatate ticks") + SP.add_argument("-F3", "--Feature3", required=False, help="Roatate ticks") + SP.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir") + SP.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="jai.html") + SP.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path") + SP.add_argument("-T", "--PlotType", required=True, help="") + SP.add_argument("-L","--Label", required=False, default=False, help="Working Directory Path") + + WC = subparsers.add_parser('WordCloud') + WC.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") + WC.add_argument("-D", "--FragSize", required=True, default=None, help="Path to target tsv file") + WC.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir") + WC.add_argument("-Hf","--htmlFname", required=False, help="HTML out file", default="report.html") + WC.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path") + + + args = parser.parse_args() + + if sys.argv[1] == "HeatMap": + HeatMapPlot(args.InFile, args.IndexColumn, args.x_label, args.y_label, args.Workdirpath, args.htmlOutDir, args.htmlFname) + + elif sys.argv[1] == "ScatterPlot": + ScatterPlot(args.InFile, args.Feature1, args.Feature2, args.Feature3, args.Label, args.PlotType, args.Workdirpath, args.htmlOutDir, args.htmlFname) + + elif sys.argv[1] == "BoxPlot": + BoxPlot(args.InFile, args.Feature, args.Label, args.Workdirpath, args.htmlOutDir, args.htmlFname) + + elif sys.argv[1] == "WordCloud": + WordCloudPlot(args.InFile, args.FragSize, args.Workdirpath, args.htmlOutDir, args.htmlFname) + + else: + print("In Correct Option:") |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/PDAUG_Basic_Plots.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/PDAUG_Basic_Plots.xml Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| b'@@ -0,0 +1,248 @@\n+<tool id="pdaug_basic_plots" name="PDAUG Basic Plots" version="0.1.0" python_template_version="3.6">\n+ <description>Basic Plots</description>\n+\n+ <requirements>\n+ <requirement type="package" version="0.25.3">pandas</requirement>\n+ <requirement type="package" version="4.10.0">plotly</requirement> \n+ <requirement type="package" version="1.8.0">wordcloud</requirement>\n+ <requirement type="package" version="3.1.2">matplotlib</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1" level="fatal" />\n+ </stdio>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+\n+ python \'$__tool_directory__/PDAUG_Basic_Plots.py\' \'$SelPlotting.Plot\' \n+\n+ #if $SelPlotting.Plot == \'HeatMap\'\n+ --InFile \'$SelPlotting.InFile\'\n+ --IndexColumn \'$SelPlotting.IndexColumn\'\n+ --x_label \'$SelPlotting.x_label\'\n+ --y_label \'$SelPlotting.y_label\'\n+ #end if \n+\n+ #if $SelPlotting.Plot == \'BoxPlot\'\n+ --InFile \'$SelPlotting.InFile\'\n+ --Feature \'$SelPlotting.Feature\' \n+ --Label \'$SelPlotting.Label\' \n+ #end if \n+\n+ #if $SelPlotting.Plot == \'ScatterPlot\'\n+ --PlotType \'$SelPlotting.PlotType.SelectPlot\'\n+ #if $SelPlotting.PlotType.SelectPlot == \'2D\'\n+ -F1 \'$SelPlotting.PlotType.Features1\'\n+ -F2 \'$SelPlotting.PlotType.Features2\'\n+ #end if\n+\n+ #if $SelPlotting.PlotType.SelectPlot == \'3D\'\n+ -F1 \'$SelPlotting.PlotType.Features1\'\n+ -F2 \'$SelPlotting.PlotType.Features2\'\n+ -F3 \'$SelPlotting.PlotType.Features3\'\n+ #end if\n+\n+ -I \'$SelPlotting.InFile\' \n+ -L \'$SelPlotting.Label\'\n+\n+ #end if \n+\n+ #if $SelPlotting.Plot == \'WordCloud\'\n+ -I \'$SelPlotting.InFile\'\n+ -D \'$SelPlotting.d\'\n+ #end if \n+\n+ --htmlOutDir \'$output.extra_files_path\'\n+ --htmlFname \'$output\'\n+ \n+ ]]></command>\n+\n+ <inputs>\n+\n+ <conditional name=\'SelPlotting\' >\n+\n+ <param name="Plot" type="select" label="Data plotting method" argument="" help="Data plotting method">\n+ <option value="HeatMap">Heat Map</option>\n+ <option value="BoxPlot">Box Plot</option>\n+ <option value="ScatterPlot">Scatter Plot</option>\n+ <option value="WordCloud">Word Cloud</option>\n+ </param>\n+\n+ <when value="HeatMap">\n+ <param name="InFile" type="data" format="tabular" label="Input file" argument= "--InFile" help="Tabular data file"/>\n+ <param name="IndexColumn" type="text" value="Index" label="Index Column" argument= "--IndexColumn" help="Column name that contains index as row/sample names "/>\n+ <param name="x_label" type="text" value="x-axis" label="Label for x-axis" argument= "--x_label" help="A label that describes x axis"/>\n+ <param name="y_label" type="text" value="y-axis" label="Label for y-axis" argument= "--y_label" help="A label that describes y axis"/>\n+ </when>\n+\n+ <when value="BoxPlot">\n+ <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile" help="Tabular data file"/>\n+ <param name="Feature" type="text" value="Feature" label="Feature name" argument= "--Features" help="Name of the feature (column name)"/>\n+ <param name="Label" type="text" value="class label" label="Class label column" argument="--Label" help="Name of the column that contains class label" />\n+ </when>\n+\n+ <when value="ScatterPlot">\n+\n+ <param name="InFile" label="Input file" type="data" format="tabular" argument= "--InFi'..b'"</filter>\n+ </data>\n+\n+ </outputs>\n+ \n+ <tests>\n+\n+ <test>\n+ <param name="Plot" value="HeatMap" />\n+ <param name="InFile" value="test1.tsv"/>\n+ <param name="IndexColumn" value="Algo"/>\n+ <param name="x_label" value="Performance"/>\n+ <param name="y_label" value="Algorithms"/>\n+ <output name="output" file="test1/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>\n+ </test>\n+\n+ <test>\n+ <param name="Plot" value="BoxPlot" />\n+ <param name="InFile" value="test2.tsv"/>\n+ <param name="Feature" value="a1"/>\n+ <param name="Label" value="class"/>\n+ <output name="output" file="test2/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>\n+ </test>\n+\n+ <test>\n+ <param name="Plot" value="ScatterPlot" />\n+ <param name="InFile" value="test2.tsv"/>\n+ <param name="SelectPlot" value="2D" />\n+ <param name="Features1" value="a1"/>\n+ <param name="Features2" value="a2"/>\n+ <param name="Label" value="class"/>\n+ <output name="output" file="test3/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>\n+ </test>\n+\n+ <test>\n+ <param name="Plot" value="ScatterPlot" />\n+ <param name="SelectPlot" value="3D" />\n+ <param name="InFile" value="test2.tsv"/>\n+ <param name="Features1" value="a1"/>\n+ <param name="Features2" value="a2"/>\n+ <param name="Features3" value="a3"/>\n+ <param name="Label" value="class"/>\n+ <output name="output" file="test4/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>\n+\n+ </test>\n+\n+ <test>\n+ <param name="Plot" value="WordCloud" />\n+ <param name="InFile" value="positive.fasta"/>\n+ <param name="d" value="4" />\n+ <output name="output" value="test5/out.png" ftype="png" compare="sim_size" delta="10000" />\n+ </test>\n+\n+ </tests>\n+ \n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+This tool generates four different types of plots. \n+\n+ * **HeatMap** Takes a data frame as input and returns heatmap. \n+ * **BoxPlot** Takes a descriptor data frame as input and returns a box plot based on the class label. \n+ * **ScatterPlot** Takes a descriptor data frame with the class label as input and compares the scatteredness based on 2D or 3D scatter plot. \n+ * **WordCloud** Calculates the ngrams from the peptide data set and plot a word cloud for ngrams to assess frequency of ngrams visually. \n+\n+-----\n+\n+**Inputs**\n+ **1** HeatMap \n+ * **--Infile** Input data frame as a tabular file.\n+ * **--IndexColumn** Number of sequence to be generated. \n+ * **--x_label** Peptide minimum length. \n+ * **--y_label_s** Peptide maximum length. \n+\n+ **2** BoxPlot\n+ * **--Infile** Input data frame as a tabular file. \n+ * **--Feature** Feature(column name) to be assessed. \n+ * **--Label** Class label column name. \n+\n+ **3** ScatterPlot\n+ * **--Infile** Input data frame as a tabular file. \n+ * **--PlotType** 2D or 3D scatter plot. \n+ * **--Feature1** First feature column name. \n+ * **--Feature2** Second feature column name.\n+ * **--Feature3** Third feature column name if 3D scatter plot option selected.\n+ * **--Label** CLass label column name.\n+\n+ **4** WordCloud\n+ * **--Infile** Input fasta file with peptides. \n+ * **--FragSize** ngram size to be calculated.\n+\n+-----\n+\n+**Outputs**\n+ * Return report html file with the respective graph]]></help>\n+\n+<citations>\n+ <citation type="bibtex">\n+\n+\n+ @article{joshi_j_2020,\n+ title = {PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},\n+ publisher = {GitHub}, \n+ journal = {GitHub repository},\n+ url = {https://github.com/jaidevjoshi83/pdaug.git},\n+ author = {Joshi J. and Blankenberg D.},\n+ year = {2020},\n+ }\n+\n+ </citation>\n+\n+</citations>\n+</tool>\n+\n+\n+\n+\n+\n+\n+\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/test-data/positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/test-data/positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/test-data/test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/test-data/test1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,9 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SGDC 0.5 0.35 0.5 0.33399999999999996 0.608 +DTC 0.608 0.7809999999999999 0.608 0.537 0.608 +GBC 0.608 0.7809999999999999 0.608 0.537 0.608 +RFC 0.5 0.25 0.5 0.33299999999999996 0.5 +LRC 0.608 0.7809999999999999 0.608 0.537 0.608 +KNC 0.5 0.25 0.5 0.33299999999999996 0.608 +GNBC 0.608 0.7809999999999999 0.608 0.537 0.608 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/test-data/test1/report_dir/report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/test-data/test1/report_dir/report.html Wed Oct 28 01:52:18 2020 +0000 |
| [ |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/test-data/test5/out.png |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Basic_Plots/test-data/test5/report_dir/report.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Basic_Plots/test-data/test5/report_dir/report.html Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,39 @@ + + + <!DOCTYPE html> + <html lang="en"> + <head> + <title>Bootstrap Example</title> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.4.0/css/bootstrap.min.css"> + <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.0/jquery.min.js"></script> + <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.4.0/js/bootstrap.min.js"></script> + <body> + <style> + div.container_1 { + width:600px; + margin: auto; + padding-right: 10; + } + div.table { + width:600px; + margin: auto; + padding-right: 10; + } + </style> + </head> + <div class="jumbotron text-center"> + <h1> Word Cloud </h1> + </div> + <div class="container"> + <div class="row"> + <div class="col-sm-4"> + <img src="Out.png" alt="Smiley face" height="1000" width="800"> + </div> + + </div> + </div> + </body> + </html> + \ No newline at end of file |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Fishers_Plot/PDAUG_Fishers_Plot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Fishers_Plot/PDAUG_Fishers_Plot.py Wed Oct 28 01:52:18 2020 +0000 |
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| b'@@ -0,0 +1,420 @@\n+import matplotlib\n+matplotlib.use(\'Agg\')\n+import os\n+import sys\n+sys.path.insert(0, os.path.abspath(\'..\'))\n+\n+import quantiprot\n+from quantiprot.utils.io import load_fasta_file\n+from quantiprot.utils.feature import Feature, FeatureSet\n+from quantiprot.metrics.aaindex import get_aa2volume, get_aa2hydropathy\n+from quantiprot.metrics.basic import average\n+\n+from matplotlib import pyplot as plt\n+\n+\n+from math import log10, floor\n+import numpy as np\n+from matplotlib import pyplot as plt\n+from scipy.stats import fisher_exact\n+from quantiprot.utils.sequence import SequenceSet, compact\n+\n+\n+def _count_frame(data, frame_range, num_bins):\n+ """\n+ Count instances in a 2D frame\n+\n+ The function discretizes the feature space into a grid of cells.\n+ Then it counts the number of instances that fall into each cell.\n+ An efficient method for counting instances is used. It performs parallel\n+ logical comparisons of data instances to vectors that hold information on\n+ grid lines.\n+\n+ Args:\n+ data (numpy.matrix): a Nx2 data matrix\n+ frame_range (numpy.matrix): a 2x2 matrix which defines feature ranges\n+ num_bins (list): a pair defining the resolution of the 2D grid\n+ Returns:\n+ cell_counts (numpy.matrix): a matrix holding counts of instances in\n+ each grid cell\n+ bin_ranges (tuple): a pair of numpy matrices holding information on\n+ bin(grid_cell) ranges\n+ """\n+ grid_x = np.linspace(start=frame_range[0, 0], stop=frame_range[1, 0],\\\n+ num=num_bins[0]+1, endpoint=True)\n+ grid_y = np.linspace(start=frame_range[0, 1], stop=frame_range[1, 1],\\\n+ num=num_bins[1]+1, endpoint=True)\n+ # copy because we add ones in the next lines\n+ bin_ranges = (np.copy(grid_x), np.copy(grid_y))\n+\n+\n+ #Count points in each grid cell\n+ grid_x[-1] += 1 # the last cell has to contain data at the border\n+ grid_y[-1] += 1 # the last cell has to contain data at the border\n+\n+ gte_x = np.matrix(data[:, 0] >= grid_x, dtype=\'float64\')\n+ lt_x = np.matrix(data[:, 0] < grid_x, dtype=\'float64\')\n+ gte_y = np.matrix(data[:, 1] >= grid_y, dtype=\'float64\')\n+ lt_y = np.matrix(data[:, 1] < grid_y, dtype=\'float64\')\n+\n+ dif_x = gte_x - lt_x\n+ dif_y = gte_y - lt_y\n+\n+ bins_x = dif_x.argmin(axis=1) - 1\n+ bins_y = dif_y.argmin(axis=1) - 1\n+\n+ coords = np.concatenate((bins_x, bins_y), axis=1)\n+\n+ cell_counts = np.zeros(shape=(len(grid_x)-1, len(grid_y)-1))\n+\n+ for i in range(coords.shape[0]):\n+ cell_counts[coords[i, 0], coords[i, 1]] += 1\n+\n+ return cell_counts, bin_ranges\n+\n+\n+def local_fisher_2d(set1, set2, features=None, \\\n+ windows_per_frame=10, overlap_factor=1, frame_range=None):\n+ """\n+ Compare local and global distribution of samples from two populations\n+ in the 2d feature space using the Fisher\'s exact test.\n+\n+ The function performs the Fisher Exact Test for comparing local and global\n+ ratia of instance counts from two different populations. It uses the\n+ \'_count_frame\' function to discretize the feature space and get instance\n+ counts. Then it scans the 2d feature space with a sliding window and\n+ performs the Fisher Exact test.\n+\n+ Args:\n+ set1 (SequenceSet or numpy.matrix): the first set with at least\n+ 2 sequence features.\n+ set2 (SequenceSet or numpy.matrix): the second set with at least\n+ 2 sequence features.\n+ features (tuple or list): strings with feature names for running\n+ the 2d Fisher test. If None then the first two features are\n+ used. Relevant only if \'set1\' or \'set2\' are SequenceSets.\n+ windows_per_frame (int): ratio between the whole feature space and\n+ the sliding window (default 10).\n+ overlap_factor (int):ratio between the size of a sliding window\n+ and a dis'..b'iewport" content="width=device-width, initial-scale=1">\n+ <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.4.0/css/bootstrap.min.css">\n+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.0/jquery.min.js"></script>\n+ <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.4.0/js/bootstrap.min.js"></script>\n+ <body>\n+ <style>\n+ div.container_1 {\n+ width:600px;\n+ margin: auto;\n+ padding-right: 10; \n+ }\n+ div.table {\n+ width:600px;\n+ margin: auto;\n+ padding-right: 10; \n+ }\n+ </style>\n+ </head>\n+ <div class="jumbotron text-center">\n+ <h1> Fisher\'s Plot </h1>\n+ </div>\n+ <div class="container">\n+ <div class="row">\n+ <div class="col-sm-4">\n+ <img src="1.png" alt="Smiley face" height="800" width="800">\n+ </div>\n+\n+ </div>\n+ </div>\n+ </body>\n+ </html>\n+ """ \n+ out_html.write(part_1)\n+ out_html.close()\n+# Load sets of amyloidogenic and non-amyloidogenic peptides:\n+\n+def run(Fasta1, Fasta2, windows_per_frame, overlap_factor, xlabel, ylabel, pop1_label, pop2_label, htmlOutDir, htmlFname, Workdirpath):\n+\n+ if not os.path.exists(htmlOutDir):\n+ os.makedirs(htmlOutDir)\n+\n+ amyload_pos_seq = load_fasta_file(Fasta1)\n+ amyload_neg_seq = load_fasta_file(Fasta2)\n+\n+ # Calculate quantitive features: volume and hydropathy\n+ mean_volume = Feature(get_aa2volume()).then(average)\n+ mean_hydropathy = Feature(get_aa2hydropathy()).then(average)\n+\n+ fs = FeatureSet("volume\'n\'hydropathy")\n+ fs.add(mean_volume)\n+ fs.add(mean_hydropathy)\n+\n+ amyload_pos_conv_seq = fs(amyload_pos_seq)\n+ amyload_neg_conv_seq = fs(amyload_neg_seq)\n+\n+ # Do local Fisher:\n+ result = local_fisher_2d(amyload_pos_conv_seq, amyload_neg_conv_seq,\n+ windows_per_frame=int(windows_per_frame), overlap_factor=int(overlap_factor))\n+\n+ # Plot local Fisher:\n+ _plot_local_fisher_2d(result, xlabel=xlabel,\n+ ylabel=ylabel,\n+ pop1_label=pop1_label,\n+ pop2_label=pop2_label,\n+ out_file_path =os.path.join(os.getcwd(), "out.png") \n+ )\n+\n+ \n+ # plt.savefig(os.path.join(Workdirpath, htmlOutDir, "1.png"))\n+\n+ HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))\n+\n+if __name__=="__main__":\n+ \n+ \n+ import argparse\n+ \n+ parser = argparse.ArgumentParser()\n+ \n+ parser.add_argument("-f1", "--Fasta1", required=True, default=None, help="First fasta file ") \n+ parser.add_argument("-f2", "--Fasta2", required=True, default=None, help="Second fasta file") \n+ parser.add_argument("-o", "--overlap_factor", required=False, default=5, help="Overlap factor") \n+ parser.add_argument("-w", "--windows_per_frame", required=False, default=5, help="Windows per frame") \n+ parser.add_argument("-x", "--xlabel", required=True, default=None, help="X label") \n+ parser.add_argument("-y", "--ylabel", required=True, default=None, help="Y label") \n+ parser.add_argument("-p1", "--pop1_label", required=True, default=None, help="First population label") \n+ parser.add_argument("-p2", "--pop2_label", required=True, default=None, help="Second population label") \n+ parser.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),\'report_dir\'), help="Path to html dir")\n+ parser.add_argument("--htmlFname", required=False, help="html output file", default="report.html")\n+ parser.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Path to output Working Directory") \n+ args = parser.parse_args()\n+\n+ run(args.Fasta1, args.Fasta2, args.windows_per_frame, args.overlap_factor, args.xlabel, args.ylabel, args.pop1_label, args.pop2_label, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+\n' |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Fishers_Plot/test-data/negative.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Fishers_Plot/test-data/negative.fasta Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 +PGRSRSAADDINPAPANM +>non-ACP250 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP252 +VMGHGLCPQGARAKAAIPAALRDHEST +>non-ACP254 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP256 +VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG +>non-ACP258 +RGGCWPRGLQQLLVPGG +>non-ACP260 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP262 +EQAERYDDMAAAMKAVTEQGHELSNEERNL +>non-ACP264 +MPNDPSDNQLK +>non-ACP266 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP268 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP270 +GHGRLVEIQGRLGVRIER +>non-ACP272 +LPFKLLLFVLLDGWTRLTH +>non-ACP274 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Fishers_Plot/test-data/out.png |
| b |
| Binary file PDAUG_Fishers_Plot/test-data/out.png has changed |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Fishers_Plot/test-data/positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Fishers_Plot/test-data/positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/PDAUG_ML_Models.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/PDAUG_ML_Models.