| Previous changeset 50:6747060cdfe6 (2014-10-27) Next changeset 52:12551ae128be (2014-10-27) |
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Commit message:
Uploaded |
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added:
reactivity_cal/.DS_Store reactivity_cal/._.DS_Store reactivity_cal/._reactivity_calculation.xml reactivity_cal/dis_f_N1Am_rrna.txt reactivity_cal/dis_f_N1Ap_rrna.txt reactivity_cal/parse_dis_react.py reactivity_cal/parse_dis_react.pyc reactivity_cal/rRNA.txt reactivity_cal/react_cal.py reactivity_cal/react_norm_function.py reactivity_cal/react_norm_function.pyc reactivity_cal/reactivity_calculation.xml reactivity_cal/read_file.py |
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| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/.DS_Store |
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| Binary file reactivity_cal/.DS_Store has changed |
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| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/._.DS_Store |
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| Binary file reactivity_cal/._.DS_Store has changed |
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| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/._reactivity_calculation.xml |
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| Binary file reactivity_cal/._reactivity_calculation.xml has changed |
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| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/dis_f_N1Am_rrna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/dis_f_N1Am_rrna.txt Mon Oct 27 01:52:17 2014 -0400 |
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| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/dis_f_N1Ap_rrna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/dis_f_N1Ap_rrna.txt Mon Oct 27 01:52:17 2014 -0400 |
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| b'@@ -0,0 +1,12 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|
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/parse_dis_react.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/parse_dis_react.py Mon Oct 27 01:52:17 2014 -0400 |
| [ |
| @@ -0,0 +1,51 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +import sys + +def parse_dist(in_file): + result = [] + distribution = {} + name = [] + f = open(in_file) + flag = 0 + for aline in f.readlines(): + line = aline.strip() + dis = line.strip() + dist = dis.split('\t') + if len(dist) > 0: + if len(dist) == 1: + if dist[0].strip().find('coverage')==-1: + if flag == 0: + name.append(line) + flag = 1 + t_name = line + else: + distribution[t_name] = 'null' + name.append(line) + flag = 1 + t_name = line + else: + distri = [] + for i in range(0, len(dist)): + distri.append(dist[i].strip()) + distribution[t_name] = distri + flag = 0 + result.append(name) + result.append(distribution) + f.close() + return result + + + + + + + + + + + + + + + |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/parse_dis_react.pyc |
| b |
| Binary file reactivity_cal/parse_dis_react.pyc has changed |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/rRNA.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/rRNA.txt Mon Oct 27 01:52:17 2014 -0400 |
| b |
