diff PDAUG_AA_Property_Based_Peptide_Generation/PDAUG_AA_Property_Based_Peptide_Generation.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /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 02:10:12 2020 +0000
@@ -0,0 +1,216 @@
+from modlamp.sequences import *
+import argparse, sys
+import pandas as pd 
+import os
+
+def Random_seq(seq_num, lenmin_s, lenmax_s, S_proba, OutFasta):
+
+    b = Random(int(seq_num), int(lenmin_s),int(lenmax_s))
+    b.generate_sequences(proba=float(S_proba))
+
+    OutPep = b.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+def Helices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    h = Helices(int(seq_num), int(lenmin_s),int(lenmax_s))
+    h.generate_sequences()
+
+    OutPep = h.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+ 
+def Kinked_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    k = Kinked(int(seq_num), int(lenmin_s),int(lenmax_s))
+    k.generate_sequences()
+
+    OutPep = k.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+def Oblique_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    o = Oblique(int(seq_num), int(lenmin_s),int(lenmax_s))
+    o.generate_sequences()
+    o.sequences
+
+    OutPep = o.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+def Centrosymmetric_seq(seq_num, lenmin_s, lenmax_s, symmetry_s, OutFasta):
+
+    s = Centrosymmetric(int(seq_num), int(lenmin_s),int(lenmax_s))
+    s.generate_sequences(symmetry=symmetry_s)
+
+    OutPep = s.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+def HelicesACP_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    helACP = HelicesACP(int(seq_num), int(lenmin_s),int(lenmax_s))
+    helACP.generate_sequences()
+
+    OutPep = helACP.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+def Hepahelices_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    h = Hepahelices(int(seq_num), int(lenmin_s),int(lenmax_s))  
+    h.generate_sequences()
+
+    OutPep = h.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+
+def AMPngrams_seq(seq_num, lenmin_s, lenmax_s, OutFasta):
+
+    s = AMPngrams(int(seq_num), int(lenmin_s),int(lenmax_s))
+    s.generate_sequences()
+
+    OutPep = s.sequences
+    OutFasta = open(OutFasta, 'w')
+
+    for i,O in enumerate(OutPep):
+        OutFasta.write(">sequence_"+str(i)+'\n')
+        OutFasta.write(O+'\n')
+
+def AmphipathicArc_seq(seq_num, lenmin_s, lenmax_s, gen_seq, hyd_gra, OutFasta):
+
+    amphi_hel = AmphipathicArc(int(seq_num), int(lenmin_s),int(lenmax_s))
+    amphi_hel.generate_sequences(int(gen_seq))
+    OutFasta = open(OutFasta, 'w')
+
+    if hyd_gra == 'true':
+
+        amphi_hel.make_H_gradient()
+        OutPep = amphi_hel.sequences
+                
+        for i,O in enumerate(OutPep):
+            OutFasta.write(">sequence_"+str(i)+'\n')
+            OutFasta.write(O+'\n')
+
+    elif hyd_gra == 'false':
+
+        OutPep = amphi_hel.sequences
+        
+        for i,O in enumerate(OutPep):
+            OutFasta.write(">sequence_"+str(i)+'\n')
+            OutFasta.write(O+'\n')
+
+if __name__=='__main__':
+
+    parser = argparse.ArgumentParser(description='Deployment tool')
+    subparsers = parser.add_subparsers()
+
+    Ran = subparsers.add_parser('Random')
+    Ran.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Ran.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Ran.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Ran.add_argument("-p","--S_proba", required=False, default='AMP', help="AA probability to be used to generate sequences,'rand', 'AMP', 'AMPnoCM', 'randnoCM', 'ACP'")
+    Ran.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    Hal = subparsers.add_parser('Helices')
+    Hal.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Hal.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Hal.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Hal.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    Kin = subparsers.add_parser('Kinked')
+    Kin.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Kin.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Kin.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Kin.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta") 
+
+    Obl = subparsers.add_parser('Oblique')
+    Obl.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Obl.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Obl.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Obl.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    Cen = subparsers.add_parser('Centrosymmetric')
+    Cen.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Cen.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Cen.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Cen.add_argument("-S","--symmetry_s", required=False, default="asymmetric", help="symmetric,asymmetric")
+    Cen.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    Hel = subparsers.add_parser('HelicesACP')
+    Hel.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Hel.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Hel.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Hel.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    Hep = subparsers.add_parser('Hepahelices')
+    Hep.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Hep.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Hep.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Hep.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    AMP = subparsers.add_parser('AMPngrams')
+    AMP.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    AMP.add_argument("-m","--n_min", required=False, default=3, help="minimum number of ngrams to take for sequence assembly")
+    AMP.add_argument("-M","--n_max", required=False, default=1, help="maximum number of ngrams to take for sequence assembly")
+    AMP.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+    
+    Arc = subparsers.add_parser('AmphipathicArc')
+    Arc.add_argument("-s","--seq_num", required=True, default=None, help="number of sequences to be generated")
+    Arc.add_argument("-m","--lenmin_s", required=False, default=7, help="")
+    Arc.add_argument("-M","--lenmax_s", required=False, default=20, help="Len max")
+    Arc.add_argument("-a","--arcsize", help="Choose among 100, 140, 180, 220, 260, or choose mixed to generate a mixture")
+    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.")
+    Arc.add_argument("-O", "--OutFasta", required=True, default=None, help="Output Fasta")
+
+    args = parser.parse_args()
+
+    if sys.argv[1] == 'Random':
+        Random_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.S_proba, args.OutFasta)
+    elif sys.argv[1] == 'Helices':
+        Helices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
+    elif sys.argv[1] == 'Kinked':
+        Kinked_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
+    elif sys.argv[1] == 'Oblique':
+        Oblique_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
+    elif sys.argv[1] == 'Centrosymmetric':
+        Centrosymmetric_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.symmetry_s, args.OutFasta)
+    elif sys.argv[1] == 'HelicesACP':
+        HelicesACP_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
+    elif sys.argv[1] == 'Hepahelices':
+        Hepahelices_seq(args.seq_num, args.lenmin_s, args.lenmax_s, args.OutFasta)
+    elif sys.argv[1] == 'AMPngrams':
+        AMPngrams_seq(args.seq_num, args.n_min, args.n_max, args.OutFasta)
+    elif sys.argv[1] == 'AmphipathicArc':
+        AmphipathicArc_seq(int(args.seq_num), int(args.lenmin_s), int(args.lenmax_s), int(args.arcsize), args.hyd_gra, args.OutFasta)
+    else:
+        print("You entered Wrong Values: ")
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