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| b"@@ -0,0 +1,1088 @@\n+\n+import numpy as np\n+import sys,os\n+from scipy import interp\n+import pandas as pd\n+\n+###############################################################\n+from sklearn.metrics import *\n+from sklearn import preprocessing\n+from sklearn.metrics import accuracy_score\n+from sklearn.metrics import precision_recall_fscore_support\n+from sklearn.metrics import roc_curve, auc\n+from sklearn.model_selection import StratifiedKFold\n+from sklearn.preprocessing import StandardScaler\n+from sklearn.preprocessing import MinMaxScaler\n+###############################################################\n+from sklearn.linear_model import LogisticRegression\n+from sklearn.naive_bayes import GaussianNB\n+from sklearn.neighbors import KNeighborsClassifier\n+from sklearn.tree import DecisionTreeClassifier\n+from sklearn.svm import SVC\n+from sklearn.ensemble import RandomForestClassifier\n+from sklearn.linear_model import SGDClassifier\n+from sklearn.ensemble import GradientBoostingClassifier\n+from sklearn.neural_network import MLPClassifier\n+###############################################################\n+from itertools import cycle\n+################################################################\n+from sklearn.model_selection import train_test_split\n+\n+\n+\n+def ReturnData(TrainFile, TestMethod, TestFile=None):\n+ \n+ if (TestFile == None) and (TestMethod == 'Internal' or 'CrossVal'):\n+\n+ df = pd.read_csv(TrainFile, sep='\\t')\n+ clm_list = df.columns.tolist()\n+ X_train = df[clm_list[0:len(clm_list)-1]].values\n+ y_train = df[clm_list[len(clm_list)-1]].values\n+ X_test = None \n+ y_test = None\n+ return X_train, y_train, X_test, y_test\n+\n+ elif (TestFile is not None) and (TestMethod == 'External'):\n+\n+ df = pd.read_csv(TrainFile, sep='\\t')\n+ clm_list = df.columns.tolist()\n+ X_train = df[clm_list[0:len(clm_list)-1]].values\n+ y_train = df[clm_list[len(clm_list)-1]].values\n+ df1 = pd.read_csv(TestFile, sep='\\t')\n+ clm_list = df1.columns.tolist()\n+ X_test = df1[clm_list[0:len(clm_list)-1]].values\n+ y_test = df1[clm_list[len(clm_list)-1]].values\n+ return X_train, y_train, X_test, y_test\n+\n+ elif (TestFile is not None) and (TestMethod == 'Predict'):\n+\n+ df = pd.read_csv(TrainFile, sep='\\t')\n+ clm_list = df.columns.tolist()\n+ X_train = df[clm_list[0:len(clm_list)-1]].values\n+ y_train = df[clm_list[len(clm_list)-1]].values\n+\n+ df = pd.read_csv(TestFile, sep='\\t')\n+ X_test = df\n+ y_test = None\n+ return X_train, y_train, X_train, y_train\n+\n+def Fit_Model(TrainData, Test_Method, Algo, Selected_Sclaer, Workdirpath, htmlOutDir, OutFile, htmlFname, NoOfFolds=None, TestSize=None, TestData=None ):\n+\n+ if not os.path.exists(htmlOutDir):\n+ os.makedirs(htmlOutDir)\n+\n+ if Test_Method == 'Internal':\n+ X,y,_,_ = ReturnData(TrainData, Test_Method)\n+\n+ mean_tpr = 0.0\n+ mean_fpr = np.linspace(0, 1, 100)\n+\n+ specificity_list = []\n+ sensitivity_list = []\n+ precison_list = []\n+ mcc_list = []\n+ f1_list = []\n+ \n+ folds = StratifiedKFold(n_splits=5)\n+ mean_tpr = 0.0\n+ mean_fpr = np.linspace(0, 1, 100)\n+\n+ ##########################\n+ accuracy_score_l = []\n+ cohen_kappa_score_l = []\n+ matthews_corrcoef_l = []\n+ precision_l = []\n+ recall_l = []\n+ f_score_l = []\n+ ##########################\n+\n+ folds = StratifiedKFold(n_splits=5)\n+\n+ for i, (train, test) in enumerate(folds.split(X, y)):\n+\n+ if Selected_Sclaer=='Min_Max':\n+ scaler = MinMaxScaler().fit(X[train])\n+ x_train = scaler.transform(X[train])\n+ x_test = scaler.transform(X[test])\n+\n+ elif Selected_Sclaer=='Standard_Scaler':\n+ scaler = preprocessing.StandardScaler().fit(X[train])\n+ x_train = "..b' args.cache_size, args.verbose, args.max_iter, args.decision_function_shape, args.randomState, args.breakties, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'SGDC\': \n+ SGD_Classifier( args.loss, args.penalty, args.alpha, args.l1_ratio, args.fit_intercept, args.max_iter, args.tol, args.shuffle, args.verbose, args.epsilon, args.n_jobs, args.random_state, args.learning_rate, args.eta0, args.power_t, args.early_stopping, args.validation_fraction, args.n_iter_no_change, args.warm_start, args.average, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'DTC\':\n+ DT_Classifier(args.criterion, args.splitter, args.max_depth, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.random_state, args.max_leaf_nodes, args.min_impurity_decrease, args.min_impurity_split, args.presort, args.ccpalpha, args.max_features, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'GBC\':\n+ GB_Classifier(args.loss, args.learning_rate, args.n_estimators, args.subsample, args.criterion, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.max_depth, args.min_impurity_decrease, args.min_impurity_split, args.init, args.random_state, args.verbose, args.max_leaf_nodes, args.warm_start, args.presort, args.validation_fraction, args.n_iter_no_change, args.tol, args.ccpalpha, args.max_features, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'RFC\':\n+ RF_Classifier( args.n_estimators, args.criterion, args.max_depth, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.max_features, args.max_leaf_nodes, args.min_impurity_decrease, args.min_impurity_split, args.bootstrap, args.oob_score, args.n_jobs, args.random_state, args.verbose, args.warm_start, args.ccp_alpha, args.max_samples, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'LRC\':\n+ LR_Classifier(args.penalty, args.dual, args.tol, args.C, args.fit_intercept, args.intercept_scaling, args.random_state, args.solver, args.max_iter, args.multi_class, args.verbose, args.warm_start, args.n_jobs, args.l1_ratio, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'KNC\':\n+ KN_Classifier(args.n_neighbors, args.weights, args.algorithm, args.leaf_size, args.p, args.metric, args.metric_params, args.n_jobs, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+elif sys.argv[1] == \'GNBC\':\n+ GNB_Classifier( args.var_smoothing, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath) \n+elif sys.argv[1] == \'MLP\' :\n+ MLP_Classifier(args.hidden_layer_sizes, args.activation, args.solver, args.alpha, args.batch_size, args.learning_rate, args.learning_rate_init, args.power_t, args.max_iter, args.shuffle, args.random_state, args.tol, args.verbose, args.warm_start, args.momentum, args.nesterovs_momentum, args.early_stopping, args.validation_fraction, args.beta_1, args.beta_2, args.epsilon, args.n_iter_no_change, args.max_fun, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.Testspt, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)\n+else:\n+ print ("option not correct")\n+ exit()\n+\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test1/SVMC.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test1/SVMC.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Algo accuracy precision recall f1 mean_auc +SVMC 0.999 0.999 0.999 0.999 0.995 |
| b |
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| b |
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| b |
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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test4/DTC.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test4/DTC.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Algo accuracy precision recall f1 mean_auc +DTC 0.997 0.997 0.997 0.997 0.993 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test4/report_dir/DTC.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test4/report_dir/DTC.html Wed Oct 28 01:52:18 2020 +0000 |
| [ |
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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test5/GBC.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test5/GBC.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +Algo accuracy precision recall f1 mean_auc +GBC 0.998 0.998 0.998 0.998 0.995 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test5/report_dir/GBC.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test5/report_dir/GBC.html Wed Oct 28 01:52:18 2020 +0000 |
| [ |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test6/RFC.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test6/RFC.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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| b |
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| b |
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| b |
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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_ML_Models/test-data/test8/KNC.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_ML_Models/test-data/test8/KNC.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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| b |
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| b |
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| b |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/PDAUG_Merge_Dataframes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/PDAUG_Merge_Dataframes.py Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,28 @@ +import glob +import pandas as pd +import sys + +files = sys.argv[1] +out_file = sys.argv[2] + + +data_frame = pd.read_csv(files.split(',')[0],sep='\t') + + +for file in files.split(',')[1:]: + + df1 = pd.read_csv(file,sep='\t') + data_frame = pd.concat([data_frame,df1]) + +final_DF = data_frame.fillna(0) + +final_DF.to_csv(out_file,sep="\t", index=False) + + + + + + + + + |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/.RData |
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| Binary file PDAUG_Merge_Dataframes/test-data/.RData has changed |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/.Rhistory --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/.Rhistory Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,11 @@ +install.pcakges("igraph") +install.packages("igraph") +library(igraph) +library(igraph) +st <- make_star(40) +st +tr <- make_tree(40, children = 3, mode = "undirected") +tr +er <- sample_gnm(n=100, m=40) +er +q() |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Blast_baseline_bacteriocin_paper-checkpoint.ipynb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Blast_baseline_bacteriocin_paper-checkpoint.ipynb Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| b'@@ -0,0 +1,2618 @@\n+{\n+ "cells": [\n+ {\n+ "cell_type": "markdown",\n+ "metadata": {},\n+ "source": [\n+ "## Import libraries"\n+ ]\n+ },\n+ {\n+ "cell_type": "code",\n+ "execution_count": 1,\n+ "metadata": {},\n+ "outputs": [\n+ {\n+ "name": "stderr",\n+ "output_type": "stream",\n+ "text": [\n+ "/home/nafizh/anaconda3/lib/python3.6/site-packages/Bio/SearchIO/__init__.py:211: BiopythonExperimentalWarning: Bio.SearchIO is an experimental submodule which may undergo significant changes prior to its future official release.\\n",\n+ " BiopythonExperimentalWarning)\\n",\n+ "/home/nafizh/anaconda3/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\\n",\n+ " from ._conv import register_converters as _register_converters\\n",\n+ "Using TensorFlow backend.\\n",\n+ "/home/nafizh/anaconda3/lib/python3.6/importlib/_bootstrap.py:205: RuntimeWarning: compiletime version 3.5 of module \'tensorflow.python.framework.fast_tensor_util\' does not match runtime version 3.6\\n",\n+ " return f(*args, **kwds)\\n"\n+ ]\n+ }\n+ ],\n+ "source": [\n+ "import os\\n",\n+ "from Bio import SearchIO\\n",\n+ "from Bio.SearchIO import HmmerIO\\n",\n+ "from Bio import SeqIO\\n",\n+ "%matplotlib inline\\n",\n+ "import matplotlib.pyplot as plt\\n",\n+ "plt.rcParams[\'figure.figsize\'] = (10.0, 7.0)\\n",\n+ "\\n",\n+ "import math\\n",\n+ "import numpy as np\\n",\n+ "#seed = 1337\\n",\n+ "seed = 42\\n",\n+ "np.random.seed(seed)\\n",\n+ "# THEANO_FLAGS=\\"dnn.conv.algo_bwd_filter=deterministic, dnn.conv.algo_bwd_data=deterministic\\"\\n",\n+ "\\n",\n+ "# %matplotlib inline\\n",\n+ "# import matplotlib.pyplot as plt\\n",\n+ "# plt.rcParams[\'figure.figsize\'] = (10.0, 7.0)\\n",\n+ "\\n",\n+ "#import numpy as np\\n",\n+ "#import matplotlib.pyplot as plt\\n",\n+ "import os\\n",\n+ "import pandas as pd\\n",\n+ "from collections import defaultdict\\n",\n+ "from Bio import SeqIO\\n",\n+ "from nltk import bigrams\\n",\n+ "from nltk import trigrams\\n",\n+ "import gensim, logging\\n",\n+ "logging.basicConfig(format=\'%(asctime)s : %(levelname)s : %(message)s\', level=logging.INFO)\\n",\n+ "\\n",\n+ "# import theano\\n",\n+ "# theano.config.device = \'gpu\'\\n",\n+ "# theano.config.floatX = \'float32\'\\n",\n+ "from keras.layers import Dropout\\n",\n+ "from keras.layers import Input, Dense, Lambda, LSTM, RepeatVector, Conv1D, MaxPooling1D, UpSampling1D\\n",\n+ "from keras.models import Model\\n",\n+ "from keras import backend as K\\n",\n+ "from keras import objectives\\n",\n+ "from keras.datasets import mnist\\n",\n+ "from keras import regularizers\\n",\n+ "from keras.layers import GaussianNoise\\n",\n+ "from keras.layers import Activation\\n",\n+ "from keras.callbacks import LearningRateScheduler, EarlyStopping\\n",\n+ "\\n",\n+ "from keras.layers.normalization import BatchNormalization\\n",\n+ "from keras.models import Sequential\\n",\n+ "from keras.layers import Dense\\n",\n+ "from keras.wrappers.scikit_learn import KerasClassifier\\n",\n+ "from keras.utils import np_utils\\n",\n+ "from keras import regularizers\\n",\n+ "#from keras.regularizers import l2, activity_l2, l1, activity_l1\\n",\n+ "from keras.optimizers import Adam, SGD\\n",\n+ "\\n",\n+ "from keras.wrappers.scikit_learn import KerasClassifier\\n",\n+ "from sklearn.decomposition import TruncatedSVD\\n",\n+ "from sklearn.manifold import TSNE\\n",\n+ "from sklearn.preprocessing import normalize\\n",\n+ "from sklearn.utils import shuffle\\n",\n+ "from sklearn.model_selection import train_test_split\\n",\n+ "from sklearn import metrics\\n",\n+ "from sklearn.model_selection import KFold\\n",\n+ "from sklearn.preprocessing import LabelEncoder\\n",\n+ "from sklearn.pipeline import Pipeline\\n",\n+ "from sklearn.metrics import precision_score\\'..b'gwePJjw8HAcHBxMdmZMSUkhISFB7cxrmKTLMLuzwaFDh3jnnXfQ6/Vo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\\n",\n+ "text/plain": [\n+ "<matplotlib.figure.Figure at 0x7f3a60385e48>"\n+ ]\n+ },\n+ "metadata": {},\n+ "output_type": "display_data"\n+ }\n+ ],\n+ "source": [\n+ "cluster_size_dict_list = [value for key, value in cluster_sizes_dict.items()]\\n",\n+ "\\n",\n+ "plt.rc(\'ytick\',labelsize=24)\\n",\n+ "plt.rc(\'xtick\',labelsize=24)\\n",\n+ "\\n",\n+ "_, ax = plt.subplots(1, 1, figsize=(12,9))\\n",\n+ "#fig.set_size_inches(12, 9)\\n",\n+ "ax.spines[\\"top\\"].set_visible(False) \\n",\n+ "ax.spines[\\"right\\"].set_visible(False)\\n",\n+ "ax.hist(cluster_size_dict_list, bins=np.arange(min(cluster_size_dict_list),max(cluster_size_dict_list)), \\n",\n+ " align=\'left\', \\n",\n+ " color=\'r\', edgecolor = \'black\')\\n",\n+ "# plt.title(\\"%i Negative bacteriocin sequences\\\\nLengths %i to %i\\" \\\\\\n",\n+ "# % (len(sizes),min(sizes),max(sizes)))\\n",\n+ "ax.set_ylabel(\'Count\',fontsize = 28)\\n",\n+ "ax.set_xlabel(\'Bacteriocin cluster sizes\',fontsize = 28)\\n",\n+ "plt.xlim(1.0, )\\n",\n+ "plt.tick_params(size = 10)\\n",\n+ "#plt.xlabel(\\"Sequence length\\")\\n",\n+ "#plt.ylabel(\\"Count\\")\\n",\n+ "# ax.figure.savefig(\'bacteriocin_cluster_sizes.eps\', format = \'eps\', dpi = 1200, bbox_inches=\\"tight\\")\\n",\n+ "# ax.figure.savefig(\'bacteriocin_cluster_sizes.png\', format = \'png\', dpi = 1200, bbox_inches=\\"tight\\")\\n",\n+ "# ax.figure.savefig(\'bacteriocin_cluster_sizes.pdf\', format = \'pdf\', dpi = 1200, bbox_inches=\\"tight\\")\\n",\n+ "#plt.show()"\n+ ]\n+ },\n+ {\n+ "cell_type": "code",\n+ "execution_count": null,\n+ "metadata": {\n+ "collapsed": true,\n+ "hidden": true\n+ },\n+ "outputs": [],\n+ "source": []\n+ }\n+ ],\n+ "metadata": {\n+ "kernelspec": {\n+ "display_name": "Python 2",\n+ "language": "python",\n+ "name": "python2"\n+ },\n+ "language_info": {\n+ "codemirror_mode": {\n+ "name": "ipython",\n+ "version": 2\n+ },\n+ "file_extension": ".py",\n+ "mimetype": "text/x-python",\n+ "name": "python",\n+ "nbconvert_exporter": "python",\n+ "pygments_lexer": "ipython2",\n+ "version": "2.7.16"\n+ }\n+ },\n+ "nbformat": 4,\n+ "nbformat_minor": 2\n+}\n' |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled-checkpoint.ipynb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled-checkpoint.ipynb Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,6 @@ +{ + "cells": [], + "metadata": {}, + "nbformat": 4, + "nbformat_minor": 2 +} |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled1-checkpoint.ipynb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/.ipynb_checkpoints/Untitled1-checkpoint.ipynb Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,89 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 42, + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Warning message in read.table(file = file, header = header, sep = sep, quote = quote, :\n", + "“incomplete final line found by readTableHeader on '/Users/joshij/Desktop/GitRepos/Peptide/align/New.csv'”\n" + ] + }, + { + "ename": "ERROR", + "evalue": "Error in data[[rowvar]]: attempt to select less than one element in get1index\n", + "output_type": "error", + "traceback": [ + "Error in data[[rowvar]]: attempt to select less than one element in get1index\nTraceback:\n", + "1. read.csv(\"/Users/joshij/Desktop/GitRepos/Peptide/align/New.csv\", \n . sep = \",\", header = TRUE, row.names = \"index\")", + "2. read.table(file = file, header = header, sep = sep, quote = quote, \n . dec = dec, fill = fill, comment.char = comment.char, ...)" + ] + } + ], + "source": [ + "m <- read.csv(\"/Users/joshij/Desktop/GitRepos/Peptide/align/New.csv\", sep=\",\",header=TRUE, row.names='index')\n", + "\n", + "\n", + "m <- as.matrix(read.table(\"/Users/joshij/Desktop/GitRepos/Peptide/align/New.csv\", sep=\",\", header=TRUE, row.names='index')[, 1:4])" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "metadata": {}, + "outputs": [], + "source": [ + "library(igraph)" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "metadata": {}, + "outputs": [ + { + "ename": "ERROR", + "evalue": "Error in mde(x): 'list' object cannot be coerced to type 'double'\n", + "output_type": "error", + "traceback": [ + "Error in mde(x): 'list' object cannot be coerced to type 'double'\nTraceback:\n", + "1. graph.adjacency(m, mode = \"undirected\", weighted = TRUE)", + "2. graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, \n . diag = diag)", + "3. `mode<-`(`*tmp*`, value = \"double\")" + ] + } + ], + "source": [ + "m <- as.matrix(read.table(\"out_1.csv\", sep=\",\", header=TRUE, row.names='index')[, 1:4])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "R", + "language": "R", + "name": "ir" + }, + "language_info": { + "codemirror_mode": "r", + "file_extension": ".r", + "mimetype": "text/x-r-source", + "name": "R", + "pygments_lexer": "r", + "version": "4.0.0" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/1.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/2.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/3.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/4.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/4.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/5.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/5.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/6.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/6.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,2 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.781 0.608 0.537 0.608 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Merge_Dataframes/test-data/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Merge_Dataframes/test-data/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,7 @@ +Algo accuracy presision recall f1 mean_auc +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 +SVMC 0.608 0.7809999999999999 0.608 0.537 0.608 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,125 @@ +import glob +import pandas as pd +import sys +import os +import argparse + +from modlamp.wetlab import CD + +parser = argparse.ArgumentParser(description='Deployment tool') +subparsers = parser.add_subparsers() + +calc_ellipticity = subparsers.add_parser('calc_ellipticity') +calc_ellipticity.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") +calc_ellipticity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") +calc_ellipticity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") +calc_ellipticity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") +calc_ellipticity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") +calc_ellipticity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") +calc_ellipticity.add_argument("-O","--OutPut", required=False, default="OutFile.tsv", help="Mutated output fasta") + +PlotData = subparsers.add_parser('PlotData') + +PlotData.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") +PlotData.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") +PlotData.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") +PlotData.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") +PlotData.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") +PlotData.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") + +Dichroweb = subparsers.add_parser("Dichroweb") +Dichroweb.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") +Dichroweb.add_argument("-T","--Type", required=True, default=None, help="Input fasta sequence") +Dichroweb.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") +Dichroweb.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") +Dichroweb.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") +Dichroweb.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") + +helicity = subparsers.add_parser('helicity') + +helicity.add_argument("-H","--DirPath", required=False, default=os.getcwd(), help="Input fasta sequence") +helicity.add_argument("-Wn","--WMin", required=True, default=None, help="Number of mutations to perform per sequence") +helicity.add_argument("-Wx","--Wmax", required=True, default=None, help="Probability of mutating a sequence") +helicity.add_argument("-A","--Amide", required=True, default=None, help="Mutated output fasta") +helicity.add_argument("-P","--Pathlen", required=True, default=None, help="Mutated output fasta") +helicity.add_argument("-t","--temperature", required=False, default=24.0, help="") +helicity.add_argument("-k","--k", required=True, default=2.4, help="") +helicity.add_argument("-I","--Induction", required=False, default=True, help="") +helicity.add_argument("-O","--OutPut", required=False, default="result.tsv", help="") + + +args = parser.parse_args() + +if sys.argv[1] == "calc_ellipticity": + + if args.Type == "calc_molar_ellipticity": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_molar_ellipticity() + df = cd.molar_ellipticity + df = pd.DataFrame(df[0]) + df.to_csv(args.OutPut, index=None, sep="\t") + + elif args.Type == "calc_meanres_ellipticity": + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_meanres_ellipticity() + df = cd.meanres_ellipticity + df = pd.DataFrame(df[0]) + df.to_csv(args.OutPut, index=None, sep="\t") + else: + pass + +if sys.argv[1] == "PlotData": + + os.system('ls temp') + + if args.Type == "mean residue ellipticity": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_meanres_ellipticity() + cd.plot(data="mean residue ellipticity", combine='solvent') + + elif args.Type == "molar ellipticity": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_molar_ellipticity() + cd.plot(data="molar ellipticity", combine='solvent') + + elif args.Type == "circular dichroism": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_molar_ellipticity() + cd.plot(data="circular dichroism", combine='solvent') + + else: + pass + +if sys.argv[1] == "Dichroweb": + + if args.Type == "mean residue ellipticity": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_meanres_ellipticity() + cd.dichroweb(data="mean residue ellipticity") + + elif args.Type == "molar ellipticity": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_molar_ellipticity() + cd.dichroweb(data='molar ellipticity') + + elif args.Type == "circular dichroism": + + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_molar_ellipticity() + cd.dichroweb(data='circular dichroism') + + +if sys.argv[1] == "helicity": + cd = CD(args.DirPath, wmin=int(args.WMin), wmax=int(args.Wmax), amide=args.Amide, pathlen=float(args.Pathlen)) + cd.calc_meanres_ellipticity() + cd.helicity(temperature=float(args.temperature), k=float(args.k), induction=args.Induction, filename=args.OutPut ) + + + + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/0.