| @@ -0,0 +1,8 @@ +>25s rRNA 3375nts +GCGACCCCAGGTCAGGCGGGATTACCCGCTGAGTTTAAGCATATCAATAAGCGGAGGAAAAGAAACTAACAAGGATTCCCTTAGTAACGGCGAGCGAACCGGGAAGAGCCCAGCTTGAAAATCGGACGTCTTCGGCGTTCGAATTGTAGTCTGGAGAAGCGTCCTCAGCGACGGACCGGGCCTAAGTTCCCTGGAAAGGGGCGCCAGAGAGGGTGAGAGCCCGTCGTGCCCGGACCCTGTCGCACCACGAGGCGCTGTCTACGAGTCGGGTTGTTTGGGAATGCAGCCCCAATCGGGCGGTAAATTCCGTCCAAGGCTAAATACGGGCGAGAGACCGATAGCGAACAAGTACCGCGAGGTAAAGATGAAAAGGACTTTGAAAAGAGAGTCAAAGAGTGCTTGAAATTGTCGGGAGGGAAGCGGATGGGGGCCGGCGATGCGTCCTGGTCGGATGCGGAACGGAGCAATCCGGTCCGCCGATCGATTCGGGGCGTGGACCGACGCGGATTACGGTGGCGGCCTAAGCCCGGGCTTTTGATACGCTTGTGGAGACGTCGCTGCCGTGATCGTGGTCTGCAGCACGCGCCTAACGGCGTGCCTCGGCATCAGCGTGCTCCGGGCGTCGGCCTGTGGGCTCCCCATTCGACCCGTCTTGAAACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGTGAGTAAACCCGTAAGGCGCAAGGAAGCTGATTGGCGGGATCCTCGCGGGTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGTGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGTAAAGCCAGAGGAAACTCTGGTGGAAGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTCGGACGCGAGTTCTATCGGGTAAAGCCAATGATTAGAGGCATTGGGGGCGCAACGCCTCGACCTATTCTCAAACTTTAAATAGGTAGGACGTGTCGGCTGCTTTGTTGAGCCGTCACACGGAATCGAGAGCTCCAAGTGGGCCATTTTTGGTAAGCAGAACTGGCGATGCGGGATGAACCGGAAGCCGGGTTACGGTGCCCAACTGCGCGCTAACCTAGAACCCACAAAGGGTGTTGGTCGATTAAGACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAATCAACTAGCCCCGAAAATGGATGGCGCTTAAGCGCGACCTATACCCGGCCGTCGGGGCAAGAGCCAGGCCTCGATGAGTAGGAGGGCGCGGCGGTCGCTGCAAAACCTAGGGCGCGAGGCGCGGAGCGGCCGTCGGTGCAGATCTTGGTGGTAGTAGCAAATATTCAAATGAGAACTTTGAAGGCCGAAGAGGGGAAAGGTTCCATGTGAACGGCACTTGCACATGGGTTAGTCGATCCTAAGAGTCGGGGGAAACCCGTCTGATAGCGCTTAAGCGAACTTCGAAAGGGGATCCGGTTAAAATTCCGGAACCGGGACGTGGCGGTTGACGGCAACGTTAGGGAGTCCGGAGACGTCGGCGGGGGCCTCGGGAAGAGTTATCTTTTCTGTTTAACAGCCTGCCCACCCTGGAAACGGCTCAGCCGGAGGTAGGGTCCAGCGGCTGGAAGAGCACCGCACGTCGCGTGGTGTCCGGTGCGCCCCCGGGCGCCCTTGAAAATCCGGAGGACCGAGTGCCGCTCACGCCCGGTCGTACTCATAACCGCATCAGGTCTCCAAGGTGAACAGCCTCTGGTCGATGGAACAATGTAGGCAAGGGAAGTCGGCAAAATGGATCCGTAACTTCGGGAAAAGGATTGGCTCTGAGGGCTGGGCTCGGGGGTCCCAGTTCCGAACCCGTCGGCTGTCAGCGGACTGCTCGAGCTGCTTCCGCGGCGAGAGCGGGTCGCCGGCTGCCGGCCGGGGGACGACTGGGAACGGCTCTCTCGGGAGCTTTCCCCGGGCGTCGAACAGTCAGCTCAGAACTGGTACGGACAAGGGGAATCCGACTGTTTAATTAAAACAAAGCATTGCGATGGTCCCTGCGGATGCTAACGCAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAACCAAGCGCGGGTAAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCCACTGTCCCTGTCTACTATCCAGCGAAACCACAGCCAAGGGAACGGGCTTGGCAGAATCAGCGGGGAAAGAAGACCCTGTTGAGCTTGACTCTAGTCCGACTTTGTGAAATGACTTGAGAGGTGTAGGATAAGTGGGAGCTTCGGCGCAAGTGAAATACCACTACTTTTAACGTTATTTTACTTACTCCGTGAATCGGAGGCCGGGGTACAACCCCTGTTTTTGGTCCCAAGGCTCGCTTCGGCGGGTCGATCCGGGCGGAGGACATTGTCAGGTGGGGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTAAGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTTCAGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACTTCGGAATTTGAAGCTAGAGGTGTCAGAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGTGTTGGATTGTTCACCCACCAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGCCCGCGTCGCGATAGTAATTCAACCTAGTACGAGAGGAACCGTTGATTCGCACAATTGGTCATCGCGCTTGGTTGAAAAGCCAGTGGCGCGAAGCTACCGTGCGCTGGATTATGACTGAACGCCTCTAAGTCAGAATCCGGGCTAGAAGCGACGCATGCGCCCGCCGCCCGATTGCCGACCCTCAGTAGGAGCTTAGGCTCCAAAGGCACGTGTCGTTGGCTAAGTCCGTTCGGCGGAACGGTCGTTCGGACCGCCTTGAATTATAATTACCACCGAGCGGCGGGTAGAATCCTTTGCAGACGACTTAAATACGCGACGGGGTATTGTAAGTGGCAGAGTGGCCTTGCTGCCACGATCCACTGAGATTCAGCCCTTTGTCGCTAAGATTCGA +>gi|20197903:2706-4513 Arabidopsis thaliana chromosome 2 BAC F23H14 genomic sequence, complete sequence +TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACGAATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGATGGTAACTACTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGCATGGCCTCTGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGTGGCCTACCATGGTGGTAACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAATACTGGGCTCTTTCGAGTCTGGTAATTGGAATGAGTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGAACCTTGGGATGGGTCGGCCGGTCCGCCTTTGGTGTGCATTGGTCGGCTTGTCCCTTCGGTCGGCGATACGCTCCTGGTCTTAATTGGCCGGGTCGTGCCTCCGGCGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCAGCGGATGTTGCTTATAGGACTCCGCTGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAATGAACGAGACCTCAGCCTGCTAACTAGCTACGTGGAGGCATCCCTTCACGGCCGGCTTCTTAGAGGGACTATGGCCGTTTAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTTCACACCTTGGCCGACAGGCCCGGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGATCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGTGGTTCGCCGCCCGCGACGTCGCGAGAAGTCCACTAAACCTTATCATTTAGAGGAAGGAGAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTG +>Arabidopsis thaliana 1 +GGATGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGTTGCATCCCTC +>gi|186498419|ref|NR_022453.1| Arabidopsis thaliana (AT2G01020) rRNA +AAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCCAAGCCTTCTGGCCGAGGGCACGTCTGCCTGGGTGTCACAA \ No newline at end of file |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/react_cal.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/react_cal.py Mon Oct 27 01:52:17 2014 -0400 |
| [ |
| @@ -0,0 +1,136 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +import sys +from Bio import SeqIO +import math +from parse_dis_react import * +from react_norm_function import * +import os + + +dist_file1 = sys.argv[1] #plus library +dist_file2 = sys.argv[2] #minus library +seq_file = sys.argv[3] #Reference library(genome/cDNA) +nt_spec = sys.argv[4] #only show reactivity for AC or ATCG +flag_in = sys.argv[5] # perform 2-8% normalization (1) or not (0) +threshold = sys.argv[6] #Threshold to cap the reactivities +output_file = sys.argv[7] + + +distri_p = parse_dist(dist_file1) +distri_m = parse_dist(dist_file2) +threshold = float(threshold) + + +ospath = os.path.realpath(sys.argv[0]) +ost = ospath.split('/') +syspath = "" +for i in range(len(ost)-1): + syspath = syspath+ost[i].strip() + syspath = syspath+'/' + +h = file(syspath+"react.txt",'w') +flag_in = int(flag_in) + +seqs = SeqIO.parse(open(seq_file),'fasta'); +nt_s = set() +for i in range(len(nt_spec)): + nt_s.add(nt_spec[i]) + +flag = 0 +trans = [] +distri_p = distri_p[1] +distri_m = distri_m[1] + +#thres = int(threshold) + + +transcripts = {} +for seq in seqs: + n = seq.id + trans.append(n) + transcripts[n] = seq.seq.tostring() + + +#print(distri_p) + + +for i in range(0, len(trans)): + h.write(trans[i]) + h.write('\n') + for j in range(len(distri_p[trans[i]])): + distri_p[trans[i]][j] = math.log((int(distri_p[trans[i]][j])+1),math.e) + for j in range(len(distri_m[trans[i]])): + distri_m[trans[i]][j] = math.log((int(distri_m[trans[i]][j])+1),math.e) + s_p = sum(distri_p[trans[i]]) + s_m = sum(distri_m[trans[i]]) + length = len(distri_p[trans[i]]) + if s_p!= 0 and s_m!= 0: + r = [] + for j in range(0, len(distri_p[trans[i]])): + f_p = (float(distri_p[trans[i]][j]))/float(s_p)*length + f_m = (float(distri_m[trans[i]][j]))/float(s_m)*length + raw_react = f_p-f_m + r.append(max(0, raw_react)) + + if s_p!= 0 and s_m!= 0: + for k in range(1,(len(r)-1)): + if transcripts[trans[i]][k-1] in nt_s: + h.write(str(r[k])) + h.write('\t') + else: + h.write('NA') + h.write('\t') + k = k+1 + if transcripts[trans[i]][k-1] in nt_s: + h.write(str(r[k])) + h.write('\n') + else: + h.write('NA') + h.write('\n') + + +h.close() + +if flag_in: + react_norm((syspath+"react.txt"),output_file, threshold) +else: + h_o = file(output_file, 'w') + f_i = open(syspath+"react.txt") + for aline in f_i.readlines(): + h_o.write(aline.strip()) + h_o.write('\n') +os.system("rm -f "+syspath+"react.txt") + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/react_norm_function.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/react_norm_function.py Mon Oct 27 01:52:17 2014 -0400 |
| [ |
| @@ -0,0 +1,82 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +import sys +from Bio import SeqIO +import math +from parse_dis_react import * + +def cap(a,value): + if a>=value: + return value + else: + return a + +def react_norm(react_file, result_file, capped_value): + print("Normalizing.....") + react1 = parse_dist(react_file) + react = react1[1] + h = file(result_file, 'w') + + capped = int(capped_value) + + all_react = [] + + + for t in react: + if react[t]!='null': + for i in range(len(react[t])): + if react[t][i]!='NA': + all_react.append(float(react[t][i])) + + + all_react.sort(reverse = True) + + + eight = all_react[int(len(all_react)*0.02):int(len(all_react)*0.1)] + meight = sum(eight)/len(eight) + + for t in react: + h.write(t) + h.write('\n') + if react[t]!='null': + for i in range((len(react[t])-1)): + if react[t][i]!='NA': + h.write(str(cap((float(react[t][i])/meight),capped))) + else: + h.write('NA') + h.write('\t') + if react[t][i+1]!='NA': + h.write(str(cap((float(react[t][i+1])/meight),capped))) + else: + h.write('NA') + h.write('\n') + + h.close() + + + + + + + + + + + + + + + + + + + + + + + + + + + + |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/react_norm_function.pyc |
| b |
| Binary file reactivity_cal/react_norm_function.pyc has changed |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/reactivity_calculation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/reactivity_calculation.xml Mon Oct 27 01:52:17 2014 -0400 |
| [ |
| @@ -0,0 +1,60 @@ +<tool id="react_cal_pipeline" name="Reactivity Calculation" version="1.0"> + <description></description> + <command interpreter="python">react_cal.py $dist_file1 $dist_file2 $seq_file $nt_spec $flag_in $threshold $output </command> + <requirements> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + </requirements> + <inputs> + <param name="dist_file1" type="data" format="txt" label="RTSC file for (+) library"/> + <param name="dist_file2" type="data" format="txt" label="RTSC file for (-) library"/> + <param name="seq_file" type="data" format="fasta" label="Reference genome/transcriptome"/> + <param name="nt_spec" type="select" label="Nucleotide specificity"> + <option value="AC">AC</option> + <option value="ATCG">AUCG</option> + </param> + <param name="flag_in" type="boolean" checked="true" truevalue = "1" falsevalue = "0" label="Normalization is performed if checked"/> + <param name="threshold" type="float" value = "7" optional = "true" label="Threshold to cap the reactivities"/> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <param name="dist_file1" value="dis_f_N1Ap_rrna.txt" /> + <param name="dist_file2" value="dis_f_N1Am_rrna.txt" /> + <param name="seq_file" value="rRNA.txt" /> + <param name="nt_spec" value="AC" /> + <param name="flag_in" value="1" /> + <param name="threshold" value="7" /> + <output name="output" file="DMS_reactivities.out" /> + + </test> + </tests> + + <help> + + +**TIPS**: + +----- + +**Input**: + +* 1. RTSC files (Output of Get RT Stop Counts) for (+) and (-) library +* 2. Reference file (fasta) used to map the reads to +* 3. Nucleotide Specificity (Type of nucleotides to have reactivity, e.g. AC for DMS and ACTG for SHAPE) +* [Optional]: +* 1. A threshold to cap the structural reactivities. {Default: 7} +* 2. Flag that determines whether to perform 2%-8% normalization {Default: Yes} + +----- + +**Output**: + +A text file with structural reactivity for each nucleotide (Reactivity file) + + + + </help> +</tool> |
| b |
| diff -r 6747060cdfe6 -r 765da0718336 reactivity_cal/read_file.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reactivity_cal/read_file.py Mon Oct 27 01:52:17 2014 -0400 |
| [ |
| @@ -0,0 +1,21 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import sys + + + +def read_t_file(in_file): + f = open(in_file); + result = []; + for aline in f.readlines(): + temp = []; + tline = aline.strip(); + tl = tline.split('\t'); + for i in range(0, len(tl)): + temp.append(tl[i].strip()); + result.append(temp); + f.close(); + return result; + + |