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/0.csv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,82 @@ +V1;V2 +260.0;-24.722610722610725 +259.0;-593.6759906759906 +258.0;-494.1794871794872 +257.0;-410.8368298368298 +256.0;-366.55944055944065 +255.0;-305.7062937062937 +254.0;-344.4428904428905 +253.0;-371.4149184149184 +252.0;-418.3100233100234 +251.0;-551.4032634032635 +250.0;-612.3869463869464 +249.0;-765.030303030303 +248.0;-856.4149184149185 +247.0;-1019.9324009324012 +246.0;-1232.0629370629372 +245.0;-1383.902097902098 +244.0;-1560.699300699301 +243.0;-1878.7482517482517 +242.0;-2123.659673659674 +241.0;-2416.666666666667 +240.0;-2765.850815850816 +239.0;-3228.927738927739 +238.0;-3747.668997668998 +237.0;-4357.342657342658 +236.0;-5233.939393939394 +235.0;-6329.34731934732 +234.0;-7478.508158508159 +233.0;-8770.04662004662 +232.0;-10285.804195804196 +231.0;-11791.282051282053 +230.0;-13279.766899766902 +229.0;-14829.58041958042 +228.0;-16370.06993006993 +227.0;-17743.752913752916 +226.0;-19018.34498834499 +225.0;-20120.629370629373 +224.0;-21116.923076923078 +223.0;-21979.463869463874 +222.0;-22708.71794871795 +221.0;-23354.079254079257 +220.0;-23866.899766899765 +219.0;-24193.9393939394 +218.0;-24557.109557109557 +217.0;-24814.219114219115 +216.0;-25031.934731934733 +215.0;-25349.88344988345 +214.0;-25744.289044289046 +213.0;-26241.25874125874 +212.0;-27040.09324009324 +211.0;-28132.40093240093 +210.0;-29622.610722610723 +209.0;-31212.121212121216 +208.0;-32520.979020979023 +207.0;-33090.90909090909 +206.0;-32665.50116550117 +205.0;-30917.48251748252 +204.0;-27818.88111888112 +203.0;-23414.21911421912 +202.0;-17853.706293706295 +201.0;-11155.547785547786 +200.0;-3263.4265734265737 +199.0;6043.286713286713 +198.0;16231.608391608392 +197.0;26713.752913752916 +196.0;36934.73193473194 +195.0;45956.41025641026 +194.0;53044.28904428904 +193.0;57816.55011655012 +192.0;60107.92540792542 +191.0;60342.89044289045 +190.0;58569.93006993008 +189.0;55043.58974358975 +188.0;50280.18648018648 +187.0;44708.85780885781 +186.0;38994.6386946387 +185.0;33251.04895104895 +184.0;28564.102564102566 +183.0;24424.708624708623 +182.0;21271.655011655017 +181.0;19615.221445221447 +180.0;14085.151515151516 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro1/1.csv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,82 @@ +V1;V2 +260.0;-90.21375291375291 +259.0;-667.4592074592074 +258.0;-484.72261072261074 +257.0;-339.2237762237762 +256.0;-353.31235431235433 +255.0;-291.4895104895105 +254.0;-355.2237762237762 +253.0;-408.4055944055944 +252.0;-472.77855477855485 +251.0;-494.01864801864804 +250.0;-506.941724941725 +249.0;-530.7249417249418 +248.0;-528.5198135198135 +247.0;-523.8764568764569 +246.0;-511.48018648018655 +245.0;-506.4428904428905 +244.0;-534.4009324009324 +243.0;-597.3496503496505 +242.0;-630.2517482517483 +241.0;-736.925407925408 +240.0;-867.7226107226107 +239.0;-1029.7435897435896 +238.0;-1091.3216783216783 +237.0;-1201.6433566433568 +236.0;-1333.927738927739 +235.0;-1441.888111888112 +234.0;-1545.4009324009326 +233.0;-1640.6503496503499 +232.0;-1721.897435897436 +231.0;-1887.7016317016316 +230.0;-1983.3146853146854 +229.0;-2051.6293706293704 +228.0;-2159.3333333333335 +227.0;-2205.988344988345 +226.0;-2288.2750582750587 +225.0;-2267.244755244755 +224.0;-2203.2470862470864 +223.0;-2122.794871794872 +222.0;-1990.3473193473194 +221.0;-1798.857808857809 +220.0;-1688.717948717949 +219.0;-1729.804195804196 +218.0;-1808.3240093240095 +217.0;-1943.20979020979 +216.0;-2030.7156177156178 +215.0;-2042.0442890442891 +214.0;-2144.5174825174827 +213.0;-2333.566433566434 +212.0;-2717.4125874125875 +211.0;-3192.0046620046624 +210.0;-3695.5710955710956 +209.0;-4442.051282051282 +208.0;-5338.368298368299 +207.0;-6389.90675990676 +206.0;-7566.177156177157 +205.0;-8868.181818181818 +204.0;-10290.55944055944 +203.0;-11561.188811188813 +202.0;-12927.97202797203 +201.0;-14257.389277389279 +200.0;-15467.948717948719 +199.0;-16368.20512820513 +198.0;-16791.794871794875 +197.0;-16856.526806526806 +196.0;-16452.167832167834 +195.0;-15712.750582750585 +194.0;-14655.967365967368 +193.0;-13285.431235431235 +192.0;-11749.627039627041 +191.0;-10088.344988344988 +190.0;-8377.785547785548 +189.0;-6856.899766899767 +188.0;-5475.477855477857 +187.0;-4284.3822843822845 +186.0;-3518.5081585081584 +185.0;-2987.552447552448 +184.0;-4163.822843822844 +183.0;-3984.3123543123547 +182.0;-3570.4895104895113 +181.0;-1223.3426573426575 +180.0;16412.727272727276 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/0.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/0.csv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,82 @@ +V1;V2 +260.0;-321.3939393939394 +259.0;-7717.787878787879 +258.0;-6424.333333333333 +257.0;-5340.878787878788 +256.0;-4765.272727272727 +255.0;-3974.181818181818 +254.0;-4477.757575757576 +253.0;-4828.393939393939 +252.0;-5438.030303030303 +251.0;-7168.242424242425 +250.0;-7961.030303030303 +249.0;-9945.39393939394 +248.0;-11133.39393939394 +247.0;-13259.121212121212 +246.0;-16016.818181818182 +245.0;-17990.727272727276 +244.0;-20289.09090909091 +243.0;-24423.727272727272 +242.0;-27607.57575757576 +241.0;-31416.666666666668 +240.0;-35956.06060606061 +239.0;-41976.06060606061 +238.0;-48719.69696969697 +237.0;-56645.454545454544 +236.0;-68041.21212121211 +235.0;-82281.51515151515 +234.0;-97220.60606060606 +233.0;-114010.60606060606 +232.0;-133715.45454545453 +231.0;-153286.6666666667 +230.0;-172636.9696969697 +229.0;-192784.54545454544 +228.0;-212810.9090909091 +227.0;-230668.78787878787 +226.0;-247238.48484848483 +225.0;-261568.18181818182 +224.0;-274520.0 +223.0;-285733.0303030303 +222.0;-295213.3333333333 +221.0;-303603.03030303033 +220.0;-310269.69696969696 +219.0;-314521.21212121216 +218.0;-319242.42424242425 +217.0;-322584.8484848485 +216.0;-325415.1515151515 +215.0;-329548.4848484848 +214.0;-334675.75757575757 +213.0;-341136.36363636365 +212.0;-351521.21212121216 +211.0;-365721.2121212121 +210.0;-385093.9393939394 +209.0;-405757.57575757575 +208.0;-422772.72727272724 +207.0;-430181.8181818182 +206.0;-424651.51515151514 +205.0;-401927.27272727276 +204.0;-361645.45454545453 +203.0;-304384.8484848485 +202.0;-232098.1818181818 +201.0;-145022.12121212122 +200.0;-42424.545454545456 +199.0;78562.72727272726 +198.0;211010.9090909091 +197.0;347278.7878787879 +196.0;480151.51515151514 +195.0;597433.3333333333 +194.0;689575.7575757577 +193.0;751615.1515151515 +192.0;781403.0303030303 +191.0;784457.5757575758 +190.0;761409.0909090909 +189.0;715566.6666666666 +188.0;653642.4242424243 +187.0;581215.1515151515 +186.0;506930.30303030304 +185.0;432263.63636363635 +184.0;371333.3333333333 +183.0;317521.2121212121 +182.0;276531.5151515152 +181.0;254997.8787878788 +180.0;183106.9696969697 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro2/1.csv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,82 @@ +V1;V2 +260.0;-1172.7787878787879 +259.0;-8676.969696969696 +258.0;-6301.39393939394 +257.0;-4409.90909090909 +256.0;-4593.060606060607 +255.0;-3789.3636363636365 +254.0;-4617.909090909091 +253.0;-5309.272727272727 +252.0;-6146.121212121212 +251.0;-6422.242424242425 +250.0;-6590.242424242425 +249.0;-6899.424242424242 +248.0;-6870.757575757575 +247.0;-6810.393939393939 +246.0;-6649.242424242425 +245.0;-6583.757575757576 +244.0;-6947.21212121212 +243.0;-7765.545454545455 +242.0;-8193.272727272728 +241.0;-9580.030303030304 +240.0;-11280.39393939394 +239.0;-13386.666666666666 +238.0;-14187.181818181818 +237.0;-15621.363636363636 +236.0;-17341.060606060604 +235.0;-18744.545454545452 +234.0;-20090.21212121212 +233.0;-21328.454545454548 +232.0;-22384.666666666664 +231.0;-24540.121212121212 +230.0;-25783.09090909091 +229.0;-26671.18181818182 +228.0;-28071.333333333336 +227.0;-28677.848484848488 +226.0;-29747.57575757576 +225.0;-29474.181818181816 +224.0;-28642.212121212124 +223.0;-27596.333333333336 +222.0;-25874.515151515152 +221.0;-23385.151515151516 +220.0;-21953.333333333332 +219.0;-22487.454545454548 +218.0;-23508.21212121212 +217.0;-25261.72727272727 +216.0;-26399.303030303032 +215.0;-26546.57575757576 +214.0;-27878.727272727276 +213.0;-30336.36363636364 +212.0;-35326.36363636363 +211.0;-41496.0606060606 +210.0;-48042.42424242424 +209.0;-57746.666666666664 +208.0;-69398.78787878789 +207.0;-83068.78787878789 +206.0;-98360.30303030302 +205.0;-115286.36363636365 +204.0;-133777.27272727274 +203.0;-150295.45454545453 +202.0;-168063.63636363635 +201.0;-185346.06060606058 +200.0;-201083.33333333334 +199.0;-212786.66666666666 +198.0;-218293.33333333334 +197.0;-219134.84848484848 +196.0;-213878.18181818182 +195.0;-204265.7575757576 +194.0;-190527.57575757577 +193.0;-172710.60606060605 +192.0;-152745.15151515152 +191.0;-131148.48484848483 +190.0;-108911.21212121211 +189.0;-89139.69696969696 +188.0;-71181.21212121213 +187.0;-55696.969696969696 +186.0;-45740.606060606064 +185.0;-38838.181818181816 +184.0;-54129.696969696975 +183.0;-51796.060606060615 +182.0;-46416.36363636364 +181.0;-15903.454545454546 +180.0;213365.45454545456 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/0.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/0.csv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Dichro3/1.csv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Halicity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Halicity.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,3 @@ +Name Solvent Helicity Induction +Peptide1 T 76.06 11.403 +Peptide1 W 6.67 0.0 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide1_T.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide1_T.csv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,85 @@ +Peptide1 +GLFDIVKKVLKLLK +33 +T +260,-0.010606 +259,-0.254687 +258,-0.212003 +257,-0.176249 +256,-0.157254 +255,-0.131148 +254,-0.147766 +253,-0.159337 +252,-0.179455 +251,-0.236552 +250,-0.262714 +249,-0.328198 +248,-0.367402 +247,-0.437551 +246,-0.528555 +245,-0.593694 +244,-0.66954 +243,-0.805983 +242,-0.91105 +241,-1.03675 +240,-1.18655 +239,-1.38521 +238,-1.60775 +237,-1.8693 +236,-2.24536 +235,-2.71529 +234,-3.20828 +233,-3.76235 +232,-4.41261 +231,-5.05846 +230,-5.69702 +229,-6.36189 +228,-7.02276 +227,-7.61207 +226,-8.15887 +225,-8.63175 +224,-9.05916 +223,-9.42919 +222,-9.74204 +221,-10.0189 +220,-10.2389 +219,-10.3792 +218,-10.535 +217,-10.6453 +216,-10.7387 +215,-10.8751 +214,-11.0443 +213,-11.2575 +212,-11.6002 +211,-12.0688 +210,-12.7081 +209,-13.39 +208,-13.9515 +207,-14.196 +206,-14.0135 +205,-13.2636 +204,-11.9343 +203,-10.0447 +202,-7.65924 +201,-4.78573 +200,-1.40001 +199,2.59257 +198,6.96336 +197,11.4602 +196,15.845 +195,19.7153 +194,22.756 +193,24.8033 +192,25.7863 +191,25.8871 +190,25.1265 +189,23.6137 +188,21.5702 +187,19.1801 +186,16.7287 +185,14.2647 +184,12.254 +183,10.4782 +182,9.12554 +181,8.41493 +180,6.04253 \ No newline at end of file |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide2_W.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/Peptide2_W.csv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/calc_meanres_ellipticity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/calc_meanres_ellipticity.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_CD_Spectral_Analysis/test-data/helicity.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_CD_Spectral_Analysis/test-data/helicity.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,7 @@ +Name,Solvent,Helicity,Induction +"Peptide1 +","W +",6.98,0.088 +"Peptide1 +","T +",79.68,0.0 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,43 @@ +from modlamp.core import BaseDescriptor +from modlamp.descriptors import PeptideDescriptor +import pandas as pd +import argparse, os + +parser = argparse.ArgumentParser() + +parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file") +parser.add_argument("-O", "--OutFile", required=True, default=None, help="Output file") +parser.add_argument("-N", "--Ngrams", required=True, default=None, help="ngrams") + +args = parser.parse_args() + +file = open(args.InFile) +lines = file.readlines() + +Index = [] +Pep = [] + + +for line in lines: + if '>' in line: + Index.append(line.strip('\n')) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + +df = pd.DataFrame() + +for i, l in enumerate(Pep): + + D = PeptideDescriptor(l) + D.count_ngrams([int(args.Ngrams)]) + + df1 = pd.DataFrame(D.descriptor, index=["sequence"+str(i),]) + df = pd.concat([df, df1], axis=0) + +df = df.fillna(0) +df.to_csv(args.OutFile, sep='\t', index=None) + + + |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Descriptors/test-data/Out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Descriptors/test-data/Out.tsv Wed Oct 28 01:52:18 2020 +0000 |
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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Descriptors/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Descriptors/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,168 @@ +from modlamp.core import BaseSequence +import pandas as pd +import os, sys +import argparse + + +parser = argparse.ArgumentParser(description='Deployment tool') +subparsers = parser.add_subparsers() + +mutateAA = subparsers.add_parser('mutateAA') +mutateAA.add_argument("-I","--InFile", required=True, default=None, help="Input fasta sequence") +mutateAA.add_argument("-N","--nr", required=True, default=None, help="Number of mutations to perform per sequence") +mutateAA.add_argument("-P","--Prob", required=True, default=None, help="Probability of mutating a sequence") +mutateAA.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Mutated output fasta") + +filterduplicates = subparsers.add_parser('filterduplicates') +filterduplicates.add_argument("-I","--InFile", required=True, default=None, help="Input file") +filterduplicates.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") + + +keepnaturalaa = subparsers.add_parser('keepnaturalaa') +keepnaturalaa.add_argument("-I","--InFile", required=True, default=None, help="Inputt file") +keepnaturalaa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") + + +filteraa = subparsers.add_parser('filteraa') +filteraa.add_argument("-I","--InFile", required=True, default=None, help="Input file") +filteraa.add_argument("-F","--FastOut", required=False, default='Out.fasta', help="Output file") +filteraa.add_argument("-A","--FilterAA", required=True, default=None, help="Filter amino acide") + +args = parser.parse_args() + +if sys.argv[1] == 'mutateAA': + + Pep = [] + Index = [] + + f = open(args.InFile) + lines = f.readlines() + + for line in lines: + if '>' in line: + line = line.strip('\n') + line = line.strip('\r') + Index.append(line) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + + b = BaseSequence(len(Pep)) + b.sequences = Pep + b.mutate_AA(int(args.nr), float(args.Prob)) + OutPep = b.sequences + + OutFasta = open(args.FastOut, 'w') + + for i,O in enumerate(OutPep): + + OutFasta.write(Index[i]+'\n') + OutFasta.write(O+'\n') + + +elif sys.argv[1] == 'filterduplicates': + + Pep = [] + Index = [] + + f = open(args.InFile) + lines = f.readlines() + + for line in lines: + if '>' in line: + line = line.strip('\n') + line = line.strip('\r') + Index.append(line) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + + b = BaseSequence(len(Pep)) + + b.sequences = Pep + + b.filter_duplicates() + + OutPep = b.sequences + + OutFasta = open(args.FastOut, 'w') + + for i,O in enumerate(OutPep): + + OutFasta.write(Index[i]+'\n') + OutFasta.write(O+'\n') + + +elif sys.argv[1] == 'keepnaturalaa': + + Pep = [] + Index = [] + + f = open(args.InFile) + lines = f.readlines() + + for line in lines: + if '>' in line: + line = line.strip('\n') + line = line.strip('\r') + Index.append(line) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + + b = BaseSequence(len(Pep)) + b.sequences = Pep + b.keep_natural_aa() + + OutFasta = open(args.FastOut, 'w') + + OutPep = b.sequences + + for i,O in enumerate(OutPep): + + OutFasta.write(Index[i]+'\n') + OutFasta.write(O+'\n') + + +elif sys.argv[1] == 'filteraa': + + Pep = [] + Index = [] + + f = open(args.InFile) + lines = f.readlines() + + for line in lines: + if '>' in line: + line = line.strip('\n') + line = line.strip('\r') + Index.append(line) + else: + line = line.strip('\n') + line = line.strip('\r') + Pep.append(line) + + + b = BaseSequence(len(Pep)) + b.sequences = Pep + + FilterAA = args.FilterAA.split(',') + + b.filter_aa(FilterAA) + + OutPep = b.sequences + + OutFasta = open(args.FastOut, 'w') + + for i,O in enumerate(OutPep): + + OutFasta.write(Index[i]+'\n') + OutFasta.write(O+'\n') + + + + + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/out1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/out1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACP0 +GFWSKIQEVGKEAAKAAAVAAGKAALGAVSEAV |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/out2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/out2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,6 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP1 +GLWSKIKKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLWSKIKEVGKEAAKKAAGKAALGAVSEAV |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/out3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/out3.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACP0 +GFWSKIQEVGKE |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/out4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/out4.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/test1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/test2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP1 +GLWSKIKKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLWSKIKEVGKEAAKKAAGKAALGAVSEAV +>ACP3 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/test3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/test3.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>ACP0 +GFWSKIQEVGKX +>ACP1 +GFWSKIQEVGKE \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Core_Functions/test-data/test4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Core_Functions/test-data/test4.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,77 @@ +import modlamp +from modlamp.datasets import load_AMPvsTM +from modlamp.datasets import load_AMPvsUniProt +from modlamp.datasets import load_ACPvsTM +from modlamp.datasets import load_ACPvsRandom +from modlamp.database import query_apd +from modlamp.database import query_camp +import os +import pandas as pd + +def DataGen(DataBaseType, OutFile, IDs): + + if DataBaseType == 'AMPvsTM': + data = load_AMPvsTM() + + elif DataBaseType == 'AMPvsUniProt': + data = load_AMPvsUniProt() + + elif DataBaseType == 'ACPvsTM': + data = load_ACPvsTM() + + elif DataBaseType == 'ACPvsRandom': + data = load_ACPvsRandom() + + elif DataBaseType == 'query_apd': + + data = query_apd([int(i) for i in IDs.split(',')]) + df = pd.DataFrame(data, columns=['Peptides']) + df.to_csv(OutFile, index=False, sep='\t') + exit() + + elif DataBaseType == 'query_camp': + data = query_camp([int(i) for i in IDs.split(',')]) + df = pd.DataFrame(data, columns=['Peptides']) + df.to_csv(OutFile, index=False, sep='\t') + exit() + + else: + print ("Enter Correct Values") + exit() + + Target = data.target.tolist() + Target_list = set(Target) + df = data.sequences + + + Target = pd.DataFrame(Target, columns=['Target']) + df = pd.DataFrame(df, columns=['Peptide']) + + df = pd.DataFrame(df) + df = pd.concat([df, Target], axis=1) + + df.to_csv(OutFile, index=False, sep='\t') + + +if __name__=="__main__": + + import argparse + parser = argparse.ArgumentParser() + + parser.add_argument("-d", "--DataBaseType", + required=True, + default=None, + help="Name of the dataset ") + + parser.add_argument("-o", "--OutFile", + required=False, + default='Out.tsv', + help="Out put file name for str descriptors") + + parser.add_argument("-L", "--List", + required=False, + default=None, + help="List of integer as ID") + + args = parser.parse_args() + DataGen(args.DataBaseType, args.OutFile, args.List) |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Access/test-data/apd.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Access/test-data/apd.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Peptides +NLCERASLTWTGNCGNTGHCDTQCRNWESAKHGACHKRGNWKCFCYFDC +VFIDILDKVENAIHNAAQVGIGFAKPFEKLINPK +GNNRPVYIPQPRPPHPRI |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Access/test-data/camp.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Access/test-data/camp.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,5 @@ +Peptides +RFRPPIRRPPIRPPFYPPFRPPIRPPIFPPIRPPFRPPLRFP +ICIFCCGCCHRSKCGMCCKT +FLSLLPSIVSGAVSLAKKLG +FLPIIAKLLGGLL |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Access/test-data/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Access/test-data/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,413 @@\n+Peptide\tTarget\n+AAGAATVLLVIVLLAGSYLAVLA\t0\n+LWIVIACLACVGSAAALTLRA\t0\n+FYRFYMLREGTAVPAVWFSIELIFGLFA\t0\n+GTLELGVDYGRAN\t0\n+KLFWRAVVAEFLATTLFVFISIGSALGFK\t0\n+HGSIGAGVDW\t0\n+ATIYLVCFCFFKQLAMIFMSVLAGNMYE\t0\n+GKLSLAATRSSE\t0\n+TSRLLLAGVALGIICSALMTWAIYF\t0\n+LGFFLVTFGFIWGMMLL\t0\n+YMLFTMIFVISSIIITVVVI\t0\n+ACFSAKVN\t0\n+LIWVAATLAGAIIAVLLVIYA\t0\n+HIPFAFAFAILAYLTLVLFRPVM\t0\n+CGLLVLLTLLLMGAIVTLGVF\t0\n+TGVYILVGVVLWTA\t0\n+LSMFIITPVMVLGTIFIFVMG\t0\n+MTLVALLVIGVSLTGYLGLKA\t0\n+QLYYQVLNFGMIVSSALMIW\t0\n+ALGALCLLLSVGSATACLLLGA\t0\n+LAVIFFFASALLYSQAAT\t0\n+MGHQLLVQLESIAITIVWSGVVAFIGYKLADLT\t0\n+ADILILSLLVIQCALGLLTIPFSA\t0\n+RHQQATFAGFIKGATWVSILSIAVLVFLALAN\t0\n+GTKWWTVGIRPMYKW\t0\n+PAIRVFATYAKWDEK\t0\n+PHVFLLFITFPILFIGWGSQS\t0\n+AGLVLWGAIIFVGWNALLLLFFW\t0\n+TQIVLLGLVTAALWAGLLTLLLLWHW\t0\n+SFIGRVFLFLMIVLPLWCGLHRMHHAMHD\t0\n+MYLGAGIALIPVIMSINYL\t0\n+FQTGFDFSD\t0\n+LISGTLGIICLSLMATLGILL\t0\n+FPFLNNLSFWFTVVGVILVNVSLG\t0\n+LDIYTRLGGMVWR\t0\n+FLIFLLVIMTVITVALLTLLF\t0\n+KDIGILYLFTAGIVGLISVCFTVYMRMELQH\t0\n+PLFYIINILVPCVLISFMINLVFYL\t0\n+HKALKTLGIIMGVFTLCWLPFFLVNIVNVF\t0\n+ANLKKLKTLMSAFLIVLGLLTFGA\t0\n+IWVGIFLLAALLAALFVCLKA\t0\n+KGAAGITGAGFITLAATLS\t0\n+VVLLAIVTLISVVQNGFFAHKV\t0\n+IAIDVLAVLVPLAAFLLDGSPDWSLYCAVWLLKPLRDS\t0\n+ALTVGTLLFLTGIGAASWAIV\t0\n+ITLIIFGVMAGVIGTILLISYGI\t0\n+WVWISLYYVAFYVVMSGIFAL\t0\n+GSNVALHVN\t0\n+GVLELGVDYGRAN\t0\n+IYLLILIILSMLCLVYASVPL\t0\n+LCSFLFVIVLFVATFYTL\t0\n+PLYFIVNVVIPCLLFSFLTGLVFYL\t0\n+ALLIAGGVGLLALAAALVLNA\t0\n+IWTWLRTTL\t0\n+PAHMIAISFFFTNALALALHGALVLSAA\t0\n+GGSLYIVGIFLPIWTFMIYIF\t0\n+GLTLGTGGR\t0\n+STVTGGYAQS\t0\n+DCFLLLVLLLYAPVGFCLLVL\t0\n+FWRAVVAEFLAMILFIFISIGSALG\t0\n+DPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAK\t0\n+LTFTEKWN\t0\n+IRDTLMRLVLTVRSN\t0\n+GKLSLAATRSTE\t0\n+GYNKFVVQYATDA\t0\n+QFHTMLMIAASGAVLIALGILCLVIQMYVSIR\t0\n+LILVLFVVLVSSVGVSLTLYA\t0\n+MASLWADYT\t0\n+DAWSGFVRGYGYDNRTN\t0\n+RWLWDFVNA\t0\n+MFVALLGLGLGQVVCSVALFF\t0\n+NMSTYVDYII\t0\n+IWVKMTFIVVLGLCFVFFWSF\t0\n+SLLISVVLVAYYLYIPLPDAI\t0\n+RKTTINGLIVAVILGVCFTGLQAYEYSHA\t0\n+IPVQLLWVNLVTDGLPATALG\t0\n+LAVIAGGVGFIMVAVLLVLFA\t0\n+MNKRNIMNLILAGGAGLPITTLALGYGAFF\t0\n+IALIVAGLSALGIATALVLNA\t0\n+NGNMWRILDHGAISL\t0\n+VAIICAAVVAVGLIVGLSVGL\t0\n+FSFLIVAGATTLFCLLHFGVI\t0\n+VGISIATIVAIIAAIYYVPW\t0\n+PLFAWSVFITAWLILLSLPVLAGAITMLLMDRNF\t0\n+LILIGAGLGVLALAAGLILTA\t0\n+LGLAAGAIYYYNTSNVFA\t0\n+QLGAGAFGGYQV\t0\n+IAIALLVILVVCSLITMSVIL\t0\n+LAFLIGGIIGGLLLLIGVSCCLW\t0\n+NGHMLRILDHGAISM\t0\n+MALILGIDRFMSECRALTNF\t0\n+AVIAGTTLAITALAVTS\t0\n+LYIVLAILCGVSIAVALALTA\t0\n+AAVTLGVLCLGLLVTVILLILQL\t0\n+LWLVIGVLTAAALAVTLIALA\t0\n+GTLLLLTAIGAASWAIVAVLL\t0\n+LLLVASVIQGLGLLLCFTYICLHFSAL\t0\n+AMIVALIVICITAVVAALV\t0\n+LVFIGTCGAVLAVALGLVLWA\t0\n+TRFGIAAKYQ\t0\n+IPWAVLIVVLITSLIIALIAL\t0\n+LWVVCAVLAGLGLTTALVLYA\t0\n+FAGRVLAGAVMMSGIGIFGLWAGIL\t0\n+LLIVLAGLAVVAVASGLILNA\t0\n+VGSIVGGIYLGFCFNAGAPAVEAFI\t0\n+MLSLGVSYR\t0\n+LTKWFFCCVCTILTMPFF\t0\n+LATIAASAIVLVVAVGLGLMA\t0\n+PIVVTGAVY\t0\n+KPHNLPMVFTGTAILYIGWFGFNAGSA\t0\n+DEFGEQLSKVISLICVAVWL\t0\n+HTLLTGVDF\t0\n+SVELIALLAISCTFFLFMHT\t0\n+LLIALLIYWTLAFITKTIKF\t0\n+FKLVIFVVLGIAIASGLMLYA\t0\n+CTLSISVLLAQTIFLFLIA\t0\n+FVIAGGTLAIPILAFVASFLL\t0\n+LLVITAIVLILSAAVGLVMYA\t0\n+LALATALIGGVAAIASLLLYA\t0\n+NPVIVIINLITLAAALLHTKTWFEL\t0\n+FIVVAGVVILAVTIALLVYFL\t0\n+IGLMCFLSIIITTVCIIMIAT\t0\n+FSVDTQLQS\t0\n+EVYILLNWIGYVNSGFNPLIYCRS\t0\n+LTLAVALIVGVSAIASLLLYA\t0\n+LYLAVVVLIGIGLTTTLVLYA\t0\n+MSTAISVLLAQAVFLLLT\t0\n+ALPGLMNKMEKAGCKRSVV\t0\n+KQFIRYLISSNVGEVVCIFL\t0\n+KYVVSSLVLVYGLIKVLTWIF\t0\n+TGVSPVFAGGVEYA\t0\n+IVIVLGILCFLLLLTVAVLVI\t0\n+KSLGILGILLGVAALCTIVALSVV\t0\n+LCLFVVTPVMVVGTAWIFL\t0\n+LYLAIVVLIGVALTATLMLYA\t0\n+LTILLAIAPVLALAVGLALYG\t0\n+FFVLLLMILILVNLAMTIWIL\t0\n+FIVLIPSVVITVIFLFFWLFM\t0\n+ILVLLILAVITIFALVCVLLV\t0\n+TYFIVLIPSVVITVIFLFFWLFM\t0\n+FLVLFIFLTSFFLNYSHTMVA\t0\n+GDKIGMFFQAMATFFGGFIIGF\t0\n+SNGVIVGTCLAFVAGMIGMAYAA\t0\n+FTFEGAARSDD\t0\n+MNYMVYFNFFACVLVPLLLMLGVYL\t0\n+AGLILLVVTLIGMSVLVRVLI\t0\n+VFLAVYLLGGITFLPLVLFTL\t0\n+LIKISALVFVTVAFFYLG\t0\n+GFFGVATFFFAALGIILIAWSAVL\t0\n+GQWEISVIWGLGVAMAIYLTA\t0\n+LWWIQAMTGFAMFFLGSVHLYIMMT\t0\n+IAVVITVVFLTLLSVVILIFF\t0\n+QVVATATFR\t0\n+MLLCFAFLWVLGIAYYMY\t0\n+IFCIIMLFALLGFL\t0\n+PLCICVAFTCLALVLVTSIVL\t0\n+LIIVLAIVVGVGAAVGLALSA\t0\n+ILVPCVLGLLLLPILAMLMALCV\t0\n+LGLLLAALICVGIATTLVLNA\t0\n+GYAAYYLVRKNFALAMPYLVE\t0\n+LPRTLAVLLVGAALAISGAVMQALF\t0\n+ILLFYVIFYGCLAGIFIGTIQ\t0\n+IMSTLLEVGYDNVKSQ\t0\n+LLAVALIIAMSISLAWQAAG'..b'GCKIKGEC\t1\n+GIFSKLAGKKLKNLLISGLKNVGKEVGMDVVRTGIDIAGCKIKGEC\t1\n+GIFSKLGRKKIKNLLISGLKNVGKEVGMDVVRTGIDIAGCKIKGEC\t1\n+GIFSLIKGAAQLIGKTVAKEAGKTGLELMACKVTKQC\t1\n+GIFTLIKGAAKLIGKTVAKEAGKTGLELMACKITNQC\t1\n+GILDAIKAIAKAAG\t1\n+GILDFAKTVVGGIRNALGI\t1\n+GILSLFTGGIKALGKTLFKMAGKAGAEHLACKATNQC\t1\n+GILSSIKGVAKGVAKNVAAQLLDTLKCKITGC\t1\n+GIMDSVKGLAKNLAGKLLDSLKCKITGC\t1\n+GIMDTIKDTAKTVAVGLLNKLKCKITGC\t1\n+GINTLKKVIQGLHEVIKLVSNHA\t1\n+GINTLKKVIQGLHEVIKLVSNHE\t1\n+GIPCGESCVWIPCISAALGCSCKNKVCYRN\t1\n+GKLQAFLAKMKEIAAQTL\t1\n+GKVWDWIKSAAKKIWSSEPVSQLKGQVLNAAKNYVAEKIGATPT\t1\n+GLADFLNKAVGKVVDFVKS\t1\n+GLFDVVKGVLKGVGKNVAGSLLEQLKCKLSGGC\t1\n+GLFKVLGSVAKHLLPHVAPIIAEKL\t1\n+GLFLDTLKGAAKDVAGKLLEGLKCKIAGCKP\t1\n+GLFLDTLKGLAGKLLQGLKCIKAGCKP\t1\n+GLFSILRGAAKFASKGLGKDLTKLGVDLVACKISKQC\t1\n+GLFSKFNKKKIKSGLFKIIKTAGKEAGLEALRTGIDVIGCKIKGEC\t1\n+GLFSKFNKKKIKSGLIKIIKTAGKEAGLEALRTGIDVIGCKIKGEC\t1\n+GLFSVLGSVAKHLLPHVAPIIAEKL\t1\n+GLFSVLGSVAKHLLPHVVPVIAEKL\t1\n+GLFTLIKGAAKLIGKTVAKEAGKTGLELMACKITNQC\t1\n+GLLDFVTGVGKDIFAQLIKQI\t1\n+GLLDSIKGMAISAGKGALQNLLKVASCKLDKTC\t1\n+GLLDSLKNLAINAAKGAGQSVLNTLSCKLSKTC\t1\n+GLLDTIKGVAKTVAASMLDKLKCKISGC\t1\n+GLLGGLLGPLLGGGGGGGGGLL\t1\n+GLLGPLLKIAAKVGSNLL\t1\n+GLLGSIFGAGKKIACALSGLC\t1\n+GLLGSLFGAGKKVACALSGLC\t1\n+GLLKRIKTLL\t1\n+GLLSGLKKVGKHVAKNVAVSLMDSLKCKISGDC\t1\n+GLLSKVLGVGKKVLCGVSGLC\t1\n+GLLSVLGSVAKHVLPHVVPVIAEHL\t1\n+GLMSSIGKALGGLIVDVLKPKTPAS\t1\n+GLNALKKVFQGIHEAIKLINNHVQ\t1\n+GLNTLKKVFQGLHEAIKLINNHVQ\t1\n+GLWNKIKEAASKAAGKAALGFVNEMV\t1\n+GLWSKIKAAGKEAAKAAAKAAGKAALNAVSEAV\t1\n+GLWSKIKEAAKTAGLMAMGFVNDMV\t1\n+GLWSTIKQKGKEAAIAAAKAAGQAALGAL\t1\n+GPLSCGRNGGVCIPIRCPVPMRQIGTCFGRPVKCCRSW\t1\n+GRLQAFLAKMKEIAAQTL\t1\n+GRPNPVNNKPTPHPRL\t1\n+GRPNPVNTKPTPYPRL\t1\n+GSGRGSCRSQCMRRHEDEPWRVQECVSQCRRRRGGGD\t1\n+GSKKPVPIIYCNRRTGKCQRM\t1\n+GVLDILKNAAKNILAHAAEQI\t1\n+GVVDILKGAGKDLLAHLVGKISEKV\t1\n+GWKDWAKKAGGWLKKKGPGMAKAALKAAMQ\t1\n+GWKDWLKKGKEWLKAKGPGIVKAALQAATQ\t1\n+GWKDWLNKGKEWLKKKGPGIMKAALKAATQ\t1\n+HGVSGHGQHGVHG\t1\n+IFGAILPLALGALKNLIK\t1\n+IIEKLVNTALGLLSGL\t1\n+IIGHLIKTALGMLGL\t1\n+ILGTILGLLKGL\t1\n+ILGTILGLLKSL\t1\n+ILPLVGNLLNDLL\t1\n+ILQKAVLDCLKAAGSSLSKAAITAIYNKIT\t1\n+INWKKIAEIGKQVLSAL\t1\n+INWKKIAEVGGKILSSL\t1\n+INWLKLGKAIIDAL\t1\n+IPRPLDPCIAQNGRCFTGICRYPYFWIGTCRNGKSCCRRR\t1\n+IWLTALKFLGKHAAKHLAKQQLSKL\t1\n+KDRPKKPGLCPPRPQKPCVKECKNDDSCPGQQKCCNYGCKDECRDPIFVG\t1\n+KTCEHLADTYRGVCFTNASCDDHCKNKAHLISGTCHNWKCFCTQNC\t1\n+KTCENLADTY\t1\n+KTCENLSGTFKGPCIPDGNCNKHCRNNEHLLSGRCRDDFRCWCTNRC\t1\n+KTCMTKKEGWGRCLIDTTCAHSCRKYGYMGGKCQGITRRCYCLLNC\t1\n+KWCFRVCYRGICYRKCR\t1\n+KWCFRVCYRGICYRRCR\t1\n+KYYGNGVSCNKKGCSVDWGKAIGIIGNNSAANLATGGAAGWSK\t1\n+LCNERPSQTWSGNCGNTAHCDKQCQDWEKASHGACHKRENHWKCFCYFNC\t1\n+LFCRKGTCHFGGCPAHLVKVGSCFGFRACCKWPWDV\t1\n+LLGRCKVKSNRFHGPCLTDTHCSTVCRGEGYKGGDCHGLRRRCMCLC\t1\n+LLGRCKVKSNRFNGPCLTDTHCSTVCRGEGYKGGDCHGLRRRCMCLC\t1\n+LLKELWTKIKGAGKAVLGKIKGLL\t1\n+LLKELWTKMKGAGKAVLGKIKGLL\t1\n+LLPILGNLLNGLL\t1\n+LLPNLLKSLL\t1\n+LMCTHPLDCSN\t1\n+LNLKGIFKKVASLLT\t1\n+LPVNEAQCRQVGGYCGLRICNFPSRFLGLCTRNHPCCSRVWV\t1\n+MSWLNFLKYIAKYGKKAVSAAWKYKGKVLEWLNVGPTLEWVWQKLKKIAGL\t1\n+QDKCKKVYENYPVSKCQLANQCNYDCKLDKHARSGECFYDEKRNLQCICDYCEY\t1\n+QGVRNHVTCRIYGGFCVPIRCPGRTRQIGTCFGRPVKCCRRW\t1\n+QKLCERPSGTWSGVCGNNNACKNQCINLEKARHGSCNYVFPAHKCICYFPC\t1\n+QQCGRQASGRLCGNRLCCSQWGYCGSTASYCGAGCQSQCRS\t1\n+QRFIHPTYRPPPQPRRPVIMRA\t1\n+RQRVEELSKFSKKGAAARRRK\t1\n+RSGRGECRRQCLRRHEGQPWETQECMRRCRRRG\t1\n+RSVCRQIKICRRRGGCYYKCTNRPY\t1\n+SAPRGCWTKSYPPKPCK\t1\n+SCTTCVCTCSCCTT\t1\n+SFGLCRLRRGFCARGRCRFPSIPIGRCSRFVQCCRRVW\t1\n+SGISGPLSCGRNGGVCIPIRCPVPMRQIGTCFGRPVKCCRSW\t1\n+SIVPIRCRSNRDCRRFCGFRGGRCTYARQCLCGY\t1\n+SKGKKANKDVELARG\t1\n+SMLSVLKNLGKVGLGFVACKINKQC\t1\n+TSYGNGVHCNKSKCWIDVSELETYKAGTVSNPKDILW\t1\n+VDKGSYLPRPTPPRPIYNRN\t1\n+VDKPDYRPRPRPPNM\t1\n+VDKPDYRPRPWPRNMI\t1\n+VDKPDYRPRPWPRPN\t1\n+VDKPDYRPRPWPRPNM\t1\n+VLPIIGNLLNSLL\t1\n+VLPLISMALGKLL\t1\n+VNPIILGVLPKFVCLITKKC\t1\n+VRNFVTCRINRGFCVPIRCPGHRRQIGTCLGPQIKCCR\t1\n+VRNHVTCRINRGFCVPIRCPGRTRQIGTCFGPRIKCCRSW\t1\n+VTCDLLSFEAKGFAANHSLCAAHCLAIGRRGGSCERGVCICRR\t1\n+VTCDLLSIKGVAEHSACAANCLSMGKAGGRCENGICLCRKTTFKELWDKRF\t1\n+VTCFCKRPVCDSGETQIGYCRLGNTFYRLCCRQ\t1\n+WLGSALKIGAKLLPSVVGLFKKKKQ\t1\n+WNPFKELERAGQRVRDAIISAGPAVATVGQAAAIARG\t1\n+WNPFKELERAGQRVRDAVISAAPAVATVGQAAAIARG\t1\n+YDLSKNCRLRGGICYIGKCPRRFFRSGSCSRGNVCCLRFG\t1\n+YSKSLPLSVLNP\t1\n+YVSCLFRGARCRVYSGRSCCFGYYCRRDFPGSIFGTCSRRNF\t1\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,115 @@ +from modlamp.plot import helical_wheel +from modlamp.plot import plot_pde +from modlamp.plot import plot_violin +from modlamp.plot import plot_aa_distr +import pandas as pd +import argparse +import sys, os + + + +parser = argparse.ArgumentParser(description='Deployment tool') +subparsers = parser.add_subparsers() + +HelWhl = subparsers.add_parser('HelWhl') + +HelWhl.add_argument("-I","--InFile", required=True, default=None, help="Input data file") +HelWhl.add_argument("-C","--colorcoding", required=False, default='rainbow', help="available: , charge, polar, simple, amphipathic, none") +HelWhl.add_argument("-L","--lineweights", required=False, default=True, help="(boolean) defines whether connection lines decrease in thickness along the sequence") +HelWhl.add_argument("-F","--filename", required=False, default="out.png", help="") +HelWhl.add_argument("-s","--seq", required=False, default=False, help="") +HelWhl.add_argument("-M","--movment", required=False, default=False, help="") +HelWhl.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") + + +PltPde = subparsers.add_parser('PltPde') +PltPde.add_argument("-I","--InFile", required=True, default=None, help="Input data file") +PltPde.add_argument("-l", "--ClmList", required=True, default=None, help="") +PltPde.add_argument("-F","--filename", required=False, default="out.png", help="filename where to safe the plot. default = None > show the plot") +PltPde.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") + +PltVio = subparsers.add_parser('PltVio') +PltVio.add_argument("-I","--InFile", required=True, default=None, help="Input data file") +PltVio.add_argument("-l", "--ClmList", required=True, default=None, help="Column list") +PltVio.add_argument("-C","--colors", required=False, default=None, help='Data to be plotted') +PltVio.add_argument("-B","--bp", required=False, default=False, help="Print a box blot inside violin") +PltVio.add_argument("-T","--title", required=False, default=None, help="Title of the plot.") +PltVio.add_argument("-a","--axlabels", required=False, default=None, help="list containing the axis labels for the plot") +PltVio.add_argument("-M","--y_max", required=False, default=1, help='y-axis maximum.') +PltVio.add_argument("-m","--y_min", required=False, default=0, help="y-axis minimum.") +PltVio.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") + + +PltAaDis = subparsers.add_parser('PltAaDis') +PltAaDis.add_argument("-I","--InFile", required=True, default=None, help="Input data file") +PltAaDis.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile") + +args = parser.parse_args() + + +if sys.argv[1] == 'HelWhl': + + f = open(args.InFile) + lines = f.readlines() + sequence = lines[1].strip('\n') + + if args.movment == 'true': + mvt = True + else: + mvt = False + + if args.seq == 'true': + sq = True + else: + sq = False + + if args.lineweights == 'true': + lw = True + else: + lw = False + + helical_wheel(sequence, colorcoding=args.colorcoding, lineweights=args.lineweights, filename=args.OutFile, seq=args.seq, moment=mvt) + + +elif sys.argv[1] == 'PltPde': + + df = pd.read_csv(args.InFile, sep="\t") + + data = df[args.ClmList.split(',')].as_matrix().T + + plot_pde(data, filename=args.OutFile) + +elif sys.argv[1] == 'PltVio': + + df = pd.read_csv(args.InFile, sep="\t") + + data = df[args.ClmList.split(',')].as_matrix().T + + c = ['#0B486B']*len(args.ClmList.split(',')) + + plot_violin(data, colors=c, bp=True, filename=args.OutFile) + + +elif sys.argv[1] == 'PltAaDis': + + f = open(args.InFile) + lines = f.readlines() + + sequences = [] + + for line in lines: + if '>' in line: + pass + else: + sequences.append(line.strip('\n')) + + plot_aa_distr(sequences, color='#0B486B', filename=args.OutFile) + + + + + + + + + |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Plotting/test-data/test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Plotting/test-data/test1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,101 @@ +a1 a2 a3 a4 class +0.745792458 0.426207561 0.191600108 0.288065693 1 +0.119121966 0.115445564 0.495149009 0.819996523 1 +0.628359245 0.368612085 0.313798062 0.969106796 1 +0.573629151 0.360519016 0.999051405 0.936534337 1 +0.462045131 0.172713201 0.761584018 0.242427539 1 +0.154977302 0.425989857 0.780108849 0.052249918 1 +0.527507264 0.1866903 0.65345531 0.802989578 1 +0.42858627 0.122042111 0.633510759 0.087143255 1 +0.047182285 0.421388314 0.50932383 0.763195243 1 +0.629380952 0.001340805 0.739114882 0.269308244 1 +0.987061141 0.799254738 0.901687538 0.656436273 1 +0.936583739 0.338280342 0.727834801 0.845588744 1 +0.347702759 0.218512242 0.393355121 0.282700471 1 +0.708462562 0.182322916 0.075067056 0.154535304 1 +0.031962605 0.834054969 0.443203056 0.605506742 1 +0.2516154 0.568625642 0.479204872 0.304473254 1 +0.246588214 0.187047247 0.897110788 0.840227568 1 +0.427269514 0.479435526 0.258422749 0.222123443 1 +0.215754123 0.525950577 0.713890537 0.495648492 1 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0.710670276 0.960584853 0 +0.237325063 0.110749999 0.275516594 0.655295659 0 +0.055801154 0.271174213 0.123738447 0.573208337 0 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Plotting/test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Plotting/test-data/test2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,8 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP1 +GLWSKIKKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLWSKIKEVGKEAAKKAAGKAALGAVSEAV +>ACP3 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Plotting/test-data/test3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Plotting/test-data/test3.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,101 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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Data_Plotting/test-data/test4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Data_Plotting/test-data/test4.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 +PGRSRSAADDINPAPANM +>non-ACP250 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP252 +VMGHGLCPQGARAKAAIPAALRDHEST +>non-ACP254 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP256 +VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG +>non-ACP258 +RGGCWPRGLQQLLVPGG +>non-ACP260 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP262 +EQAERYDDMAAAMKAVTEQGHELSNEERNL +>non-ACP264 +MPNDPSDNQLK +>non-ACP266 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP268 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP270 +GHGRLVEIQGRLGVRIER +>non-ACP272 +LPFKLLLFVLLDGWTRLTH +>non-ACP274 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Global_Descriptors/.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Global_Descriptors/.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +"" +0 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Global_Descriptors/PDAUG_Peptide_Global_Descriptors.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,117 @@ +from modlamp.descriptors import * +import os +import pandas as pd + +def Descriptor_calcultor(DesType, inputfile, ph, amide,OutFile ): + + list_pep_name = [] + f = open(inputfile) + lines = f.readlines() + + for line in lines: + if ">" in line: + pass + else: + list_pep_name.append(line.strip('\n')) + + desc = GlobalDescriptor(list_pep_name) + + if DesType == "Length": + desc.length() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Weight": + + desc.calculate_MW() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Charge": + desc.calculate_charge(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "ChargeDensity": + desc.charge_density(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "IsoelectricPoint": + desc.isoelectric_point(amide=amide) + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "InstabilityIndex": + desc.instability_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "Aromaticity": + desc.aromaticity() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "AliphaticIndex": + desc.aliphatic_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "BomanIndex": + desc.boman_index() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "HydrophobicRatio": + desc.hydrophobic_ratio() + df = desc.descriptor + dfN = desc.featurenames + + elif DesType == "All": + desc.calculate_all(ph=int(ph), amide=amide) + df = desc.descriptor + dfN = desc.featurenames + else: + pass + + df = desc.descriptor + dfN = desc.featurenames + dfOut = pd.DataFrame(df,columns=dfN) + + dfOut.to_csv(OutFile, index=False, sep='\t') + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-t", "--DesType", + required=True, + default=None, + help="Descriptors Type") + + parser.add_argument("-i", "--InFile", + required=True, + default=None, + help="Peptide File") + + parser.add_argument("-p", "--Ph", + required=False, + default=7.0, + help="Ph 0-14") + + parser.add_argument("-a", "--Amide", + required=False, + default="True", + help="True or False") + + parser.add_argument("-O", "--OutFile", + required=False, + default="out.tsv", + help="True or False") + + + args = parser.parse_args() + + Descriptor_calcultor(args.DesType, args.InFile, args.Ph, args.Amide, args.OutFile) |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Global_Descriptors/test-data/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Global_Descriptors/test-data/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,139 @@\n+Length\tMW\tCharge\tChargeDensity\tpI\tInstabilityInd\tAromaticity\tAliphaticInd\tBomanInd\tHydrophRatio\n+33.0\t3833.74\t3.795\t0.0009898949850537595\t10.03125\t63.451515151515146\t0.09090909090909091\t115.15151515151516\t0.5603030303030305\t0.5454545454545454\n+34.0\t3727.11\t-1.001\t-0.0002685727011008529\t4.43505859375\t43.670588235294126\t0.08823529411764706\t43.23529411764706\t1.9917647058823529\t0.3235294117647059\n+18.0\t1788.15\t2.996\t0.0016754746525738892\t13.55859375\t40.550000000000004\t0.05555555555555555\t108.33333333333331\t-0.5277777777777778\t0.4444444444444444\n+28.0\t3036.42\t1.094\t0.00036029271312927727\t9.43701171875\t49.610714285714295\t0.07142857142857142\t70.0\t1.4278571428571425\t0.35714285714285715\n+21.0\t2199.45\t-1.07\t-0.00048648525767805596\t3.9296875\t29.85714285714286\t0.0\t111.42857142857142\t1.0095238095238097\t0.42857142857142855\n+34.0\t3689.37\t3.864\t0.0010473332845445157\t9.955322265625\t20.40882352941177\t0.029411764705882353\t97.3529411764706\t1.4858823529411767\t0.35294117647058826\n+13.0\t1401.6\t-0.069\t-4.922945205479453e-05\t6.28125\t93.56923076923078\t0.0\t97.6923076923077\t1.6992307692307689\t0.38461538461538464\n+26.0\t2978.24\t-1.0\t-0.0003357687761899646\t4.58935546875\t51.846153846153854\t0.11538461538461539\t68.07692307692308\t2.5303846153846155\t0.38461538461538464\n+21.0\t2531.74\t-0.999\t-0.00039459028178248954\t4.666015625\t24.804761904761904\t0.047619047619047616\t79.04761904761904\t4.30047619047619\t0.3333333333333333\n+30.0\t3671.28\t5.025\t0.0013687324311956594\t11.23828125\t89.66033333333333\t0.2\t74.66666666666666\t1.4336666666666662\t0.36666666666666664\n+18.0\t1797.22\t1.929\t0.0010733243565061595\t10.03125\t1.8055555555555547\t0.0\t168.33333333333331\t-0.7383333333333333\t0.6111111111111112\n+37.0\t4489.59\t3.96\t0.0008820404535826211\t10.2333984375\t44.878378378378386\t0.16216216216216217\t142.43243243243245\t-0.7545945945945945\t0.5675675675675675\n+25.0\t2504.82\t1.028\t0.0004104087319647719\t8.76171875\t90.01199999999999\t0.04\t51.2\t0.8763999999999998\t0.36\n+24.0\t2793.81\t1.194\t0.00042737337184704755\t9.7275390625\t64.35000000000001\t0.041666666666666664\t20.416666666666664\t5.572083333333334\t0.08333333333333333\n+37.0\t4180.030000000001\t2.996\t0.0007167412674071716\t11.2880859375\t42.77297297297297\t0.10810810810810811\t128.91891891891893\t-0.05243243243243245\t0.4594594594594595\n+24.0\t2705.2599999999998\t3.86\t0.0014268499146107953\t10.68359375\t56.52083333333335\t0.125\t101.66666666666666\t0.3158333333333334\t0.4583333333333333\n+13.0\t1428.75\t1.996\t0.0013970253718285214\t13.55078125\t63.938461538461546\t0.0\t164.6153846153846\t0.21999999999999995\t0.6153846153846154\n+20.0\t2481.99\t4.996\t0.0020129009383599455\t12.58203125\t27.415000000000003\t0.1\t126.5\t2.55\t0.5\n+38.0\t3846.5\t3.928\t0.0010211880930716235\t11.572265625\t67.88157894736841\t0.05263157894736842\t97.63157894736841\t0.15473684210526317\t0.42105263157894735\n+34.0\t3297.91\t4.997\t0.0015152020522088232\t12.58203125\t84.26764705882351\t0.0\t100.88235294117648\t0.6679411764705883\t0.47058823529411764\n+13.0\t1319.59\t1.095\t0.0008298031964473814\t12.25\t138.72307692307695\t0.0\t30.0\t-0.010769230769230812\t0.23076923076923078\n+19.0\t2324.8\t4.929\t0.00212018238128011\t11.94287109375\t140.16315789473683\t0.05263157894736842\t107.89473684210525\t3.7010526315789476\t0.42105263157894735\n+33.0\t3845.8\t6.996\t0.001819127359717094\t12.7998046875\t53.71212121212121\t0.06060606060606061\t174.54545454545456\t0.8466666666666666\t0.5757575757575758\n+13.0\t1523.62\t0.998\t0.0006550189679841431\t10.58203125\t52.04615384615385\t0.15384615384615385\t7.6923076923076925\t4.195384615384616\t0.23076923076923078\n+34.0\t3496.1\t1.996\t0.000570921884385458\t12.1005859375\t44.17941176470589\t0.058823529411764705\t123.23529411764706\t-0.060000000000000095\t0.47058823529411764\n+18.0\t2142.54\t4.996\t0.0023318117748093387\t13.80078125\t39.522222222222226\t0.05555555555555555\t81.1111111111111\t2.7783333333333338\t0.2777777777777778\n+28.0\t3162.91\t3.793\t0.0011992121179546684\t10.529296875\t88.95357142857144\t0.07142857142857142\t136.07142857142856\t-0.03678571428571437\t0.5714285714285714\n+17.0\t1756.0\t-1.001\t-0.0005700455580865603\t4.150390625\t87.4294'..b'34482758620689655\t101.37931034482759\t2.560344827586206\t0.41379310344827586\n+39.0\t4304.1900000000005\t5.092\t0.0011830332768767175\t10.71923828125\t-1.2307692307692295\t0.15384615384615385\t130.0\t-0.5758974358974357\t0.46153846153846156\n+34.0\t3621.3\t3.996\t0.0011034711291525142\t12.1552734375\t76.77647058823528\t0.029411764705882353\t123.23529411764707\t0.5847058823529411\t0.3235294117647059\n+38.0\t3944.43\t0.929\t0.00023552198923545357\t8.60546875\t37.489736842105266\t0.13157894736842105\t46.8421052631579\t1.0836842105263156\t0.4473684210526316\n+24.0\t2808.35\t5.027\t0.0017900190503320457\t12.5751953125\t30.070833333333336\t0.08333333333333333\t93.74999999999997\t1.8133333333333332\t0.5\n+37.0\t3970.48\t-2.999\t-0.0007553242932844392\t3.85400390625\t44.127027027027026\t0.0\t58.10810810810811\t2.005405405405405\t0.3783783783783784\n+14.0\t1624.91\t-0.072\t-4.431014640810875e-05\t5.90625\t26.992857142857144\t0.21428571428571427\t118.57142857142856\t-0.8014285714285715\t0.5\n+21.0\t2443.84\t2.929\t0.0011985236349351838\t11.2216796875\t68.41904761904762\t0.14285714285714285\t79.04761904761904\t1.4666666666666668\t0.3333333333333333\n+33.0\t3489.99\t0.932\t0.0002670494757864636\t8.7001953125\t45.63939393939393\t0.030303030303030304\t80.0\t1.6799999999999993\t0.3939393939393939\n+33.0\t3753.61\t4.928\t0.001312869477649516\t11.6767578125\t48.21818181818182\t0.15151515151515152\t115.15151515151516\t-0.79030303030303\t0.3939393939393939\n+28.0\t2794.43\t-0.004\t-1.4314189297996373e-06\t6.5\t25.335714285714285\t0.07142857142857142\t188.57142857142856\t-2.130357142857143\t0.7142857142857143\n+11.0\t1282.6399999999999\t1.927\t0.001502370111644733\t9.6748046875\t-2.499999999999997\t0.18181818181818182\t177.2727272727273\t-1.957272727272727\t0.7272727272727273\n+23.0\t2246.54\t5.095\t0.002267932019906167\t13.86328125\t27.30434782608696\t0.0\t73.04347826086956\t2.0630434782608695\t0.5217391304347826\n+18.0\t2206.5099999999998\t0.098\t4.4414029394836193e-05\t7.703125\t31.249999999999996\t0.0\t129.99999999999997\t3.2727777777777773\t0.3333333333333333\n+38.0\t4012.57\t3.995\t0.0009956212601898533\t12.4033203125\t88.79473684210524\t0.13157894736842105\t59.473684210526315\t0.9107894736842105\t0.47368421052631576\n+18.0\t1839.01\t0.997\t0.0005421395207203876\t10.58203125\t94.75\t0.0\t43.888888888888886\t2.883888888888888\t0.3333333333333333\n+24.0\t2682.34\t0.996\t0.00037131758091815356\t9.7353515625\t0.7625000000000008\t0.08333333333333333\t223.33333333333331\t-1.78\t0.6666666666666666\n+27.0\t2757.17\t2.128\t0.0007718058734136814\t10.0205078125\t37.24444444444445\t0.0\t76.29629629629629\t1.32\t0.4444444444444444\n+29.0\t3012.65\t0.86\t0.00028546296449969295\t8.0888671875\t55.06896551724138\t0.06896551724137931\t144.82758620689654\t-0.8844827586206897\t0.6206896551724138\n+31.0\t3141.71\t5.928\t0.0018868705259237803\t12.69970703125\t65.65806451612903\t0.03225806451612903\t97.74193548387098\t1.1216129032258066\t0.45161290322580644\n+17.0\t1793.12\t2.928\t0.0016329080039261176\t12.1005859375\t65.27058823529413\t0.058823529411764705\t85.88235294117648\t0.8123529411764705\t0.29411764705882354\n+25.0\t2761.2\t3.997\t0.001447559032304795\t11.4951171875\t90.212\t0.04\t50.8\t2.4636\t0.24\n+30.0\t3435.68\t-3.897\t-0.0011342732734131234\t4.270751953125\t50.57\t0.03333333333333333\t52.33333333333333\t3.3416666666666663\t0.3333333333333333\n+11.0\t1257.3799999999999\t-0.003\t-2.385913566304538e-06\t6.6875\t51.97272727272727\t0.0\t35.45454545454546\t3.4490909090909088\t0.18181818181818182\n+25.0\t2845.46\t1.93\t0.0006782734601786705\t10.59765625\t30.988000000000007\t0.12\t148.0\t-0.3963999999999999\t0.6\n+29.0\t3257.87\t-0.001\t-3.069490188374613e-07\t6.9375\t41.60689655172414\t0.10344827586206896\t141.3793103448276\t-0.07000000000000005\t0.5517241379310345\n+18.0\t2044.3799999999999\t3.097\t0.0015148847083223276\t12.10009765625\t38.794444444444444\t0.0\t118.88888888888889\t2.8877777777777776\t0.3333333333333333\n+19.0\t2281.79\t2.095\t0.0009181388296030749\t11.400390625\t15.952631578947368\t0.15789473684210525\t158.94736842105263\t-0.45894736842105277\t0.5263157894736842\n+28.0\t2915.63\t0.996\t0.0003416071312203537\t12.25\t45.892857142857146\t0.03571428571428571\t191.07142857142856\t-2.048571428571429\t0.6785714285714286\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Global_Descriptors/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Global_Descriptors/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 +PGRSRSAADDINPAPANM +>non-ACP250 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP252 +VMGHGLCPQGARAKAAIPAALRDHEST +>non-ACP254 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP256 +VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG +>non-ACP258 +RGGCWPRGLQQLLVPGG +>non-ACP260 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP262 +EQAERYDDMAAAMKAVTEQGHELSNEERNL +>non-ACP264 +MPNDPSDNQLK +>non-ACP266 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP268 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP270 +GHGRLVEIQGRLGVRIER +>non-ACP272 +LPFKLLLFVLLDGWTRLTH +>non-ACP274 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Length_Distribution/PDAUG_Peptide_Length_Distribution.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,31 @@ +import matplotlib.pyplot as plt +import Bio +from Bio import SeqIO +import os + + +def LegnthDestribution(InFile, OutFile): + + + sizes = [len(rec.seq) for rec in SeqIO.parse(InFile, "fasta")] + + plt.hist(sizes, bins=20) + plt.title("%i Negative bacteriocin sequences\nLengths %i to %i" \ + % (len(sizes),min(sizes),max(sizes))) + plt.xlabel("Sequence length (bp)") + plt.ylabel("Count") + + plt.savefig(OutFile) + + + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-I", "--InFile", required=True, default=None, help="Input file name") + parser.add_argument("-O", "--OutFile", required=False, default="Out.png", help="Input file name") + args = parser.parse_args() + LegnthDestribution(args.InFile, args.OutFile) |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Length_Distribution/test-data/out.png |
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| Binary file PDAUG_Peptide_Length_Distribution/test-data/out.png has changed |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Length_Distribution/test-data/positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Length_Distribution/test-data/positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Ngrams/PDAUG_Peptide_Ngrams.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,82 @@ +import matplotlib +matplotlib.use('Agg') +import os +import sys +sys.path.insert(0, os.path.abspath('..')) +import quantiprot +from quantiprot.utils.io import load_fasta_file +from quantiprot.utils.feature import Feature, FeatureSet +from quantiprot.metrics.aaindex import get_aa2hydropathy +from quantiprot.metrics.basic import identity +from quantiprot.metrics.ngram import pattern_match, pattern_count +from quantiprot.analysis.ngram import ngram_count +from quantiprot.analysis.ngram import zipf_law_fit +from matplotlib import pyplot as plt + + +def Run_ngrams(fasta1, fasta2, OutFile ): + + alphasyn_seq = load_fasta_file(fasta1) + amyload_pos_seq = load_fasta_file(fasta2) + + fs_aa = FeatureSet("aa patterns") + fs_aa.add(identity) + fs_aa.add(pattern_match, pattern='VT', padded=True) + fs_aa.add(pattern_count, pattern='VT') + + result_seq = fs_aa(alphasyn_seq) + + fs_hp = FeatureSet("hydropathy patterns") + fs_hp.add(Feature(get_aa2hydropathy())) + fs_hp.add(Feature(get_aa2hydropathy()).then(pattern_match, pattern=[0.0, 2.0], + metric='taxi', radius=1.0)) + result_seq2 = fs_hp(alphasyn_seq) + result_freq = ngram_count(alphasyn_seq, n=2) + result_fit = zipf_law_fit(amyload_pos_seq, n=3, verbose=True) + + counts = sorted(result_fit["ngram_counts"], reverse=True) + ranks = range(1, len(counts)+1) + + slope = result_fit["slope"] + harmonic_num = sum([rank**-slope for rank in ranks]) + fitted_counts = [(rank**-slope) / harmonic_num * sum(counts) for rank in ranks] + + plt.plot(ranks, counts, 'k', label="empirical") + plt.plot(ranks, fitted_counts, 'k--', + label="Zipf's law\nslope: {:.2f}".format((slope))) + plt.xlabel('rank') + plt.ylabel('count') + plt.xscale('log') + plt.yscale('log') + plt.legend() + + plt.savefig(OutFile) + +if __name__=="__main__": + + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-f1", "--Fasta1", + required=True, + default=None, + help="First fasta file") + + parser.add_argument("-f2", "--Fasta2", + required=True, + default=None, + help="Second fasta file") + + + parser.add_argument("--OutFile", + required=True, + help="HTML out file", + default="report.html") + + + args = parser.parse_args() + + Run_ngrams(args.Fasta1, args.Fasta2, args.OutFile) + |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Ngrams/test-data/out.png |
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| Binary file PDAUG_Peptide_Ngrams/test-data/out.png has changed |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Ngrams/test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Ngrams/test-data/test1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Ngrams/test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Ngrams/test-data/test2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 +PGRSRSAADDINPAPANM +>non-ACP250 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP252 +VMGHGLCPQGARAKAAIPAALRDHEST +>non-ACP254 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP256 +VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG +>non-ACP258 +RGGCWPRGLQQLLVPGG +>non-ACP260 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP262 +EQAERYDDMAAAMKAVTEQGHELSNEERNL +>non-ACP264 +MPNDPSDNQLK +>non-ACP266 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP268 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP270 +GHGRLVEIQGRLGVRIER +>non-ACP272 +LPFKLLLFVLLDGWTRLTH +>non-ACP274 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/PDAUG_Peptide_Sequence_Analysis.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/PDAUG_Peptide_Sequence_Analysis.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| b'@@ -0,0 +1,231 @@\n+import modlamp\n+from modlamp.analysis import *\n+\n+from plotly.subplots import make_subplots\n+import plotly.graph_objects as go\n+from modlamp.analysis import GlobalAnalysis\n+from modlamp.analysis import *\n+\n+import pandas as pd\n+import os, sys\n+import argparse\n+\n+parser = argparse.ArgumentParser(description=\'Deployment tool\')\n+subparsers = parser.add_subparsers()\n+\n+CalcAAFreq = subparsers.add_parser(\'CalcAAFreq\')\n+CalcAAFreq.add_argument("-I","--InFile", required=True, default=None, help="")\n+CalcAAFreq.add_argument("-T","--PlotFile", required=False, default=\'out.pdf\', help="out.pdf")\n+CalcAAFreq.add_argument("--OutFile", required=False, default=\'Out.tsv\', help="Out.tsv")\n+\n+H = subparsers.add_parser(\'H\')\n+H.add_argument("-I","--InFile", required=True, default=None, help="")\n+H.add_argument("-S","--Scale", required=False, default=\'eisenberg\', help="hydrophobicity scale to use. For available scales, see modlamp.descriptors.PeptideDescriptor.")\n+H.add_argument("--OutFile", required=False, default=\'Out.tsv\', help="Out.tsv")\n+\n+uH = subparsers.add_parser(\'uH\')\n+uH.add_argument("-I","--InFile", required=True, default=None, help="")\n+uH.add_argument("-S","--Scale", required=False, default=\'eisenberg\', help="hydrophobicity scale to use. For available scales, see modlamp.descriptors.PeptideDescriptor.")\n+uH.add_argument("-W", "--Window", required=False, default=1000, help="")\n+uH.add_argument("-A", "--Angle", required=False, default=100, help="")\n+uH.add_argument("-M", "--Modality", required=False, default=\'max\', help="")\n+uH.add_argument("--OutFile", required=False, default=\'Out.tsv\', help="Out.tsv")\n+\n+charge = subparsers.add_parser(\'charge\')\n+charge.add_argument("-I","--InFile", required=True, default=None, help="")\n+charge.add_argument("-p", "--ph", required=False, default=7.0, help="")\n+charge.add_argument("-A", "--Amide", required=False, default=True, help="")\n+charge.add_argument("--OutFile", required=False, default=\'Out.tsv\', help="Out.tsv")\n+\n+Len = subparsers.add_parser(\'Len\')\n+Len.add_argument("-I","--InFile", required=True, default=None, help="")\n+Len.add_argument("--OutFile", required=False, default=\'Out.tsv\', help="Out.tsv")\n+\n+PlotSaummary = subparsers.add_parser(\'PlotSummary\')\n+PlotSaummary.add_argument("-I1","--InFile1", required=True, default=None, help="")\n+PlotSaummary.add_argument("-I2", "--InFile2", required=True, default=None, help="Out.tsv")\n+PlotSaummary.add_argument("--PlotFile", required=False, default=\'Out.pdf\', help="out.pdf")\n+PlotSaummary.add_argument("--htmlFname", required="False", default=\'report.html\', help="Output file")\n+PlotSaummary.add_argument("-O","--htmlOutDir", required=False, default=os.path.join(os.getcwd(),\'report_dir\'), help="HTML Out Dir")\n+PlotSaummary.add_argument("-Wp","--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")\n+PlotSaummary.add_argument("-fn", "--First_lib_name", required=True, help="Name of the fist peptide data")\n+PlotSaummary.add_argument("-sn", "--Second_lib_name", required=True, help="Name of the second peptide data")\n+\n+\n+args = parser.parse_args()\n+\n+\n+\n+def SummaryPlot(Lib_1, Lib_2, First_lib_name, Second_lib_Name, Workdirpath, htmlOutDir, htmlFname):\n+\n+ if not os.path.exists(htmlOutDir):\n+ os.makedirs(htmlOutDir)\n+\n+\n+ AA = [\'A\',\'C\',\'D\',\'E\',\'F\',\'G\',\'H\',\'I\',\'K\',\'L\',\'M\',\'N\',\'P\',\'Q\',\'R\',\'S\',\'T\',\'V\',\'W\',\'Y\']\n+\n+ Pep1, Index1 = ReturnPeptide(Lib_1)\n+ Pep2, Index2 = ReturnPeptide(Lib_2)\n+\n+ fig = make_subplots(\n+ rows=2, cols=3,\n+ specs=[[{"type": "xy"}, {"type": "histogram"}, {"type": "box"} ],[{"type": "violin"}, {"type": "violin"}, {"type": "scatter3d"} ]],\n+ subplot_titles=(" Amino Acid Fraction", "Global Charge", "Length Distribution", "Global Hydrophobicity", "Global Hydrophobic Movement", "Scatter Plot"))\n+\n+\n+ #########################################\n+ g = GlobalAnalysis([Pep1, Pep2])\n+ df = g.calc_aa_freq(plot=False)\n+\n+ data1 = g.aafreq[0]\n+ data2 = '..b'ace(go.Violin(y=h2,box_visible=True, name=Second_lib_Name, marker_color=\'#FF7F0E\', meanline_visible=True), row=2, col=1)\n+ #################################################################\n+\n+ #####################################\n+ uH = GlobalAnalysis([Pep1, Pep2])\n+ uH.calc_uH()\n+\n+ uh1 = uH.uH[0]\n+ uh2 = uH.uH[1]\n+\n+ fig.add_trace(go.Violin( y=uh1,box_visible=True, name =First_lib_name, marker_color=\'#1F77B4\', meanline_visible=True), row=2, col=2)\n+ fig.add_trace(go.Violin(y=uh2,box_visible=True, name=Second_lib_Name, marker_color=\'#FF7F0E\', meanline_visible=True), row=2, col=2)\n+ #######################################\n+\n+\n+ ############################################\n+ fig.add_trace(go.Scatter3d(x=h1, y=uh1, z=charge1, marker_color=\'#1F77B4\', mode=\'markers\', name=First_lib_name, marker_size=3.0),row=2, col=3)\n+ fig.add_trace(go.Scatter3d(x=h2, y=uh2, z=charge2, marker_color=\'#FF7F0E\', mode=\'markers\', name=Second_lib_Name, marker_size=3.0), row=2, col=3)\n+ fig.update_layout(scene = dict(xaxis_title=\'Hydrophobicity\', yaxis_title=\'Hydrophobic Movement\', zaxis_title=\'Charge\'),uniformtext_minsize=4, font=dict(\n+ family="Times New Roman",\n+ size=12,\n+ color="black"))\n+ ###########################################\n+\n+ fig.update_xaxes(title_text="Amino Acid", row=1, col=1)\n+ fig.update_xaxes(title_text="Global Charge", row=1, col=2)\n+ fig.update_xaxes(title_text="Peptide dataset", showgrid=False, row=1, col=3)\n+ fig.update_xaxes(title_text="Peptide dataset", row=2, col=1)\n+ fig.update_xaxes(title_text="Peptide dataset", row=2, col=2)\n+\n+ fig.update_yaxes(title_text="Fraction", row=1, col=1)\n+ fig.update_yaxes(title_text="Fraction", row=1, col=2)\n+ fig.update_yaxes(title_text="Length", row=1, col=3)\n+ fig.update_yaxes(title_text="Global hydrophobicity", row=2, col=1)\n+ fig.update_yaxes(title_text="Global hydrophobic Movement", row=2, col=2)\n+ fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))\n+ #fig.show()\n+\n+def ReturnPeptide(Infile):\n+\n+ file = open(Infile)\n+ lines = file.readlines()\n+\n+ Index = []\n+ Pep = []\n+\n+ for line in lines:\n+ if \'>\' in line:\n+ line = line.strip(\'\\n\')\n+ line = line.strip(\'\\r\')\n+ Index.append(line.strip(\'\\n\'))\n+ else:\n+ line = line.strip(\'\\n\')\n+ line = line.strip(\'\\r\')\n+ Pep.append(line)\n+ return Pep, Index\n+\n+if sys.argv[1] == \'CalcAAFreq\':\n+\n+ Pep, Index = ReturnPeptide(args.InFile)\n+ g = GlobalAnalysis(Pep)\n+ g.calc_aa_freq(plot=False, color=\'#83AF9B\')\n+ df1 = pd.DataFrame(g.aafreq[0], columns=[\'aa_freq\'])\n+ df1.to_csv(args.OutFile, sep=\'\\t\', index=None)\n+\n+elif sys.argv[1] == \'H\':\n+\n+ Pep, _ = ReturnPeptide(args.InFile)\n+ g = GlobalAnalysis(Pep)\n+ g.calc_H(args.Scale)\n+ df1 = pd.DataFrame(g.H[0].T, columns=[\'H\'])\n+ df1.to_csv(args.OutFile, sep=\'\\t\', index=None)\n+\n+elif sys.argv[1] == \'uH\':\n+\n+ Pep, _ = ReturnPeptide(args.InFile)\n+\n+ g = GlobalAnalysis(Pep)\n+ g.calc_uH(int(args.Window), int(args.Angle), args.Modality)\n+ df1 = pd.DataFrame(g.uH[0].T, columns=[\'uH\'])\n+ df1.to_csv(args.OutFile, sep=\'\\t\', index=None)\n+ \n+elif sys.argv[1] == \'charge\':\n+\n+ Pep, _ = ReturnPeptide(args.InFile)\n+\n+ g = GlobalAnalysis(Pep)\n+\n+ if args.Amide == \'true\':\n+ amide = True\n+ else:\n+ amide = False\n+\n+ g.calc_charge(float(args.ph), amide)\n+ df1 = pd.DataFrame(g.charge[0].T, columns=[\'charge\'])\n+ df1.to_csv(args.OutFile, sep=\'\\t\', index=None)\n+\n+elif sys.argv[1] == \'Len\':\n+\n+ Pep, _ = ReturnPeptide(args.InFile)\n+ df1 = pd.DataFrame([len(x) for x in Pep], columns=[\'c\'])\n+ df1.to_csv( args.OutFile, sep=\'\\t\', index=None)\n+\n+elif sys.argv[1] == "PlotSummary":\n+\n+ SummaryPlot(args.InFile1, args.InFile2, args.First_lib_name, args.Second_lib_name, args.Workdirpath, args.htmlOutDir, args.htmlFname)\n+\n+\n+\n+\n+\n+\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/ACPs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/ACPs.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP_1 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP_2 +GLFDIIKKIAESI +>ACP_3 +GLLDIVKKVVGAFGSL +>ACP_4 +GLFDIVKKVVGALGSL +>ACP_5 +GLFDIVKKVVGTLAGL +>ACP_6 +GLFDIAKKVIGVIGSL +>ACP_7 +GLFDIVKKIAGHIAGSI +>ACP_8 +GLFDIVKKIAGHIVSSI +>ACP_9 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP_10 +HGVSGHGQHGVHG +>ACP_11 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP_12 +KWKLFKKIKFLHSAKKF +>ACP_13 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP_14 +GIGTKILGGVKTALKGALKELASTYAN +>ACP_15 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP_16 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP_17 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP_18 +FLPLLAGLAANFLPTIICKISYKC +>ACP_19 +FVQWFSKFLGRIL +>ACP_20 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP_21 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP_22 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP_23 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP_24 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP_25 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP_26 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP_27 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP_28 +ECRRLCYKQRCVTYCRGR +>ACP_29 +LKLKSIVSWAKKVL +>ACP_30 +KWCFRVCYRGICYRRCR +>ACP_31 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP_32 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP_33 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP_34 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP_35 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP_36 +GLFVGVLAKVAAHVVPAIAEHF +>ACP_37 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP_38 +GFVDFLKKVAGTIANVVT +>ACP_39 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP_40 +TRSSRAGLQFPVGRVHRLLRK +>ACP_41 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP_42 +GLFDVIKKVASVIGGL +>ACP_43 +GLFDIIKKVASVVGGL +>ACP_44 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP_45 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP_46 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP_47 +GLLGPLLKIAAKVGSNLL +>ACP_48 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP_49 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP_50 +FFHHIFRGIVHVGKTIHRLVTG +>ACP_51 +KLAKLAKKLAKLAK +>ACP_52 +KTCENLADTFRGPCFATSNC +>ACP_53 +IDWKKLLDAAKQIL +>ACP_54 +FLIGMTQGLICLITRKC +>ACP_55 +ILPILSLIGGLLGK +>ACP_56 +GLLGLLGSVVSHVVPAIVGHF +>ACP_57 +GLLGLLGSVVSHVLPAITQHL +>ACP_58 +GIKCRFCCGCCTPGICGVCCRF +>ACP_59 +QSHLSLCRWCCNCCRSNKGC +>ACP_60 +ILGPVISTIGGVLGGLLKNL +>ACP_61 +FLPILASLAAKFGPKLFCLVTKKC +>ACP_62 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP_63 +LLGMIPLAISAISALSKL +>ACP_64 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP_65 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP_66 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP_67 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP_68 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP_69 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP_70 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP_71 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP_72 +GFKDLLKGAAKALVKTVLF +>ACP_73 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP_74 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP_75 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP_76 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP_77 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP_78 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP_79 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP_80 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP_81 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP_82 +FLPVIAGVAANFLPKLFCAISKKC +>ACP_83 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP_84 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP_85 +VNWKKVLGKIIKVAK +>ACP_86 +VNWKKILGKIIKVAK +>ACP_87 +FFSLLPSLIGGLVSAIK +>ACP_88 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP_89 +KWKLFKKIPKFLHLAKKF +>ACP_90 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP_91 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP_92 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP_93 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP_94 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP_95 +FVDLKKIANIINSIFGK +>ACP_96 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP_97 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP_98 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP_99 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP_100 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP_101 +GMWSKILGHLIR +>ACP_102 +GKWMSLLKHILK +>ACP_103 +GFGMALKLLKKVL +>ACP_104 +GTGLPMSERRKIMLMMR +>ACP_105 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP_106 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP_107 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP_108 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP_109 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP_110 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP_111 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP_112 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP_113 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP_114 +FLGWLFKWASK +>ACP_115 +FLKWLFKWAKK +>ACP_116 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP_117 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP_118 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP_119 +KWKLFKKIGAVLKVL +>ACP_120 +GACFSIAHECGA +>ACP_121 +TCCATGACGTTCCTGACGTT +>ACP_122 +KRFKQDGGASHASPASS +>ACP_123 +KRAKAAGGWSHWSPWSSC +>ACP_124 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP_125 +FLGALFKVASKVLPSVKCAITKKC +>ACP_126 +GIGKFLKKAKKFGKAFVKILKK +>ACP_127 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP_128 +VECYGPNRPQF +>ACP_129 +KRFKQDGGWSHWSPWSSC +>ACP_130 +RQVFQVAYIIIKA +>ACP_131 +KAFDITYVRLKF +>ACP_132 +DFKLFAVTIKYR +>ACP_133 +DFKLFAVYIKYR +>ACP_134 +WHSDMEWWYLLG +>ACP_135 +HTMYYHHYQHHL +>ACP_136 +RLVSYNGIIFFLK +>ACP_137 +GRENYHGCTTHWGFTLC +>ACP_138 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/non_ACPs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/non_ACPs.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP_1 +VIADDLPPTCIRP +>non-ACP_2 +MAEALLLRATFYLLIGSANAAKPD +>non-ACP_3 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP_4 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP_5 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP_6 +RHVGLLCATGPQRWRF +>non-ACP_7 +VGKSSKMLQHIDYRMRCILQDGRIFIGTFKA +>non-ACP_8 +LPGGLRVLVQTGH +>non-ACP_9 +RPKFALAQAQKCFALYRQAYTANNSSQVQAAMKGFEE +>non-ACP_10 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP_11 +LHRAQDYRRELDTLQSLLTTSQSSELQAAAALLKC +>non-ACP_12 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP_13 +KAEVCMAVPWLSLQ +>non-ACP_14 +KMQGSRMDEQRCS +>non-ACP_15 +LVTPPKALLKPLSIPNQ +>non-ACP_16 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP_17 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP_18 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP_19 +EWRDLKGRADINKDDVV +>non-ACP_20 +SWVEENRASFQPPVCNKLMHR +>non-ACP_21 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP_22 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP_23 +FYQNRAAAFEQLQKWKEVAQDCT +>non-ACP_24 +VFHRVRWAPELGASLG +>non-ACP_25 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP_26 +RPEPGGCCCRRTVRANGC +>non-ACP_27 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP_28 +ASRQLLVAPPEAL +>non-ACP_29 +LKEERQRQKKEARIAAMASAEGQDSAEAQD +>non-ACP_30 +QTLVHNGGRLPPDLQLSAEDSSSTPS +>non-ACP_31 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP_32 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP_33 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP_34 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP_35 +RANALIKRGTMCMQQQQPMLSTQ +>non-ACP_36 +LLSLIGFCWAQYDP +>non-ACP_37 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP_38 +NWLCLSRAQQLNGDLDKARHAYQ +>non-ACP_39 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP_40 +MNRLLQKGTSLVPSWRTR +>non-ACP_41 +GHGRLVEIQGRLGVRIER +>non-ACP_42 +YKELYYRLLTSPAADAGNTL +>non-ACP_43 +RNKLDLETLTDILEHQIR +>non-ACP_44 +WPGILVGGARVASCRYPALGPRLA +>non-ACP_45 +EPSTGLMLVEESRWVHLGRELLPATAP +>non-ACP_46 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP_47 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP_48 +GNMEKAIDMFNKAINLAKSEMEMAHLYSLC +>non-ACP_49 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP_50 +NTNVTPHLLAGMRLIAVQQPEDPLRVL +>non-ACP_51 +MQESLRLQQQALEAR +>non-ACP_52 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP_53 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP_54 +FSPQRDRFQAEGS +>non-ACP_55 +TGCCIAGRLANLDDQNLTVAL +>non-ACP_56 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ +>non-ACP_57 +ISRGLLLLAALCCLAPSFL +>non-ACP_58 +GSILGFLQIATVLTVLLLLLK +>non-ACP_59 +AAAALRARILQVSSKVN +>non-ACP_60 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP_61 +LLRSCPLQGSPGRPRSV +>non-ACP_62 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP_63 +CQNGRRANRTVRFARTA +>non-ACP_64 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP_65 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP_66 +TLDRDGTLVRLRFTMVALITVCCPLVAFFF +>non-ACP_67 +LFLTGCKVDLYTGISQKEGNEMLALL +>non-ACP_68 +QGKAGEVIVTGLRTEQLSLSDAKLLLEAAMR +>non-ACP_69 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP_70 +VDREQLVQKARLAEQAERYDD +>non-ACP_71 +IACLLPRVSNLELKQGKAGEVIVTGLR +>non-ACP_72 +SHLELNNGTKMPTLGLGT +>non-ACP_73 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP_74 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP_75 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP_76 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP_77 +PAIQPVLSGLSRIVNGEEA +>non-ACP_78 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP_79 +RQQEFLLLNGWLQLQCGHAERACILLD +>non-ACP_80 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP_81 +ERFTSNQMFFDLAQASASGGLNNKKI +>non-ACP_82 +AARQIGSCLMRCRTLDTTSP +>non-ACP_83 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP_84 +PGRSRSAADDINPAPANM +>non-ACP_85 +WVTVRSQQRGLFPAI +>non-ACP_86 +PNFSMETWLLLV +>non-ACP_87 +ENWRKQKRERWEKIQADKERRARLQAEAQE +>non-ACP_88 +PRPPSKTYRGAFQN +>non-ACP_89 +PTDSPLDRAIQHLQRLTIQELPDPPTDLPESNSNQ +>non-ACP_90 +VAGTTAVAGQVPIMGAVKFGGDVCAAG +>non-ACP_91 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP_92 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP_93 +ARPRLDLQLVQRFVRIQKVF +>non-ACP_94 +TKGNDIADLDAVAQTLKKPADDANKAVN +>non-ACP_95 +LWARSKNDQLRISFPPGLCWG +>non-ACP_96 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP_97 +EAAMAAAAAPGSGNGVGGGGGTAG +>non-ACP_98 +AASVNPLAAVELQRLSAQER +>non-ACP_99 +ATRAAAARLVGTAASRTPAAARH +>non-ACP_100 +LNPDPCKPLAFI +>non-ACP_101 +LWRLCIGLHSAPRFLVAMAYLKYYQGTPC +>non-ACP_102 +LDRDGTLVRLRFTLVALVTVCCPLVAFLFCVL +>non-ACP_103 +VTLLFKLYCLA +>non-ACP_104 +LSITRGLLLLAALCCLAPIS +>non-ACP_105 +RKRLKEERQRQKKEARIAA +>non-ACP_106 +VVMNSLRVILQAS +>non-ACP_107 +PDPPADSPLDQTIQHLQGLTIQELPDPPTHLPE +>non-ACP_108 +QYLRIRTVQPEPDYGAAV +>non-ACP_109 +KHRTVLFRRWMAIICCLI +>non-ACP_110 +VSVDNPNDLMLMQWSLIRITIQEE +>non-ACP_111 +QQIQGGKELKDALAQL +>non-ACP_112 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP_113 +PPMPSAPPVHPPP +>non-ACP_114 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP_115 +ARTLNNKLSLSKPKFSGFT +>non-ACP_116 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP_117 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP_118 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP_119 +RSVKGLVALITGGASGL +>non-ACP_120 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP_121 +LLAAGFCPAVLCH +>non-ACP_122 +LGSGHHDGSGDSLEMSSLDRAQ +>non-ACP_123 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP_124 +HHKDSSIHHLRLSANDAEDSLRM +>non-ACP_125 +LRLIHFLHQTTDPYPQGPGTANQRRRR +>non-ACP_126 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP_127 +ELNPKYVKALFRRAKAHE +>non-ACP_128 +LTMMAPAVAQQTDDETFV +>non-ACP_129 +AKLRRKHDKAMDEYEAMNKKLTAQK +>non-ACP_130 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP_131 +APARRVLQVKRVMQESSLSPAHL +>non-ACP_132 +SLINQQITQVGHGGQAGRLTETNPLTENS +>non-ACP_133 +NATSSQDQFAKWARLNRKYEQLSQ +>non-ACP_134 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP_135 +LIWTIFILHIAIFLVNTIGAATIDNLLWLLYLKLP +>non-ACP_136 +GWVTTLGPGSRGYRAPPPPRRSRE +>non-ACP_137 +QRRQNDSSVFLAIMVAAAVES +>non-ACP_138 +QQEKEFLESYPQNCPPDALPGTPGNLD |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/out1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/out1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +H +0.1475757575757576 +0.3215384615384615 +0.44875 +0.44875 +0.45687500000000003 +0.48624999999999996 +0.4235294117647058 +0.4129411764705882 +-0.10278350515463919 +0.15153846153846157 +-0.296 +-0.14411764705882354 +-0.0019230769230769162 +0.20703703703703702 +0.2162962962962963 +0.28814814814814815 +0.24777777777777776 +0.4795833333333333 +0.35076923076923083 +0.03171428571428572 +-0.035128205128205144 +0.04405405405405406 +-0.1698809523809524 +0.17913043478260865 +0.11269230769230772 +0.28448275862068967 +0.07433333333333328 +-0.6266666666666666 +0.14071428571428576 +-0.43117647058823527 +-0.19765957446808508 +0.4856 +0.5168 +0.3433333333333333 +0.4583333333333333 +0.5745454545454545 +0.3282608695652174 +0.3733333333333333 +0.17192307692307696 +-0.3457142857142857 +0.1076 +0.4675 +0.4675 +-0.16962962962962963 +0.08749999999999998 +-0.3174358974358975 +0.4411111111111112 +-0.050120481927710826 +-0.025555555555555557 +0.24727272727272726 +-0.15142857142857138 +-0.066 +0.07142857142857142 +0.34882352941176475 +0.6842857142857143 +0.6666666666666666 +0.5438095238095239 +0.18681818181818183 +-0.231 +0.5955 +0.35541666666666666 +0.08687500000000001 +0.5977777777777777 +0.15000000000000002 +0.19517241379310335 +0.1663333333333333 +0.33566666666666667 +0.19225806451612903 +0.21999999999999997 +-0.2715662650602409 +0.28916666666666674 +0.2563157894736842 +-0.10543478260869568 +-0.12173913043478261 +-0.15695652173913047 +-0.43962962962962954 +-0.21695652173913044 +0.12199999999999997 +0.38833333333333336 +0.4166666666666667 +0.4054166666666666 +0.4258333333333333 +0.35625 +0.14285714285714288 +0.055333333333333366 +0.07533333333333335 +0.6094117647058823 +-0.21846153846153846 +-0.058333333333333334 +-0.2692857142857143 +0.20566666666666658 +0.00366666666666667 +0.1886206896551724 +0.13266666666666665 +0.24470588235294113 +0.2412903225806451 +0.23933333333333323 +0.264516129032258 +0.27419354838709675 +0.12766666666666668 +0.23583333333333334 +0.12916666666666668 +0.3400000000000001 +-0.16058823529411767 +0.33214285714285713 +0.19161290322580643 +0.0384 +0.12482758620689656 +0.2403125 +0.2882142857142857 +0.24965517241379304 +0.06206896551724138 +0.26321428571428573 +0.37636363636363634 +0.07636363636363636 +-0.034615384615384596 +0.0023076923076923396 +0.026500000000000013 +0.16733333333333336 +0.3899999999999999 +0.2585 +-0.24882352941176467 +-0.053333333333333316 +-0.29405405405405405 +0.23041666666666671 +-0.05090909090909091 +0.2141666666666667 +-0.11818181818181818 +-0.18722222222222226 +0.2615384615384615 +0.03583333333333333 +0.03583333333333331 +0.06166666666666661 +0.31583333333333335 +-0.031666666666666655 +0.3292307692307693 +0.02470588235294122 +-0.005333333333333309 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test1/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test1/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,21 @@ +aa_freq +0.07522371364653244 +0.07690156599552572 +0.019574944071588368 +0.024049217002237135 +0.047818791946308725 +0.10123042505592841 +0.02069351230425056 +0.07774049217002237 +0.10486577181208054 +0.08612975391498881 +0.007829977628635347 +0.03159955257270693 +0.04893736017897092 +0.018456375838926176 +0.0447427293064877 +0.06823266219239374 +0.04390380313199105 +0.06180089485458613 +0.018176733780760627 +0.0220917225950783 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 +PGRSRSAADDINPAPANM +>non-ACP250 +LLSALTLETWVLLAVILVLLYRLG +>non-ACP252 +VMGHGLCPQGARAKAAIPAALRDHEST +>non-ACP254 +FLVSIAGLLYALVQLGQPCDCLPPLRAAA +>non-ACP256 +VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG +>non-ACP258 +RGGCWPRGLQQLLVPGG +>non-ACP260 +APATPPRPLKRKKLQFTDVTPESSP +>non-ACP262 +EQAERYDDMAAAMKAVTEQGHELSNEERNL +>non-ACP264 +MPNDPSDNQLK +>non-ACP266 +TELLLAITVFCLGFWVVRALRTQVP +>non-ACP268 +LTADLLGAPFFTLPKELQLALLERQTVFL +>non-ACP270 +GHGRLVEIQGRLGVRIER +>non-ACP272 +LPFKLLLFVLLDGWTRLTH +>non-ACP274 +QALWLVLVLSMPPVLVAAVVGTLVSLVQ |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test2/out2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test2/out2.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,139 @@ +H +0.1475757575757576 +0.3215384615384615 +0.44875 +0.44875 +0.45687500000000003 +0.48624999999999996 +0.4235294117647058 +0.4129411764705882 +-0.10278350515463919 +0.15153846153846157 +-0.296 +-0.14411764705882354 +-0.0019230769230769162 +0.20703703703703702 +0.2162962962962963 +0.28814814814814815 +0.24777777777777776 +0.4795833333333333 +0.35076923076923083 +0.03171428571428572 +-0.035128205128205144 +0.04405405405405406 +-0.1698809523809524 +0.17913043478260865 +0.11269230769230772 +0.28448275862068967 +0.07433333333333328 +-0.6266666666666666 +0.14071428571428576 +-0.43117647058823527 +-0.19765957446808508 +0.4856 +0.5168 +0.3433333333333333 +0.4583333333333333 +0.5745454545454545 +0.3282608695652174 +0.3733333333333333 +0.17192307692307696 +-0.3457142857142857 +0.1076 +0.4675 +0.4675 +-0.16962962962962963 +0.08749999999999998 +-0.3174358974358975 +0.4411111111111112 +-0.050120481927710826 +-0.025555555555555557 +0.24727272727272726 +-0.15142857142857138 +-0.066 +0.07142857142857142 +0.34882352941176475 +0.6842857142857143 +0.6666666666666666 +0.5438095238095239 +0.18681818181818183 +-0.231 +0.5955 +0.35541666666666666 +0.08687500000000001 +0.5977777777777777 +0.15000000000000002 +0.19517241379310335 +0.1663333333333333 +0.33566666666666667 +0.19225806451612903 +0.21999999999999997 +-0.2715662650602409 +0.28916666666666674 +0.2563157894736842 +-0.10543478260869568 +-0.12173913043478261 +-0.15695652173913047 +-0.43962962962962954 +-0.21695652173913044 +0.12199999999999997 +0.38833333333333336 +0.4166666666666667 +0.4054166666666666 +0.4258333333333333 +0.35625 +0.14285714285714288 +0.055333333333333366 +0.07533333333333335 +0.6094117647058823 +-0.21846153846153846 +-0.058333333333333334 +-0.2692857142857143 +0.20566666666666658 +0.00366666666666667 +0.1886206896551724 +0.13266666666666665 +0.24470588235294113 +0.2412903225806451 +0.23933333333333323 +0.264516129032258 +0.27419354838709675 +0.12766666666666668 +0.23583333333333334 +0.12916666666666668 +0.3400000000000001 +-0.16058823529411767 +0.33214285714285713 +0.19161290322580643 +0.0384 +0.12482758620689656 +0.2403125 +0.2882142857142857 +0.24965517241379304 +0.06206896551724138 +0.26321428571428573 +0.37636363636363634 +0.07636363636363636 +-0.034615384615384596 +0.0023076923076923396 +0.026500000000000013 +0.16733333333333336 +0.3899999999999999 +0.2585 +-0.24882352941176467 +-0.053333333333333316 +-0.29405405405405405 +0.23041666666666671 +-0.05090909090909091 +0.2141666666666667 +-0.11818181818181818 +-0.18722222222222226 +0.2615384615384615 +0.03583333333333333 +0.03583333333333331 +0.06166666666666661 +0.31583333333333335 +-0.031666666666666655 +0.3292307692307693 +0.02470588235294122 +-0.005333333333333309 |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test3/out3.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test3/out3.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test5/out5.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test5/out5.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Sequence_Analysis/test-data/test6/out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Sequence_Analysis/test-data/test6/out.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.py Wed Oct 28 01:52:18 2020 +0000 |
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| @@ -0,0 +1,73 @@ +import tempfile +import pandas as pd +import shutil +import sys +import glob +import fragbuilder +import openbabel +from fragbuilder import peptide + +import os + + +def read_pep_file(pep_infile): + + file = open(pep_infile) + lines = file.readlines() + + Index = [] + list_pep_name = [] + + for line in lines: + if '>' in line: + Index.append(line.strip('\n')) + else: + line = line.strip('\n') + line = line.strip('\r') + list_pep_name.append(line.strip('\n')) + + return list_pep_name + +def structure_gen(pep_seq, out_dir): + + if not os.path.exists(os.path.join(out_dir, 'DataFile')): + os.makedirs(os.path.join(out_dir, 'DataFile')) + + b = len(pep_seq) + + for seq in pep_seq: + + pep = peptide.Peptide(seq, nterm = "charged", cterm = "neutral") + pep.regularize() + pep.write_pdb(os.path.join(out_dir, 'DataFile', seq+".pdb")) + + obConversion = openbabel.OBConversion() + obConversion.SetInAndOutFormats("pdb", "sdf") + mol = openbabel.OBMol() + obConversion.ReadFile(mol, os.path.join(out_dir, 'DataFile', seq+".pdb")) + + mol.AddHydrogens() + + +def main_process(str_pep_file, out_dir): + + my_pep = read_pep_file(str_pep_file) + structure_gen(my_pep, out_dir) + + +if __name__=="__main__": + + + import argparse + parser = argparse.ArgumentParser() + + parser.add_argument("-p", "--pep", required=True, default=None, help="pep file") + parser.add_argument("-o", "--OutDir", required=None, default=os.getcwd(), help="Path to out file") + + args = parser.parse_args() + main_process(args.pep, args.OutDir) + + + + + |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Structure_Builder/test-data/DataFile/GLF.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Structure_Builder/test-data/DataFile/GLF.pdb Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,104 @@ +COMPND 532b43383ef54805b372df2052770b55.xyz +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +ATOM 1 H1 GLY A 1 -0.947 -3.845 0.857 1.00 0.00 H +ATOM 2 H2 GLY A 1 -0.713 -3.892 -0.803 1.00 0.00 H +ATOM 3 N GLY A 1 -0.621 -3.315 0.040 1.00 0.00 N +ATOM 4 H3 GLY A 1 0.386 -3.137 0.204 1.00 0.00 H +ATOM 5 CA GLY A 1 -1.319 -1.994 -0.077 1.00 0.00 C +ATOM 6 C GLY A 1 -0.309 -0.872 0.134 1.00 0.00 C +ATOM 7 HA1 GLY A 1 -1.785 -1.954 -1.064 1.00 0.00 H +ATOM 8 HA2 GLY A 1 -2.074 -1.955 0.712 1.00 0.00 H +ATOM 9 O GLY A 1 0.593 -1.038 0.954 1.00 0.00 O +ATOM 10 N LEU A 2 -0.429 0.219 -0.671 1.00 0.00 N +ATOM 11 H LEU A 2 -1.117 0.254 -1.426 1.00 0.00 H +ATOM 12 CA LEU A 2 0.459 1.393 -0.605 1.00 0.00 C +ATOM 13 HA LEU A 2 0.332 1.829 0.390 1.00 0.00 H +ATOM 14 CB LEU A 2 1.922 1.033 -0.902 1.00 0.00 C +ATOM 15 C LEU A 2 -0.074 2.337 -1.694 1.00 0.00 C +ATOM 16 HB1 LEU A 2 2.267 0.267 -0.198 1.00 0.00 H +ATOM 17 HB2 LEU A 2 1.979 0.568 -1.897 1.00 0.00 H +ATOM 18 CG LEU A 2 2.914 2.212 -0.852 1.00 0.00 C +ATOM 19 O LEU A 2 -0.481 1.887 -2.764 1.00 0.00 O +ATOM 20 HG LEU A 2 2.626 2.959 -1.601 1.00 0.00 H +ATOM 21 CD2 LEU A 2 2.950 2.886 0.520 1.00 0.00 C +ATOM 22 CD1 LEU A 2 4.316 1.715 -1.216 1.00 0.00 C +ATOM 23 HD21 LEU A 2 3.225 2.174 1.305 1.00 0.00 H +ATOM 24 HD22 LEU A 2 3.682 3.701 0.530 1.00 0.00 H +ATOM 25 HD23 LEU A 2 1.983 3.322 0.784 1.00 0.00 H +ATOM 26 HD11 LEU A 2 4.319 1.250 -2.208 1.00 0.00 H +ATOM 27 HD12 LEU A 2 5.030 2.544 -1.232 1.00 0.00 H +ATOM 28 HD13 LEU A 2 4.674 0.973 -0.493 1.00 0.00 H +ATOM 29 N PHE A 3 -0.097 3.669 -1.378 1.00 0.00 N +ATOM 30 H PHE A 3 0.245 4.000 -0.480 1.00 0.00 H +ATOM 31 CA PHE A 3 -0.582 4.687 -2.325 1.00 0.00 C +ATOM 32 HA PHE A 3 0.142 4.669 -3.141 1.00 0.00 H +ATOM 33 CB PHE A 3 -2.047 4.467 -2.753 1.00 0.00 C +ATOM 34 C PHE A 3 -0.462 6.046 -1.641 1.00 0.00 C +ATOM 35 HB1 PHE A 3 -2.452 3.593 -2.222 1.00 0.00 H +ATOM 36 HB2 PHE A 3 -2.657 5.319 -2.420 1.00 0.00 H +ATOM 37 CG PHE A 3 -2.358 4.263 -4.224 1.00 0.00 C +ATOM 38 O PHE A 3 -0.686 6.268 -0.459 1.00 0.00 O +ATOM 39 CD2 PHE A 3 -3.706 4.066 -4.576 1.00 0.00 C +ATOM 40 CD1 PHE A 3 -1.405 4.261 -5.249 1.00 0.00 C +ATOM 41 HD2 PHE A 3 -4.477 4.061 -3.809 1.00 0.00 H +ATOM 42 CE2 PHE A 3 -4.083 3.880 -5.907 1.00 0.00 C +ATOM 43 CE1 PHE A 3 -1.784 4.075 -6.582 1.00 0.00 C +ATOM 44 HD1 PHE A 3 -0.345 4.400 -5.059 1.00 0.00 H +ATOM 45 HE2 PHE A 3 -5.130 3.733 -6.160 1.00 0.00 H +ATOM 46 CZ PHE A 3 -3.121 3.887 -6.910 1.00 0.00 C +ATOM 47 HE1 PHE A 3 -1.027 4.082 -7.363 1.00 0.00 H +ATOM 48 HZ PHE A 3 -3.412 3.745 -7.949 1.00 0.00 H +ATOM 49 OXT PHE A 3 -0.036 7.020 -2.465 1.00 0.00 O +ATOM 50 HXT PHE A 3 0.006 7.834 -1.917 1.00 0.00 H +CONECT 1 3 +CONECT 2 3 +CONECT 3 2 5 4 1 +CONECT 4 3 +CONECT 5 7 3 6 8 +CONECT 6 9 5 10 +CONECT 7 5 +CONECT 8 5 +CONECT 9 6 +CONECT 10 11 6 12 +CONECT 11 10 +CONECT 12 14 15 10 13 +CONECT 13 12 +CONECT 14 17 16 18 12 +CONECT 15 19 29 12 +CONECT 16 14 +CONECT 17 14 +CONECT 18 22 14 20 21 +CONECT 19 15 +CONECT 20 18 +CONECT 21 18 23 24 25 +CONECT 22 26 28 27 18 +CONECT 23 21 +CONECT 24 21 +CONECT 25 21 +CONECT 26 22 +CONECT 27 22 +CONECT 28 22 +CONECT 29 15 31 30 +CONECT 30 29 +CONECT 31 32 29 34 33 +CONECT 32 31 +CONECT 33 31 37 36 35 +CONECT 34 38 31 49 +CONECT 35 33 +CONECT 36 33 +CONECT 37 40 33 39 +CONECT 38 34 +CONECT 39 37 42 41 +CONECT 40 44 43 37 +CONECT 41 39 +CONECT 42 46 39 45 +CONECT 43 47 40 46 +CONECT 44 40 +CONECT 45 42 +CONECT 46 43 48 42 +CONECT 47 43 +CONECT 48 46 +CONECT 49 34 50 +CONECT 50 49 +MASTER 0 0 0 0 0 0 0 0 50 0 50 0 +END |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Peptide_Structure_Builder/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Peptide_Structure_Builder/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>sequences_0 +GLF \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/PDAUG_Sequence_Based_Peptide_Generation.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,154 @@ +import sys +import itertools +import pandas as pd +import random +import os +from itertools import permutations +from random import shuffle +import argparse, sys +import pandas as pd + + +def MutatedPeptides(input_file, index_list, AA, outputFile): + + + index_list = [int(x) for x in index_list.split(',')] + out_put = [] + AA = AA.split(',') + l = len(index_list) + + replacements = [x for x in itertools.permutations(AA,l)] + + + counter = 0 + to_modify = [x for x in input_file] + + for replacement in replacements: + for i,index in enumerate(index_list): + to_modify[index_list[i]-1] = replacement[i] + + counter = counter + 1 + out_put.append("".join(to_modify).upper()) + + w = open(outputFile, 'w') + + for i, f in enumerate(out_put): + + + w.write(">sequence_"+str(i)+'\n') + w.write(f+'\n') + +def RandomPeptides(AAs, pep_length, out_pep_num, outputFile): + + + if int(pep_length) > 20: + print ("Max peptide lenth 20") + exit() + else: + pass + + if int(out_pep_num) > 10000: + print ("Max peptide library 10000") + exit() + else: + pass + + out_pep_lib = [] + raw = AAs.split(',') + + for x in range(int(out_pep_num)): + un_seq = [] + for i in range(int(pep_length)): + un_seq.append(random.choice(raw)) + out_pep_lib.append("".join(un_seq)) + + + w = open(outputFile, 'w') + + + for i, f in enumerate(out_pep_lib): + + w.write(">sequence_"+str(i)+'\n') + w.write(f+'\n') + +def SlidingWindowPeptide(infile, window_size, frag_size, outputFile): + + + if int(window_size) > 10: + print ("Max window_size 10") + exit() + else: + pass + if int(frag_size) > 20: + print ("Max frag size is 20") + exit() + else: + pass + + + pep_list = [] + + f = open(infile) + + lines = f.readlines() + + flines = [] + + for line in lines: + if '>' in line: + pass + else: + flines.append(line.strip('\n')) + sequence = "".join(flines) + + for i in range(int(frag_size)): + if int(frag_size) == len(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]): + pep_list.append(sequence[i*int(window_size):i*int(window_size)+int(frag_size)]) + else: + break + + w = open(outputFile, 'w') + + + for i, f in enumerate(pep_list): + + w.write(">sequence_"+str(i)+'\n') + w.write(f+'\n') + +if __name__=='__main__': + + parser = argparse.ArgumentParser(description='Deployment tool') + subparsers = parser.add_subparsers() + + Mp = subparsers.add_parser('MutatedPeptides') + Mp.add_argument("-s","--sequence") + Mp.add_argument("-m","--mutation_site_list") + Mp.add_argument("-a","--AA_list") + Mp.add_argument("-d", "--outputFile", required=None, default='out.fasta', help="Path to out file") + + Rp = subparsers.add_parser('RandomPeptides') + Rp.add_argument("-a","--AA_list") + Rp.add_argument("-l","--pep_length") + Rp.add_argument("-o","--out_pep_lenght") + Rp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") + + Sp = subparsers.add_parser('SlidingWindowPeptide') + Sp.add_argument("-i","--InFile") + Sp.add_argument("-w","--winSize") + Sp.add_argument("-s","--FragSize") + Sp.add_argument("-d", "--outputFile", required=None, default=os.path.join(os.getcwd(),'report_dirr'), help="Path to out file") + + args = parser.parse_args() + + if sys.argv[1] == 'MutatedPeptides': + MutatedPeptides(args.sequence, args.mutation_site_list, args.AA_list, args.outputFile) + + elif sys.argv[1] == 'RandomPeptides': + RandomPeptides(args.AA_list, args.pep_length, args.out_pep_lenght, args.outputFile) + + elif sys.argv[1] == 'SlidingWindowPeptide': + SlidingWindowPeptide(args.InFile, args.winSize, args.FragSize, args.outputFile) + + else: + print("In Correct Option:") + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Based_Peptide_Generation/test-data/out1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/test-data/out1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>sequence_0 +KGLKLLKKKLLK +>sequence_1 +KYLKLLKKKLLK |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Based_Peptide_Generation/test-data/out2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/test-data/out2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +>sequence_0 +FKFGG +>sequence_1 +GDDLGGV +>sequence_2 +GVKKK +>sequence_3 +GFDDFV +>sequence_4 +GGLFKF +>sequence_5 +VKDVG +>sequence_6 +FFKDDIL |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Based_Peptide_Generation/test-data/out3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/test-data/out3.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +>sequence_0 +MNRLTFA +>sequence_1 +LTFAVFL +>sequence_2 +AVFLSAL +>sequence_3 +LSALGFL +>sequence_4 +LGFLVCA +>sequence_5 +LVCAAGN +>sequence_6 +AAGNPCC |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Based_Peptide_Generation/test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Based_Peptide_Generation/test-data/test1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,10 @@ +>AHC69389.1 COX-2 [Pagrus major] +MNRLTFAVFLSALGFLVCAAGNPCCSEPCQNRGVCTALGSDNYECDCTRTGYRGQNCTTPEFLTWLKVSL +KPSPNTVHYILTHFKDFWNIINNISFLRDAIMRYVLTSRSHMIDSPPTFNADYGYKNWEAYSNLSYYTRT +LPPVPEDCPTPMGVEGKKELPDAKILAEKLLMRREFIPDPQGTSLMFAFFAQHFTHQFFKSDMKRGPAFT +AAQGHGVDLSHIYGDNLVRQHKLRLFKDGKLKHQILDGEMYPPTVKEVGAEMHHPPHVPDAYRFAVGHEA +FGLVPGLMMYATIWLREHNRVCDVLKEVHPDWDDERLFQTTRLILIGETIKIVIEDYVQHLSGYNFKLKF +DPELLFNQRFQYQNRIASEFNTLYHWHPLMPDSFHIEEKEYSYKEFVFNTSVVTEHGISNLVESFSKQIA +GRVAGGRNVPGPIMYVAIKSIENSRKMRYQSLNAYRKRFSLKPYSSFEDMTGEKEMAAVLEEMYGHIDAM +ELYPGLLVEKPRENAIFGETMVEMGAPFSLKGLMGNPICSPEYWKPSTFGGTVGFDIVNTASLQRLVCNN +ANGPCPVASFHVPDVKETGSMIINSSTSNSRSSDINPTVILKERTTEL \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Network/PDAUG_Sequence_Network.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Network/PDAUG_Sequence_Network.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,53 @@ +import Levenshtein +import matplotlib.pyplot as plt +import networkx as nx +import os + + +def SeqSimilarityNetwork(InFile, OutFile): + + f = open(InFile) + lines = f.readlines() + + record = [] + seq = [] + + G = nx.Graph() + + for line in lines: + + if ">" in line: + record.append(line.strip('\n')) + else: + seq.append(line.strip('\n')) + + for x, i in enumerate(seq): + for X, I in enumerate(seq): + L = Levenshtein.ratio(i, I ) + if L >= 0.4: + G.add_edge(record[x], record[X], weight=float(Levenshtein.ratio(i, I ))) + + elarge = [(u, v) for (u, v, d) in G.edges(data=True) if d['weight'] >= 0.4] + + pos = nx.spring_layout(G) + nx.draw_networkx_nodes(G, pos, node_size=10) + nx.draw_networkx_edges(G, pos, edgelist=elarge,width=1) + plt.axis('off') + + plt.savefig(OutFile) + + + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-I", "--InFile", required=True, default=None, help="Path to target tsv file") + parser.add_argument("-O","--OutFile", required=False, help="HTML out file", default="out.png") + args = parser.parse_args() + + SeqSimilarityNetwork(args.InFile, args.OutFile) + + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Network/test-data/out.png |
| b |
| Binary file PDAUG_Sequence_Network/test-data/out.png has changed |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Network/test-data/positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Network/test-data/positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Property_Based_Descriptors/Out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/Out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,158 @@ +import pandas as pd +from pydpi.pypro import PyPro +import os + + +def BinaryDescriptor(seq): + + BinaryCode = { + + 'A':"1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'C':"0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'D':"0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'E':"0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'F':"0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'G':"0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'H':"0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0", + 'I':"0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0", + 'K':"0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0", + 'L':"0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0", + 'M':"0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0", + 'N':"0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0", + 'P':"0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0", + 'Q':"0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0", + 'R':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0", + 'S':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0", + 'T':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0", + 'V':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0", + 'W':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0", + 'Y':"0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1", + } + + lines = [] + Df = [] + + + for s in seq: + des = [] + for n in s: + des.append(BinaryCode[n.upper()]) + lines.append(','.join(des).split(',')) + + df = pd.DataFrame(lines) + + return df + +def Decriptor_generator(InFile, Lamda, Weight, DesType, Out_file): + + list_pep_name = [] + f = open(InFile) + lines = f.readlines() + + for line in lines: + if ">" in line: + pass + else: + list_pep_name.append(line.strip('\n')) + + out_df = pd.DataFrame() + + for seq in list_pep_name: + + protein = PyPro() + protein.ReadProteinSequence(seq) + + if DesType == 'PAAC': + DS = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'APAAC': + DS = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'CTD': + DS = protein.GetCTD() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'DPComp': + DS = protein.GetDPComp() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'GearyAuto': + DS = protein.GetGearyAuto() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'MoranAuto': + DS = protein.GetMoranAuto() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'MoreauBrotoAuto': + DS = protein.GetMoreauBrotoAuto() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'QSO': + DS = protein.GetQSO() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'SOCN': + DS = protein.GetSOCN() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'TPComp': + DS = protein.GetTPComp() + df = pd.DataFrame(DS, index=[0]) + elif DesType == 'All': + DS_1 = protein.GetPAAC(lamda=int(Lamda), weight=float(Weight)) + DS_2 = protein.GetAPAAC(lamda=int(Lamda), weight=float(Weight)) + DS_3 = protein.GetCTD() + DS_4 = protein.GetDPComp() + DS_5 = protein.GetGearyAuto() + DS_6 = protein.GetMoranAuto() + DS_7 = protein.GetMoreauBrotoAuto() + DS_8 = protein.GetQSO() + DS_9 = protein.GetSOCN() + DS_10 = protein.GetTPComp() + + DS = {} + + for D in (DS_1, DS_2, DS_3, DS_4, DS_5, DS_6, DS_7, DS_8, DS_9, DS_10): + DS.update(D) + + df = pd.DataFrame(DS, index=[0]) + + if DesType == 'BinaryDescriptor': + out_df = BinaryDescriptor(list_pep_name) + else: + out_df = pd.concat([out_df, df], axis=0) + + + out_df.to_csv(Out_file, index=False, sep='\t') + + +if __name__=="__main__": + + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-I", "--InFile", + required=True, + default=None, + help="pep file") + + parser.add_argument("-l", "--Lamda", + required=False, + default=50, + help="pep file") + + parser.add_argument("-w", "--Weight", + required=False, + default=0.5, + help="pep file") + + parser.add_argument("-t", "--DesType", + required=True, + default=None, + help="out put file name for str Descriptors") + + parser.add_argument("-O", "--Out_file", + required=False, + default="Out.tsv", + help="Path to target tsv file") + + args = parser.parse_args() + Decriptor_generator(args.InFile, args.Lamda, args.Weight, args.DesType, args.Out_file) + + \ No newline at end of file |
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| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Property_Based_Descriptors/test-data/Out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/test-data/Out.tsv Wed Oct 28 01:52:18 2020 +0000 |
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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Property_Based_Descriptors/test-data/Out1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/test-data/Out1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Sequence_Property_Based_Descriptors/test-data/positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Sequence_Property_Based_Descriptors/test-data/positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,16 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,57 @@ +import os +import argparse + + +def TSVtoFASTA(InFile, Method, Positive, Negative, OutFile): + + if Method == 'WithClassLabel': + + f = open(InFile) + lines = f.readlines() + + of1 = open(Positive,'w') + of2 = open(Negative,'w') + + n = 0 + m = 0 + + for line in lines: + + if '1' in line.split('\t')[1].strip('\n'): + n= n+1 + of1.write('>peptide_'+str(n)+'\n') + of1.write(line.split('\t')[0]+'\n') + + if '0' in line.split('\t')[1].strip('\n'): + m= m+1 + of2.write('>peptide_'+str(m)+'\n') + of2.write(line.split('\t')[0]+'\n') + + elif Method == 'NoClassLabel': + + f = open(InFile) + lines = f.readlines() + of1 = open(OutFile,'w') + + for i, line in enumerate(lines[1:]): + of1.write('>peptide_'+str(i)+'\n') + of1.write(line.split('\t')[0]+'\n') + + else: + pass + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + + parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv") + parser.add_argument("-P", "--Postvs", required=False, default='Positive.fasta', help="Path to target tsv file") + parser.add_argument("-N", "--Negtvs", required=False, default='Negative.fasta', help="Path to target tsv file") + parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file") + parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file") + args = parser.parse_args() + + TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile) + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/test-data/test1.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/test-data/test1.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,24 @@ +Peptides Class_label +GLFDIVKKVVGALG 0 +KLLKLLKKKLLK 0 +KLLLLKLLK 0 +GLFDIVKKVVGALG 0 +GLFDIVKKVVGALG 0 +KLLKLLKKKLLK 0 +KLLLLKLLK 0 +GLFDIVKKVVGALG 0 +GLFDIVKKVVGALG 0 +KLLKLLKKKLLK 0 +KLLLLKLLK 0 +GLFDIVKKVVGALG 0 +GLFDIVKKVVGALG 1 +KLLKLLKKKLLK 1 +KLLLLKLLK 1 +GLFDIVKKVVGALG 1 +GLFDIVKKVVGALG 1 +KLLKLLKKKLLK 1 +KLLLLKLLK 1 +GLFDIVKKVVGALG 1 +KLLKLLKKKLLK 1 +KLLLLKLLK 1 +GLFDIVKKVVGALG 1 \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/test-data/test1/Negative.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/test-data/test1/Negative.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,24 @@ +>peptide_1 +GLFDIVKKVVGALG +>peptide_2 +KLLKLLKKKLLK +>peptide_3 +KLLLLKLLK +>peptide_4 +GLFDIVKKVVGALG +>peptide_5 +GLFDIVKKVVGALG +>peptide_6 +KLLKLLKKKLLK +>peptide_7 +KLLLLKLLK +>peptide_8 +GLFDIVKKVVGALG +>peptide_9 +GLFDIVKKVVGALG +>peptide_10 +KLLKLLKKKLLK +>peptide_11 +KLLLLKLLK +>peptide_12 +GLFDIVKKVVGALG |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/test-data/test1/Positive.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/test-data/test1/Positive.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,22 @@ +>peptide_1 +GLFDIVKKVVGALG +>peptide_2 +KLLKLLKKKLLK +>peptide_3 +KLLLLKLLK +>peptide_4 +GLFDIVKKVVGALG +>peptide_5 +GLFDIVKKVVGALG +>peptide_6 +KLLKLLKKKLLK +>peptide_7 +KLLLLKLLK +>peptide_8 +GLFDIVKKVVGALG +>peptide_9 +KLLKLLKKKLLK +>peptide_10 +KLLLLKLLK +>peptide_11 +GLFDIVKKVVGALG |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/test-data/test2.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/test-data/test2.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,24 @@ +Peptides +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG +KLLKLLKKKLLK +KLLLLKLLK +GLFDIVKKVVGALG \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_TSVtoFASTA/test-data/test2/Out.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_TSVtoFASTA/test-data/test2/Out.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,69 @@ +>peptide_0 +GLFDIVKKVVGALG + +>peptide_1 +KLLKLLKKKLLK + +>peptide_2 +KLLLLKLLK + +>peptide_3 +GLFDIVKKVVGALG + +>peptide_4 +GLFDIVKKVVGALG + +>peptide_5 +KLLKLLKKKLLK + +>peptide_6 +KLLLLKLLK + +>peptide_7 +GLFDIVKKVVGALG + +>peptide_8 +GLFDIVKKVVGALG + +>peptide_9 +KLLKLLKKKLLK + +>peptide_10 +KLLLLKLLK + +>peptide_11 +GLFDIVKKVVGALG + +>peptide_12 +GLFDIVKKVVGALG + +>peptide_13 +KLLKLLKKKLLK + +>peptide_14 +KLLLLKLLK + +>peptide_15 +GLFDIVKKVVGALG + +>peptide_16 +GLFDIVKKVVGALG + +>peptide_17 +KLLKLLKKKLLK + +>peptide_18 +KLLLLKLLK + +>peptide_19 +GLFDIVKKVVGALG + +>peptide_20 +KLLKLLKKKLLK + +>peptide_21 +KLLLLKLLK + +>peptide_22 +GLFDIVKKVVGALG + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Uversky_Plot/PDAUG_Uversky_Plot.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,61 @@ +import matplotlib +matplotlib.use('Agg') +import os +import sys +sys.path.insert(0, os.path.abspath('..')) +from quantiprot.utils.io import load_fasta_file +from quantiprot.utils.feature import Feature, FeatureSet +from quantiprot.utils.sequence import compact +from quantiprot.metrics.aaindex import get_aa2charge, get_aa2hydropathy +from quantiprot.metrics.basic import average, average_absolute +from matplotlib import pyplot as plt + + + +def Run_Uverskey(Fasta1, Fasta2, OutFile): + + + amyload_seq = load_fasta_file(Fasta1) + disprot_seq = load_fasta_file(Fasta2) + + net_abs_charge = Feature(get_aa2charge(default=0)).then(average_absolute) + mean_hydropathy = Feature(get_aa2hydropathy(default=0)).then(average) + + uversky_fs = FeatureSet("uversky") + uversky_fs.add(mean_hydropathy, name="mean_hydropathy") + uversky_fs.add(net_abs_charge, name="net_abs_charge") + + amyload_uversky_seq = uversky_fs(amyload_seq) + disprot_uversky_seq = uversky_fs(disprot_seq) + + + amyload_data_x = amyload_uversky_seq.columns(feature="mean_hydropathy")[0] + amyload_data_y = amyload_uversky_seq.columns(feature="net_abs_charge")[0] + plt.plot(amyload_data_x, amyload_data_y,'.', label="Amyload") + + disprot_data = compact(disprot_uversky_seq).columns() + plt.plot(disprot_data[0], disprot_data[1],'.', label="Disprot") + + plt.plot([-0.78, 0.835], [0.0, 0.5],'k') + plt.xlabel("mean hydrophobicity") + plt.ylabel("net abs charge") + plt.legend() + + plt.savefig(OutFile) + + + +if __name__=="__main__": + + import argparse + + parser = argparse.ArgumentParser() + parser.add_argument("-f1", "--Fasta1", required=True, default=None, help="pep file") + parser.add_argument("-f2", "--Fasta2", required=True, default=None, help="out put file name for str Descriptors") + parser.add_argument("--OutFile", required=False, help="HTML out file", default="out.png") + + + + args = parser.parse_args() + + Run_Uverskey(args.Fasta1, args.Fasta2, args.OutFile) |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Uversky_Plot/test-data/out.png |
| b |
| Binary file PDAUG_Uversky_Plot/test-data/out.png has changed |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Uversky_Plot/test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Uversky_Plot/test-data/test1.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>ACP0 +GLWSKIKEVGKEAAKAAAKAAGKAALGAVSEAV +>ACP2 +GLFDIIKKIAESI +>ACP4 +GLLDIVKKVVGAFGSL +>ACP6 +GLFDIVKKVVGALGSL +>ACP8 +GLFDIVKKVVGTLAGL +>ACP10 +GLFDIAKKVIGVIGSL +>ACP12 +GLFDIVKKIAGHIAGSI +>ACP14 +GLFDIVKKIAGHIVSSI +>ACP16 +AACARFIDDFCDTLTPNIYRPRDNGQRCYAVNGHRCDFTVFNTNNGGNPIRASTPNCKTVLRTAANRCPTGGRGKINPNAPFLFAIDPNDGDCSTNF +>ACP18 +HGVSGHGQHGVHG +>ACP20 +FKCRRWQWRMKKLGAPSITCVRRAF +>ACP22 +KWKLFKKIKFLHSAKKF +>ACP24 +KSSAYSLQMGATAIKQVKKLFKKWGW +>ACP26 +GIGTKILGGVKTALKGALKELASTYAN +>ACP28 +GIGGKILSGLKTALKGAAKELASTYLH +>ACP30 +GIGGVLLSAGKAALKGLAKVLAEKYAN +>ACP32 +SIGAKILGGVKTFFKGALKELASTYLQ +>ACP34 +FLPLLAGLAANFLPTIICKISYKC +>ACP36 +FVQWFSKFLGRIL +>ACP38 +KWKIFKKIEKVGRNIRNGIIKAGPAVAVLGEAKAL +>ACP40 +GWLKKIGKKIERVGQHTRDATIQTIGVAQQAANVAATLK +>ACP42 +KWKLFKKIEKVGQNIRDGIIKAGPAVAVVGQATQIAK +>ACP44 +SQLGDLGSGAGQGGGGGGSIRAAGGAFGKLEAAREEEFFYKKQKEQLERLKNDQIHQAEFHHQQIKEHEEAIQRHKDFLNNLHK +>ACP46 +GIGKFLHSAKKFGKAFVGEIMNS +>ACP48 +GIGAVLKVLTTGLPALISWIKRKRQQ +>ACP50 +ALWKNMLKGIGKLAGQAALGAVKTLVGAE +>ACP52 +ACYCRIPACIAGERRYGTCIYQGRLWAFCC +>ACP54 +ECRRLCYKQRCVTYCRGR +>ACP56 +LKLKSIVSWAKKVL +>ACP58 +KWCFRVCYRGICYRRCR +>ACP60 +KSCCRNTWARNCYNVCRLPGTISREICAKKCDCKIISGTTCPSDYPK +>ACP62 +GLLSVLGSVAKHVLPHVVPVIAEHL +>ACP64 +GLLSVLGSVVKHVIPHVVPVIAEHL +>ACP66 +GLFKVLGSVAKHLLPHVAPVIAEK +>ACP68 +GLFGVLGSIAKHVLPHVVPVIAEK +>ACP70 +GLFVGVLAKVAAHVVPAIAEHF +>ACP72 +GLFVGLAKVAAHNNPAIAEHFQA +>ACP74 +GFVDFLKKVAGTIANVVT +>ACP76 +GLLQTIKEKLESLESLAKGIVSGIQA +>ACP78 +TRSSRAGLQFPVGRVHRLLRK +>ACP80 +FFGWLIKGAIHAGKAIHGLIHRRRH +>ACP82 +GLFDVIKKVASVIGGL +>ACP84 +GLFDIIKKVASVVGGL +>ACP86 +GRFKRFRKKFKKLFKKLSPVIPLLHLG +>ACP88 +GGLRSLGRKILRAWKKYGPIIVPIIRIG +>ACP90 +RRRPRPPYLPRPRPPPFFPPRLPPRIPPGFPPRFPPRFP +>ACP92 +GLLGPLLKIAAKVGSNLL +>ACP94 +GLICESCRKIIQKLEDMVGPQPNEDTVTQAASQVCDKLKILRGLCKKIMRSFLRRISWDILTGKKPQAICVDIKICKEKTGLI +>ACP96 +DHYNCVSSGGQCLYSACPIFTKIQGTCYRGKAKCCK +>ACP98 +FFHHIFRGIVHVGKTIHRLVTG +>ACP100 +KLAKLAKKLAKLAK +>ACP102 +KTCENLADTFRGPCFATSNC +>ACP104 +IDWKKLLDAAKQIL +>ACP106 +FLIGMTQGLICLITRKC +>ACP108 +ILPILSLIGGLLGK +>ACP110 +GLLGLLGSVVSHVVPAIVGHF +>ACP112 +GLLGLLGSVVSHVLPAITQHL +>ACP114 +GIKCRFCCGCCTPGICGVCCRF +>ACP116 +QSHLSLCRWCCNCCRSNKGC +>ACP118 +ILGPVISTIGGVLGGLLKNL +>ACP120 +FLPILASLAAKFGPKLFCLVTKKC +>ACP122 +GLWSKIKEAAKAAGKAALNAVTGLVNQGDQPS +>ACP124 +LLGMIPLAISAISALSKL +>ACP126 +GLPVCGETCVGGTCNTPGCSCSWPVCTRN +>ACP128 +GVPICGETCTLGTCYTAGCSCSWPVCTRN +>ACP130 +GIPCGESCVWIPCISSAIGCSCKSKVCYRN +>ACP132 +GIPCAESCVWIPCTVTALIGCGCSNKVCYN +>ACP134 +GTFPCGESCVFIPCLTSAIGCSCKSKVCYKN +>ACP136 +GLLPCAESCVYIPCLTTVIGCSCKSKVCYKN +>ACP138 +GRDYRTCLTIVQKLKKMVDKPTQRSVSNAATRVCRTGRSRWRDVCRNFMRRYQSRVTQGLVAGETAQQICEDLRLCIPSTGPL +>ACP140 +GETDPNTQLLNDLGNNMAWGAALGAPGGLGSAALGAAGGALQTVGQGLIDHGPVNVFIPVLIGPSWNGSGSGYNSATSSSGSGS +>ACP142 +GFKDLLKGAAKALVKTVLF +>ACP144 +KSCCPNTTGRNIYNACRLTGAPRPTCAKLSGCKIISGSTCPSDYPK +>ACP146 +KSCCPNTTGRNIYNTCRFGGGSREVCARISGCKIISASTCPSDYPK +>ACP148 +KSCCPNTTGRNIYNTCRLTGSSRETCAKLSGCKIISASTCPSNYPK +>ACP150 +MRKEFHNVLSSGQLLADKRPARDYNRK +>ACP152 +KSCCKNTTGRNIYNTCRFAGGSRERCAKLSGCKIISASTCPSDYPK +>ACP154 +FIFHIIKGLFHAGKMIHGLVTRRRH +>ACP156 +FLPAIVGAAAKFLPKIFCAISKKC +>ACP158 +FLPIIAGVAAKVLPKIFCAISKKC +>ACP160 +FLPIIAGIAAKFLPKIFCTISKKC +>ACP162 +FLPVIAGVAANFLPKLFCAISKKC +>ACP164 +FLPIIAGAAAKVVQKIFCAISKKC +>ACP166 +GLMDTIKGVAKTVAASWLDKLKCKITGC +>ACP168 +VNWKKVLGKIIKVAK +>ACP170 +VNWKKILGKIIKVAK +>ACP172 +FFSLLPSLIGGLVSAIK +>ACP174 +RFRLPFRRPPIRIHPPPFYPPFRRFL +>ACP176 +KWKLFKKIPKFLHLAKKF +>ACP178 +YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGSG +>ACP180 +GIPCGESCVFIPCITGAIGCSCKSKVCYRN +>ACP182 +GEFLKCGESCVQGECYTPGCSCDWPICKKN +>ACP184 +GLPTCGETCTLGTCYVPDCSCSWPICMKN +>ACP186 +GLPVCGETCFGGTCNTPGCTCDPWPVCTRN +>ACP188 +FVDLKKIANIINSIFGK +>ACP190 +GSIPCGESCVFIPCISSVIGCACKSKVCYKN +>ACP192 +GIPCGESCVFIPCISSVIGCSCSSKVCYRN +>ACP194 +GSIPCGESCVFIPCISAVIGCSCSNKVCYKN +>ACP196 +GSIPCEGSCVFIPCISAIIGCSCSNKVCYKN +>ACP198 +GIPCGESCVFIPCLTSAIDCSCKSKVCYRN +>ACP200 +GMWSKILGHLIR +>ACP202 +GKWMSLLKHILK +>ACP204 +GFGMALKLLKKVL +>ACP206 +GTGLPMSERRKIMLMMR +>ACP208 +GIACGESCVFLGCFIPGCSCKSKVCYFN +>ACP210 +GVIPCGESCVFIPCISSVLGCSCKNKVCYRD +>ACP212 +KLCGETCFKFKCYTPGCSCSYPFCK +>ACP214 +GDACGETCFTGICFTAGCSCNPWPTCTRN +>ACP216 +GIPCAESCVWIPPCTITALMGCSCKNNVCYNN +>ACP218 +IPCGESCVWIPCITAIAGCSCKNKVCYT +>ACP220 +AIPCGESCVWIPCISTVIGCSCSNKVCYR +>ACP222 +GEYCGESCYLIPCFTPGCYCVSRQCVNKN +>ACP224 +IPCGESCVWIPCISGMFGCSCKDKVCYS +>ACP226 +FLGWLFKWASK +>ACP228 +FLKWLFKWAKK +>ACP230 +KWKSFLKTFKSAKKTVLHTALKAISS +>ACP232 +KWKSFLKTFKSLKKTVLHTLLKAISS +>ACP234 +MPFLFCNVNDVCNFASRNDYSCNYYSNSYSFWLASLNPER +>ACP236 +KWKLFKKIGAVLKVL +>ACP238 +GACFSIAHECGA +>ACP240 +TCCATGACGTTCCTGACGTT +>ACP242 +KRFKQDGGASHASPASS +>ACP244 +KRAKAAGGWSHWSPWSSC +>ACP246 +LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES +>ACP248 +FLGALFKVASKVLPSVKCAITKKC +>ACP250 +GIGKFLKKAKKFGKAFVKILKK +>ACP252 +GIGKFLKKAKKGIGAVLKVLTTGL +>ACP254 +VECYGPNRPQF +>ACP256 +KRFKQDGGWSHWSPWSSC +>ACP258 +RQVFQVAYIIIKA +>ACP260 +KAFDITYVRLKF +>ACP262 +DFKLFAVTIKYR +>ACP264 +DFKLFAVYIKYR +>ACP266 +WHSDMEWWYLLG +>ACP268 +HTMYYHHYQHHL +>ACP270 +RLVSYNGIIFFLK +>ACP272 +GRENYHGCTTHWGFTLC +>ACP274 +ASSSYPLIHWRPWAR |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Uversky_Plot/test-data/test2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Uversky_Plot/test-data/test2.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| @@ -0,0 +1,276 @@ +>non-ACP0 +MTISLIWGIAMVVCCCIWVIFDRRRRKAGEPPL +>non-ACP2 +MFATPLRQPTNASGARPAVSMDGQETPFQYEITD +>non-ACP4 +LLWRKVAGATVGPGPVPA +>non-ACP6 +DSPDPMNGASSNALIAKMNSAKLLYQHY +>non-ACP8 +NNQEVIDAISQAISQTPGCVL +>non-ACP10 +KKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEG +>non-ACP12 +CSRLLPSLAQEEG +>non-ACP14 +KNDFAALQAKLDADAAEIEKWWSDSR +>non-ACP16 +VDREQLVQKARLAEQAERYDD +>non-ACP18 +RPLRRVVLFYQGKLCSMAGNFWQSSHYLQW +>non-ACP20 +GAAGERKLCLLSLLLIGA +>non-ACP22 +MFRKLLKMWILLRPTHWLILIALCAVTCAGYWLLWSE +>non-ACP24 +HLRGPADSGWMPQAAPCLSGAPQAS +>non-ACP26 +NNPNNSNSHLRPHAYNNSRRDDSD +>non-ACP28 +VVILASLSVMFLVSLWQQKIRERLPPGPTPLPFIGNY +>non-ACP30 +ICLSCLISFFLWNQNRAKGKLPPG +>non-ACP32 +VVMNSLRVILQAS +>non-ACP34 +ARPRLDLQLVQRFVRIQKVF +>non-ACP36 +MLAKGLSLRSVLAKGCQPFLSPTWQSSVLATGGGANIS +>non-ACP38 +AAGLPGAALPLRKRPLRAPSPEPAAPRGAAGLVV +>non-ACP40 +PPMPSAPPVHPPP +>non-ACP42 +SCPIDKRRPLIAFLRRLRD +>non-ACP44 +RLGLWASGLILILGFLKLLRLLLRRQRLARAMD +>non-ACP46 +FSPQRDRFQAEGS +>non-ACP48 +GTLWALVFLGILVGMVVPSPAGTRANNTLLDSRG +>non-ACP50 +MNRLLQKGTSLVPSWRTR +>non-ACP52 +MTTSLIWGIAIAACCCLWLILGIRRRQT +>non-ACP54 +ATLANGMSLQPPLEEVS +>non-ACP56 +PLTATNSGLAVNN +>non-ACP58 +VRACHKVCRCLLSGFGGRVDAGQPELLTER +>non-ACP60 +TAGILLLLLLGTLEGS +>non-ACP62 +MEPSILLLLALLVGFLLLLVRGH +>non-ACP64 +MKNCFQLLCNLKVPAAGFKNTVKS +>non-ACP66 +SVIHTQAHASGLQQVPQLVPAGPGGGGKAVAPSKQSK +>non-ACP68 +KPLGLLKPSSLMKVSGRFKAHQDA +>non-ACP70 +ARTLNNKLSLSKPKFSGFT +>non-ACP72 +LLLVIIWTLFGPSGLGEELLSLSLASLLPAPASPGPP +>non-ACP74 +WPGILVGGARVASCRYPALGPRLA +>non-ACP76 +RSVKGLVALITGGASGL +>non-ACP78 +AAAALRARILQVSSKVN +>non-ACP80 +TGCCIAGRLANLDDQNLTVAL +>non-ACP82 +GSILGFLQIATVLTVLLLLLK +>non-ACP84 +AARQIGSCLMRCRTLDTTSP +>non-ACP86 +WGCRGRRWAFARVDGGSCHRRGAPTGSTSNQIR +>non-ACP88 +YAKPGAVRSPAQILQWQVLPNTVPAKS +>non-ACP90 +RMAGPWLSLHEARLLGTRGAAAPKAV +>non-ACP92 +SISNRAAVPEHGVAPDAERL +>non-ACP94 +PNFSMETWLLLV +>non-ACP96 +PRPPSKTYRGAFQN +>non-ACP98 +SVLVKGCQPFLSAPRECPGHPRVGT +>non-ACP100 +LVTPPKALLKPLSIPNQ +>non-ACP102 +KMQGSRMDEQRCS +>non-ACP104 +VIADDLPPTCIRP +>non-ACP106 +LPGGLRVLVQTGH +>non-ACP108 +GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL +>non-ACP110 +RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD +>non-ACP112 +QQEKEFLESYPQNCPPDALPGTPGNLD +>non-ACP114 +APARRVLQVKRVMQESSLSPAHL +>non-ACP116 +KVAPGGPTGYPGNLTAEQEQKLGELKMILL +>non-ACP118 +FLASYPQKCPAGSLPGTPGNTDE +>non-ACP120 +MDAKARNCLLQHREALEKDIKTSY +>non-ACP122 +ASRQLLVAPPEAL +>non-ACP124 +MISNGIGTVTTGKRSMCLFPLLLIGLWGC +>non-ACP126 +MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC +>non-ACP128 +AVFGLGGVGLSVIMGCKAAGASRIIAVDIN +>non-ACP130 +PNAKQSILQKNPDDVVIVAAYRTA +>non-ACP132 +AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP +>non-ACP134 +LLAAGFCPAVLCH +>non-ACP136 +AASVNDEQHQRIIKYGRALVLDIVEQ +>non-ACP138 +IARLREDGIQKRVIQEGRGELPDFQDG +>non-ACP140 +FIVVMNILALTLPFLAAEVQN +>non-ACP142 +CQNGRRANRTVRFARTA +>non-ACP144 +WVTVRSQQRGLFPAI +>non-ACP146 +LLRSCPLQGSPGRPRSV +>non-ACP148 +LNDGHFMPVLGFGTYAPPEVPRNRAVEV +>non-ACP150 +HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT +>non-ACP152 +RPEPGGCCCRRTVRANGC +>non-ACP154 +SWVEENRASFQPPVCNKLMHR +>non-ACP156 +VFHRVRWAPELGASLG +>non-ACP158 +RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ +>non-ACP160 +LLQRARLAEQAERYDDMASAMKAVTELNEPLS +>non-ACP162 +ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA +>non-ACP164 +AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ +>non-ACP166 +QRRQNDSSVFLAIMVAAAVES +>non-ACP168 +CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS +>non-ACP170 +LVLLTVQNSALILTLNYSRIMPGYD +>non-ACP172 +TVLSPPQRFKRILQAMMLAVAVV +>non-ACP174 +ISRGLLLLAALCCLAPSFL +>non-ACP176 +VAGTESAQGPPGPAASLELWLNKATDPS +>non-ACP178 +QYLRIRTVQPEPDYGAAV +>non-ACP180 +ASPTQTPPTTSTIRVARRSRVALVAM +>non-ACP182 +TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ +>non-ACP184 +LSITRGLLLLAALCCLAPIS +>non-ACP186 +ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ +>non-ACP188 +LLLLSWVALGPRSLEGADPGTPGEAEGPACP +>non-ACP190 +LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP +>non-ACP192 +GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI +>non-ACP194 +RHVGLLCATGPQRWRF +>non-ACP196 +AAVALARPKPPLRHQEHLQNEPDS +>non-ACP198 +SRVNDQSQASRNGLKGKVLTLDTMNPCV +>non-ACP200 +AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK +>non-ACP202 +LCTSGLWTAQASTNESSNSHRGLAPTNV +>non-ACP204 +PAIQPVLSGLSRIVNGEEA +>non-ACP206 +GCQASLSTAQERLGHPGVPTREGVR +>non-ACP208 +RKVLILTLVVAACGFVLWSSNGR +>non-ACP210 +GRVRSRCPGPALLLLLALAARPALAGPPAAALQ +>non-ACP212 +CRITKPALLVLNQETAKVVQT +>non-ACP214 +KAEVCMAVPWLSLQ +>non-ACP216 +SHLELNNGTKMPTLGLGT +>non-ACP218 +LLLPEAAAERDAREKLALWDRRPDTTAPL +>non-ACP220 +LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS +>non-ACP222 +LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD +>non-ACP224 +AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR +>non-ACP226 +SLFWAARPLQRCGQLVRMAIRAQH +>non-ACP228 +MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA +>non-ACP230 +LLSLIGFCWAQYDP +>non-ACP232 +LWARSKNDQLRISFPPGLCWG +>non-ACP234 +PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG +>non-ACP236 +IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG +>non-ACP238 +LDAASPGPLALLGLLFAATLLLSALFLL +>non-ACP240 +VTLLFKLYCLA +>non-ACP242 +ATRAAAARLVGTAASRTPAAARH +>non-ACP244 +RNKLDLETLTDILEHQIR +>non-ACP246 +RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF +>non-ACP248 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| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Descriptor/PDAUG_Word_Vector_Descriptor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Descriptor/PDAUG_Word_Vector_Descriptor.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,59 @@ +import numpy as np +import os +import pandas as pd +from Bio import SeqIO +from nltk import bigrams +from nltk import trigrams +import gensim +import argparse + +parser = argparse.ArgumentParser() + +parser.add_argument("-M", "--ModelInput", required=True, default=None, help="Path to target tsv file") +parser.add_argument("-R", "--row", required=True, default=None, help="Path to target tsv file") +parser.add_argument("-I", "--InputFasta", required=True, default=6, help="Path to target tsv file") +parser.add_argument("-O", "--OutFile", required=False, default='model.txt', help="Path to target tsv file") +parser.add_argument("-P", "--positive", required=True, help="Path to target tsv file") +parser.add_argument("-N", "--negative", required=True, help="Path to target tsv file") + +args = parser.parse_args() + +seed = 42 +np.random.seed(seed) + +new_model = gensim.models.KeyedVectors.load_word2vec_format(args.ModelInput, binary=False) + +import time +t0 = time.time() + +temp_word = np.zeros(shape=(int(args.row), 200)) + +for index, seqs in enumerate(SeqIO.parse(args.InputFasta, 'fasta')): + seq_sum = 0 + tri_seq = trigrams(seqs.seq) + for item in ((tri_seq)): + tri_str = item[0] + item[1] + item[2] + if tri_str not in list(new_model.wv.vocab): + continue + seq_sum = seq_sum + new_model[tri_str] + + temp_word[index] = seq_sum + +t1 = time.time() + + +temp_word = temp_word + + +clm = [x for x in range(0,temp_word.shape[1])] +y_temp_word = np.vstack((np.ones((int(args.positive), 1)), np.zeros((int(args.negative),1)))) + +c, r = y_temp_word.shape +y_temp_word = y_temp_word.reshape(c,) + +class_label = pd.DataFrame(y_temp_word, columns=["Class_label"]) + +df = pd.DataFrame(temp_word, columns=clm) +df = pd.concat([df,class_label], axis=1) + +df.to_csv(args.OutFile, index=None, sep="\t") \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Descriptor/test-data/Out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Descriptor/test-data/Out.tsv Wed Oct 28 01:52:18 2020 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Descriptor/test-data/model.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Descriptor/test-data/model.txt Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,567 @@\n+566 200\n+SLK 0.001365332 -0.0017459366 -0.00080282777 0.0011080382 -0.0020799749 0.0023665277 0.00064222724 -0.00020277791 -0.0024961173 0.0017166281 0.0016223168 -0.00068261253 -0.0018985914 0.002186477 -0.001368902 -0.0022669677 -0.0009672694 0.0020265202 -0.00024468428 -0.0013020429 -0.0017395875 0.0016356348 -0.00079645164 0.0023032813 0.0024860792 -0.002388357 -0.0014398484 0.00140585 -0.0003748012 -0.0018963028 -0.00017838413 -0.00024190723 0.00024986145 0.002378538 -0.0017191146 0.0023616562 0.001670377 -0.0006269774 -0.0010054546 -0.0011329858 -0.002181357 -0.0020793916 0.002035759 -0.0010104823 0.001482032 -0.0010092463 0.001162038 -0.0023821024 0.00028114635 9.705908e-05 0.0016195059 -0.00094875274 0.0009430515 -0.002029896 0.0018548059 0.0015280207 -0.00028816742 -6.1781415e-05 -0.00077087915 0.0020475688 8.588983e-05 0.00056099205 6.22821e-05 -0.0013446079 -0.0014237356 0.00075389433 -0.00020252455 -0.00095345493 -0.0007824703 -6.162045e-05 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-0.000932948 0.0011330452 0.00060474453 -0.00040816146 0.0024577135 0.0020908166 -0.00016210739 -0.0013720029 0.0022247606 -0.0004630553 -0.002023366 0.0010714133 0.0010599708 0.0024086582 1.5625536e-05 -0.00033240227 0.0007969802 0.0024127767 -0.0005245974 0.0023930564 -0.002065922 -0.00049742655 0.00075228175 0.0012057236 -0.0021796646 -0.0017681125 0.002240387 -0.0015084597 2.8815777e-05 0.00062441436 0.0017449431 -0.00060599134 -0.00016037462 -0.0019211516 -0.00083369436 -0.0017688617 -0.0012831012 0.0018926467 -0.00082292286 0.00015296093 -0.00056383596 -0.000414889 -0.0004348078 -0.0021617427 -0.0022588358 -0.0018406851 -0.00062651787 0.0017154918 0.0023480973 -0.0023299463 0.00028671883 0.0012787611 -0.0020714088 0.0011408264 -0.0013465516 0.0015014345 -0.0017432373\n+LVC -1.2101434e-05 -0.0022298675 0.001447321 -0.0013246932 0.00057933765 -0.002318466 0.001946672 -0.0009749499 -0.0020036546 -0.00085358316 -0.0008264022 -0.0002964486 0.000796339 0.0021234967 0.0016650832 0.0008551463 -0.0019276019 0.0011267059 2.823315e-05 -0.0015146568 -0.001965077 0.0006863515 -0.0015384579 0.0024484461 0.0018394345 -0.00084675086 -6.0793493e-05 0.002531608 0.0024579482 0.00036317756 0.00021481325 -0.0014953372 -0.0010072981 -0.0020482857 -0.0017800514 -0.0012966199 0.0017186782 0.0011799947 0.0007498256 -0.0021813198 0.0006652456 0.0021067823 -2.0717955e-05 0.002445156 -0.002240867 0.00045164707 0.0018858616 -0.0023328154 0.0011247616 -0.0003575369 0.0011778875 -0.0008954814 -0.0017944037 0.0015972335 0.0008786754 0.000983835 -0.00030637544 0.0005728325 0.002248167 0.0008306682 0.00105836 0.0018650618 0.0022743535 0.00028581268 0.00071605446 -0.00024169416 0.0011736357 0.0006689531 -0.0018869323 -0.00023115014 0.0009952596 -0.0015211194 0.0015442141 -0.000500582 -0.0014211049 -0.0018496842 -0.000335584 -0.0007210559 0.00015120191 0.00039644202 0.0010430668 -0.00044082105 -0.0017261596 0.0001878975 -6.498627e-06 -0.00041374264 -0.0022203664 0.0018215046 0.00023135482 0.00062350027 0.0021234509'..b'9329166 0.00083683885 -0.0012966121 -0.000420821 0.0012175398 -0.0014267633 0.001252249 0.0016301421 -0.0019441452 -0.0007565895 0.0023559122 -7.5507046e-06 -0.0013640765 -0.0014484831 0.0013146921 -0.00070724834 0.0006098803 0.001090075 0.0017408988 -0.001816694 0.00065133127 0.0014607466 -0.0019121281 -0.0019158301 0.00092410535 0.0023605211 0.0004920717 0.00088350684 0.0010997092 3.324904e-06 0.0021491952 0.0011182296 -9.8608805e-05 0.0020175215 0.0016764243 1.0548103e-05 -0.0017188648 -0.00072903285 0.0024229095 -0.0010821237 0.0009385571 -0.0013538856 -0.0016275204 -0.0018933859 0.000107686 0.0013027365 -0.0019094732 -0.00116395 0.0007673889 0.0023619593 0.0007082056 0.00045266104 -0.0020115129 0.002031747 -0.0019755852 0.00026481098 0.0003243022 -0.0020673268 0.0014138616 0.00065170706 -0.0011964287 -0.002201478 -0.0012715297 -0.0010389787 -0.0014538697 -0.0018862948 0.0010369697 0.0020708728 0.000986399 1.6503946e-05 -0.00059497467 0.0005850068 -0.0005638295 -0.002096313 0.002155895 -0.0017137764 0.0019099646 0.00109993 -0.0009016919 -0.00026621978 0.0011989886 -0.00095179136 3.3868637e-05 0.001603786 0.0006490003 0.000836424 0.0014219693 0.0015205769 0.0006233736 -0.0026071914 -0.0017951333 0.0010369756 -7.279905e-06 -0.00030341622 0.0020297645\n+RTT 0.0008749674 0.00096788583 0.00046035784 0.0016080411 -0.0014414618 0.0014620025 -4.0255152e-05 0.00045544843 0.001784968 0.0023198745 -4.6789242e-05 -0.0008355484 0.000529331 -0.0012765506 0.00095468503 0.0014647499 -0.00076876057 0.0010658011 0.0016611569 0.0013699844 0.0023904063 0.0012192386 0.0011243214 -0.0012805273 -0.0006703495 -0.0012319596 0.00051839405 0.001952754 0.0008436256 -0.0015916091 -0.0011713775 0.000609642 -0.0014617583 0.0022987772 -0.0008756762 -0.0002850732 -9.186468e-05 0.0015565944 0.0021467975 0.001879534 -0.0009571439 0.0025193726 0.00070011965 0.00014257328 -0.0012639355 -0.0017070648 0.00011292961 0.001955303 -0.0023525355 -0.0024229723 0.0016758887 -0.001555089 -0.0012256737 -0.0014706277 -0.0011813928 -0.0008920257 -0.00070989813 0.0016142618 6.2340194e-05 -0.0013028994 -0.00041547752 0.0017577651 -0.0013958853 0.00019386491 -0.0011342029 0.0009555548 0.0015859862 0.0010165847 0.0023251616 0.0024807346 -0.0001621106 0.0009780871 -0.0021544576 -0.0016797123 -0.0019976767 0.0023287062 -0.0005807063 -0.0010508454 -0.0011735009 0.0009913616 -0.0023642706 0.0010660653 -0.0011858979 0.00059610215 0.0008311239 -0.00092363905 0.0013755945 0.00037625633 0.002422985 -0.0016978119 -0.0013139286 0.000529977 -0.0011911308 -0.0023673559 0.00020641256 -0.0015232897 -0.0002883984 -0.0012487182 -0.00046426966 -0.0009833992 0.0018450054 0.0002375337 0.001846433 -0.0017698813 -0.002041315 -0.0008291253 -0.0005597482 0.0011917122 0.00015343283 -0.0011826177 0.002399056 0.0006649859 -0.0017162617 -0.00086710486 0.00016337876 -0.0008963979 -0.0014059466 -0.0023056318 -0.00063665456 0.0013866306 0.001834191 0.0024510582 -0.0008367855 9.572251e-07 0.0019129917 -0.00024920254 -0.002109615 0.0014992991 0.002470077 -0.0015247426 0.0021252346 0.0003277864 -0.00013354525 0.00068446604 0.0024241658 -0.001372545 0.0012075508 -0.0018025833 -0.00038149007 0.00037644224 0.0018547113 0.0018578246 -0.0020145597 -1.42324225e-05 0.0021410969 0.00025578332 8.691112e-05 -0.0017239064 -0.0012059687 -0.0019051972 0.00064171746 0.0024287626 0.0007367608 0.0012890009 0.0012271192 0.00032794752 0.0010868037 -0.0010993943 0.00021350925 0.001333526 -5.4828255e-05 0.0011917402 0.0011615263 0.001149004 0.00055940665 0.00021172808 0.0007953479 -0.00045935702 -0.0015195387 0.0016530926 0.0018495353 0.0010670543 0.00029422963 -0.0010919494 0.0010870786 -0.0021665462 -0.0007957788 -0.002275716 -0.0012395901 -0.001598635 0.00031872877 -0.00020240767 -0.0020836846 -0.00056924846 -0.0019875302 -0.0013354532 -0.0006294266 0.0022098403 -0.0008797699 -0.00035938426 -0.0023506682 0.0018134243 0.0018999709 0.0014204925 -0.00048301555 -0.001929654 0.0013711938 0.00044136978 -0.00092774484 0.0009801525\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Descriptor/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Descriptor/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,552 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+>non-ACP\n+KMQGSRMDEQRCS\n+>non-ACP\n+VIADDLPPTCIRP\n+>non-ACP\n+LPGGLRVLVQTGH\n+>non-ACP\n+GWIWRWGWGRRCLGRPGLPGPGPGPATPLFLLLL\n+>non-ACP\n+RGIRGSSAARPSGRRRDPAGRTTETGFNIFTQHD\n+>non-ACP\n+QQEKEFLESYPQNCPPDALPGTPGNLD\n+>non-ACP\n+APARRVLQVKRVMQESSLSPAHL\n+>non-ACP\n+KVAPGGPTGYPGNLTAEQEQKLGELKMILL\n+>non-ACP\n+FLASYPQKCPAGSLPGTPGNTDE\n+>non-ACP\n+MDAKARNCLLQHREALEKDIKTSY\n+>non-ACP\n+ASRQLLVAPPEAL\n+>non-ACP\n+MISNGIGTVTTGKRSMCLFPLLLIGLWGC\n+>non-ACP\n+MTLRNFGMGKRSIEDRVQEEARCLVEELRKTNASPC\n+>non-ACP\n+AVFGLGGVGLSVIMGCKAAGASRIIAVDIN\n+>non-ACP\n+PNAKQSILQKNPDDVVIVAAYRTA\n+>non-ACP\n+AMELLLTATIFYLVLWVVKAFRLQVPKGLKSPPGP\n+>non-ACP\n+LLAAGFCPAVLCH\n+>non-ACP\n+AASVNDEQHQRIIKYGRALVLDIVEQ\n+>non-ACP\n+IARLREDGIQKRVIQEGRGELPDFQDG\n+>non-ACP\n+FIVVMNILALTLPFLAAEVQN\n+>non-ACP\n+CQNGRRANRTVRFARTA\n+>non-ACP\n+WVTVRSQQRGLFPAI\n+>non-ACP\n+LLRSCPLQGSPGRPRSV\n+>non-ACP\n+LNDGHFMPVLGFGTYAPPEVPRNRAVEV\n+>non-ACP\n+HLGRPSAPTIVAQPVSGLASPASFQPEQFQYTLDNNVLT\n+>non-ACP\n+RPEPGGCCCRRTVRANGC\n+>non-ACP\n+SWVEENRASFQPPVCNKLMHR\n+>non-ACP\n+VFHRVRWAPELGASLG\n+>non-ACP\n+RAKVLTLDGMNPRVRRVEYAVRGPIVQRALELEQELRQ\n+>non-ACP\n+LLQRARLAEQAERYDDMASAMKAVTELNEPLS\n+>non-ACP\n+ALIQKLNSDPQFVLAQNVGTTHDLLDICLKRATVQRA\n+>non-ACP\n+AALPMLWTGLVLLGLLGFPQTPAQGHDTVQPNFQQ\n+>non-ACP\n+QRRQNDSSVFLAIMVAAAVES\n+>non-ACP\n+CNAPGCGQRFTNEDHLAVHKHKHEMTLKFGPARTDS\n+>non-ACP\n+LVLLTVQNSALILTLNYSRIMPGYD\n+>non-ACP\n+TVLSPPQRFKRILQAMMLAVAVV\n+>non-ACP\n+ISRGLLLLAALCCLAPSFL\n+>non-ACP\n+VAGTESAQGPPGPAASLELWLNKATDPS\n+>non-ACP\n+QYLRIRTVQPEPDYGAAV\n+>non-ACP\n+ASPTQTPPTTSTIRVARRSRVALVAM\n+>non-ACP\n+TIWRNQHTYKMATSASANLSKIVKKNYMELPQDGKVQ\n+>non-ACP\n+LSITRGLLLLAALCCLAPIS\n+>non-ACP\n+ILLSIWRQSSGRGKLPPGPIPLPIIGNIFQ\n+>non-ACP\n+LLLLSWVALGPRSLEGADPGTPGEAEGPACP\n+>non-ACP\n+LRVKRAMQEASFMPPLLPPAAHQRFSTVPAVP\n+>non-ACP\n+GLLLLAGLCCLVFGIMAEDAQVAQGPSQQI\n+>non-ACP\n+RHVGLLCATGPQRWRF\n+>non-ACP\n+AAVALARPKPPLRHQEHLQNEPDS\n+>non-ACP\n+SRVNDQSQASRNGLKGKVLTLDTMNPCV\n+>non-ACP\n+AAALGPGVLQATRAFHTGQPRLAPLPPLPEYGGK\n+>non-ACP\n+LCTSGLWTAQASTNESSNSHRGLAPTNV\n+>non-ACP\n+PAIQPVLSGLSRIVNGEEA\n+>non-ACP\n+GCQASLSTAQERLGHPGVPTREGVR\n+>non-ACP\n+RKVLILTLVVAACGFVLWSSNGR\n+>non-ACP\n+GRVRSRCPGPALLLLLALAARPALAGPPAAALQ\n+>non-ACP\n+CRITKPALLVLNQETAKVVQT\n+>non-ACP\n+KAEVCMAVPWLSLQ\n+>non-ACP\n+SHLELNNGTKMPTLGLGT\n+>non-ACP\n+LLLPEAAAERDAREKLALWDRRPDTTAPL\n+>non-ACP\n+LLALSLVLLYRYATYSHGFFKKLGIPGPKPLPLFGNVLS\n+>non-ACP\n+LLSLWRQSSGRGKLPPGPTPLPVIGNILQIGIKD\n+>non-ACP\n+AFKSMEVANFYYEADCLAAAYGGKAAPAAPPADRPGPR\n+>non-ACP\n+SLFWAARPLQRCGQLVRMAIRAQH\n+>non-ACP\n+MRPPRTLTSTATMSALSTSMPMEIDDVMDEDAVNGQA\n+>non-ACP\n+LLSLIGFCWAQYDP\n+>non-ACP\n+LWARSKNDQLRISFPPGLCWG\n+>non-ACP\n+PQGFDVDRDAKKLNKACKGMGTNEAAIIEILSG\n+>non-ACP\n+IFCLILWVVKAWQPRLPKGLKSPPGPWGWPLLG\n+>non-ACP\n+LDAASPGPLALLGLLFAATLLLSALFLL\n+>non-ACP\n+VTLLFKLYCLA\n+>non-ACP\n+ATRAAAARLVGTAASRTPAAARH\n+>non-ACP\n+RNKLDLETLTDILEHQIR\n+>non-ACP\n+RRLVLQARTYAQAAASPAPAAGPGQMSFTFASPTQVFF\n+>non-ACP\n+PGRSRSAADDINPAPANM\n+>non-ACP\n+LLSALTLETWVLLAVILVLLYRLG\n+>non-ACP\n+VMGHGLCPQGARAKAAIPAALRDHEST\n+>non-ACP\n+FLVSIAGLLYALVQLGQPCDCLPPLRAAA\n+>non-ACP\n+VRSVRAAVGGLRAISAPSAPCLPRPWGLRAG\n+>non-ACP\n+RGGCWPRGLQQLLVPGG\n+>non-ACP\n+APATPPRPLKRKKLQFTDVTPESSP\n+>non-ACP\n+EQAERYDDMAAAMKAVTEQGHELSNEERNL\n+>non-ACP\n+MPNDPSDNQLK\n+>non-ACP\n+TELLLAITVFCLGFWVVRALRTQVP\n+>non-ACP\n+LTADLLGAPFFTLPKELQLALLERQTVFL\n+>non-ACP\n+GHGRLVEIQGRLGVRIER\n+>non-ACP\n+LPFKLLLFVLLDGWTRLTH\n+>non-ACP\n+QALWLVLVLSMPPVLVAAVVGTLVSLVQ\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Model/PDAUG_Word_Vector_Model.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Model/PDAUG_Word_Vector_Model.py Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,38 @@ +import nltk +from nltk import trigrams +import pandas as pd +from Bio import SeqIO +import gensim, logging +import argparse + +parser = argparse.ArgumentParser() + +parser.add_argument("-I", "--Input", required=True, default=None, help="Path to target fasta file") +parser.add_argument("-M", "--min_count", required=False, default=0, help="Path to target tsv file") +parser.add_argument("-W", "--window", required=False, default=5, help="Path to target tsv file") +parser.add_argument("-O", "--OutFile", required=False, default='model.txt', help="Path to target tsv file") + +args = parser.parse_args() + +class ProteinSeq(object): + def __init__(self): + pass + def __iter__(self): + for index, record in enumerate(SeqIO.parse(args.Input, 'fasta')): + for loop_num in range(0, 3): + Ngram_list = [] + tri_tokens = trigrams(record.seq) + for index1, item in enumerate(tri_tokens): + if index1 % 3 == loop_num: + tri_pep = item[0] + item[1] + item[2] + Ngram_list.append(tri_pep) + yield Ngram_list +#min_count = 0 +size = 200 +#window = 5 +sg = 1 + +sentences = ProteinSeq() +model = gensim.models.Word2Vec(sentences, min_count=int(args.min_count), size=size, window=int(args.window), sg = sg, workers = 10) +model.wv.save_word2vec_format(args.OutFile, binary=False) + |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Model/test-data/model.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Model/test-data/model.txt Wed Oct 28 01:52:18 2020 +0000 |
| b |
| b'@@ -0,0 +1,567 @@\n+566 200\n+SLK -0.0010030628 0.000100835154 -0.0019347421 -0.00076493184 0.0014542947 0.0014068135 0.00084618153 0.0020921843 -0.0019026415 -0.0006590894 0.0022805685 -0.00096782576 -0.0024763828 0.0007323335 0.00061047205 -0.0022421663 -0.000654532 -0.0011798553 -0.00060771394 -0.00050038786 -0.0007698266 0.00084362755 -0.0011791416 -0.0016665208 -0.0005201962 0.0019055296 -1.512186e-05 -0.0019836018 -0.0012254894 -0.0022825655 0.0010594992 0.0018288207 -0.0006668121 0.0021907832 0.00094542024 -0.00170071 0.00183659 -0.0005609948 -0.0008470077 0.0024044297 -0.0006272259 -0.0015420591 -0.0015622115 0.0022688601 0.00055790844 0.00022420083 0.0021307333 -0.002215041 -9.6654316e-05 0.0014316123 0.0010925673 0.0023748777 0.0017993941 -0.0010667549 -0.0010471892 0.001276248 -0.0010441451 -0.0013733016 -0.0017143694 0.0008117987 -0.002100952 0.0005481462 0.0012565582 -0.00027537628 0.00060161017 0.0005101376 -0.00082007336 0.0009339486 -0.0017269732 -0.00015142813 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-0.0006066804 0.00245605'..b'924 0.0021821025 -0.0014032001 -0.0009744811 0.0010769261 -0.00034137678 0.000214921 0.0024331359 -0.0020255684 0.0020676758 0.0017541476 0.0018737108 0.0015129836 0.0010686504 0.002332911 0.0001992582 0.0011322168 0.0003263395 -0.0009947193 0.0022501221 -0.0023565881 -0.00039700672 0.0021902514 0.0018467497 -0.0018980933 0.0003773999 -0.0011028886 -0.0024948912 0.00058945455 -0.0011515784 0.0015930029 -0.0005651209 4.1423882e-05 0.0017315708 6.154556e-05 0.00067807746 -0.0007624985 0.0014497186 -0.0011262009 -0.00094811886 0.0007234749 0.0002620769 -0.0007772993 0.0017874188 -0.0015540041 -0.0023920804 0.0006855838 -0.0010742402 -0.00021710082 0.0011857314 -0.0023305858 0.0023731578 0.0012189841 -0.00069491967 -0.0010127571 0.0005580876 0.001036492 -0.0021085378 -0.0003845184 -0.0019605139 0.0022725107 0.0018582217 -0.00018812898 0.0006322817 -0.0024015135 0.002275918 -0.0012636826 -0.0023785608 0.0020010332 -0.002370117 -0.00044299682 -0.00078391156 0.0023472942 -0.0018125535 0.0020114002 -0.002014159 0.0012666982 0.0021298465 -0.0011994458 0.002128024 -0.001189568 0.0019846351 -0.0021721057 -0.0020807649 -8.474351e-05 0.0020009486 -0.0002868331 -0.0011943501 0.0020324918 -0.0020747124 0.00047011115 -0.0021956079 0.00034764616 -0.0018886229 0.0018471953 0.00047610325\n+RTT 0.000800459 0.0022807189 0.000614407 0.00043291523 0.0013266976 0.0016516823 -0.00017887352 0.0001774865 0.0022674256 0.0007991084 -0.0017937184 -0.0012809283 0.00034525068 0.0010474691 -0.0011773593 -0.00020316518 0.00071664935 0.0004490933 0.0005864967 0.0023711638 0.0012197499 -0.0009967296 0.0012682456 0.0015518359 0.000651693 0.0008096255 0.0004684565 -0.001262113 -0.0011209914 0.00018294278 -0.00013294513 0.00014597994 0.00041009023 -0.0013152343 -0.00050766 0.00033145904 0.00056744565 0.0008613704 0.0007503846 -0.001847496 -0.0016863405 0.0022872342 0.0009217861 -0.0011331631 0.0013246123 -0.002163321 0.0023381775 -0.0013936638 0.0022097866 -0.0023730479 0.0014418369 -0.0015951154 -0.0017479687 -1.1758027e-05 0.0012897338 0.0007854197 0.00087452476 -0.0019004125 0.0017956524 0.0019462679 0.0014046035 0.0014048805 -0.001382155 -0.0015547818 0.0009136546 0.0013969156 -0.002408568 -0.00095783925 -0.0012149756 0.0013561236 0.00081642164 -0.0005703783 -0.0020031298 0.00029171846 -0.0018983197 0.0008232627 -0.00067786424 0.0015696628 0.0005483555 -0.0008685772 -0.0004985128 0.0015814694 -0.0019487073 -0.00022380968 -0.0024199411 -0.0018035958 -0.001738709 -0.001768671 0.0023001665 0.0011826147 0.0013505309 -0.001520888 -0.0022249857 0.0015392177 8.096851e-05 0.00019641909 -0.00217602 -0.0008343077 0.00033551097 -0.00075170374 -0.0019082596 0.0015030898 -0.0021043406 -0.00062664493 0.0012989572 -0.0019294041 0.00089970586 -0.0021291745 0.00081388105 -0.0014019778 0.002488779 -0.00050189596 -2.1637376e-05 0.0010064129 -0.000278038 0.0019295008 0.00056200475 0.0023637 -0.0021872418 -0.0007958102 -0.0016448909 0.0002751693 0.0017254049 0.0006061145 -0.00071685784 0.0024198801 -0.0014178854 0.0017153893 0.0022203254 0.0025270556 -0.00053209305 0.0022114152 0.0022816851 -0.0013134214 0.0017226143 0.002457915 0.0014352301 -0.00053877925 0.0018859431 0.001810429 -0.0024067212 -0.0019813501 -0.002387521 -0.00020712892 0.0013106425 0.0007510423 -0.0016320832 0.0011793209 0.00049539725 0.0010422879 0.0012776309 0.0008611337 -0.0022205974 -0.00247682 0.0006492324 -0.0011322489 -0.0010332862 -0.0014822948 6.4873646e-05 0.0014633074 -0.00056768797 -0.0018850511 -0.00024886813 -0.0012680636 0.0023715075 0.0012950113 -2.916198e-06 -0.0024495733 -0.0020298546 0.0012903305 0.00018515662 0.0012265041 0.0001239143 -0.00017969421 -0.0018547528 0.0004504478 0.0021181984 -0.0017624114 -0.00014107149 0.0016415552 -0.00047895184 0.00086379354 0.002456045 -0.00063980406 0.001173198 -0.0021613056 0.0022272768 0.0012139239 0.00215961 0.0012713169 6.230853e-05 -0.00018173548 -0.0012579496 -0.0013567571 0.00051431364 -0.0023164214 0.0014994337 0.0011433125 0.00029282333 -0.0015467361\n' |
| b |
| diff -r 000000000000 -r 7d247e27ff11 PDAUG_Word_Vector_Model/test-data/test.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PDAUG_Word_Vector_Model/test-data/test.fasta Wed Oct 28 01:52:18 2020 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +>AHC69389.1 COX-2 [Pagrus major] +MNRLTFAVFLSALGFLVCAAGNPCCSEPCQNRGVCTALGSDNYECDCTRTGYRGQNCTTPEFLTWLKVSL +KPSPNTVHYILTHFKDFWNIINNISFLRDAIMRYVLTSRSHMIDSPPTFNADYGYKNWEAYSNLSYYTRT +LPPVPEDCPTPMGVEGKKELPDAKILAEKLLMRREFIPDPQGTSLMFAFFAQHFTHQFFKSDMKRGPAFT +AAQGHGVDLSHIYGDNLVRQHKLRLFKDGKLKHQILDGEMYPPTVKEVGAEMHHPPHVPDAYRFAVGHEA +>jai +FGLVPGLMMYATIWLREHNRVCDVLKEVHPDWDDERLFQTTRLILIGETIKIVIEDYVQHLSGYNFKLKF +DPELLFNQRFQYQNRIASEFNTLYHWHPLMPDSFHIEEKEYSYKEFVFNTSVVTEHGISNLVESFSKQIA +GRVAGGRNVPGPIMYVAIKSIENSRKMRYQSLNAYRKRFSLKPYSSFEDMTGEKEMAAVLEEMYGHIDAM +ELYPGLLVEKPRENAIFGETMVEMGAPFSLKGLMGNPICSPEYWKPSTFGGTVGFDIVNTASLQRLVCNN +ANGPCPVASFHVPDVKETGSMIINSSTSNSRSSDINPTVILKERTTEL |
