Mercurial > repos > galaxyp > cravatool
diff cravat_submit.py @ 0:83181dabeb90 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
author | galaxyp |
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date | Fri, 18 May 2018 13:25:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cravat_submit.py Fri May 18 13:25:29 2018 -0400 @@ -0,0 +1,287 @@ +import requests +import json +import time +import urllib +import sys +import csv +import re +import math +from difflib import SequenceMatcher +from xml.etree import ElementTree as ET +import sqlite3 + +try: + input_filename = sys.argv[1] + input_select_bar = sys.argv[2] + GRCh_build = sys.argv[3] + probed_filename = sys.argv[4] + output_filename = sys.argv[5] + file_3 = sys.argv[6] + file_4 = sys.argv[7] + file_5 = sys.argv[8] +except: + # Filenames for testing. + input_filename = 'test-data/[VCF-BEDintersect__on_data_65_and_data_6].vcf' + probed_filename = 'test-data/[PepPointer].bed' + input_select_bar = 'VEST' + GRCh_build = 'GRCh38' + output_filename = 'combined_variants.tsv' + file_3 = 'test-results/Gene_Level_Analysis.tsv' + file_4 = 'test-results/Variant_Non-coding.Result.tsv' + file_5 = 'test-results/Input_Errors.Result.tsv' + matches_filename = 'matches.tsv' + +def getSequence(transcript_id): + server = 'http://rest.ensembl.org' + ext = '/sequence/id/' + transcript_id + '?content-type=text/x-seqxml%2Bxml;multiple_sequences=1;type=protein' + req = requests.get(server+ext, headers={ "Content-Type" : "text/plain"}) + + if not req.ok: + return None + + root = ET.fromstring(req.content) + for child in root.iter('AAseq'): + return child.text + + +write_header = True + +GRCh37hg19 = 'off' +if GRCh_build == 'GRCh37': + GRCh37hg19 = 'on' + +#plugs in params to given URL +submit = requests.post('http://staging.cravat.us/CRAVAT/rest/service/submit', files={'inputfile':open(input_filename)}, data={'email':'znylund@insilico.us.com', 'analyses': input_select_bar, 'hg19': GRCh37hg19}) + +#Makes the data a json dictionary, takes out only the job ID +jobid = json.loads(submit.text)['jobid'] + +#out_file.write(jobid) +submitted = json.loads(submit.text)['status'] +#out_file.write('\t' + submitted) + +input_file = open(input_filename) + +# Loads the proBED file as a list. +if (probed_filename != 'None'): + proBED = [] + with open(probed_filename) as tsvin: + tsvreader = csv.reader(tsvin, delimiter='\t') + for i, row in enumerate(tsvreader): + proBED.append(row) + +#loops until we find a status equal to Success, then breaks +while True: + check = requests.get('http://staging.cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid}) + status = json.loads(check.text)['status'] + resultfileurl = json.loads(check.text)['resultfileurl'] + #out_file.write(str(status) + ', ') + if status == 'Success': + #out_file.write('\t' + resultfileurl) + break + else: + time.sleep(2) + +#out_file.write('\n') + +#creates three files +file_1 = 'Variant_Result.tsv' +file_2 = 'Additional_Details.tsv' +#file_3 = time.strftime("%H:%M") + 'Combined_Variant_Results.tsv' + +#Downloads the tabular results +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv", file_1) +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv", file_2) +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Gene_Level_Analysis.Result.tsv", file_3) +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Non-coding.Result.tsv", file_4) +urllib.urlretrieve("http://staging.cravat.us/CRAVAT/results/" + jobid + "/" + "Input_Errors.Result.tsv", file_5) + +#opens the Variant Result file and the Variant Additional Details file as csv readers, then opens the output file (galaxy) as a writer +with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout: + tsvreader_2 = csv.reader(tsvin_2, delimiter='\t') + tsvout = csv.writer(tsvout, delimiter='\t') + + headers = [] + duplicate_indices = [] + n = 12 #Index for proteogenomic column start + reg_seq_change = re.compile('([A-Z]+)(\d+)([A-Z]+)') + SOtranscripts = re.compile('([A-Z]+[\d\.]+):([A-Z]+\d+[A-Z]+)') + pep_muts = {} + pep_map = {} + rows = [] + + for row in tsvreader_2: + if row != [] and row[0][0] != '#': + #checks if the row begins with input line + if row[0] == 'Input line': + vad_headers = row + else: + # Initially screens through the output Variant Additional Details to catch mutations on same peptide region + genchrom = row[vad_headers.index('Chromosome')] + genpos = int(row[vad_headers.index('Position')]) + aa_change = row[vad_headers.index('Protein sequence change')] + input_line = row[vad_headers.index('Input line')] + + for peptide in proBED: + pepseq = peptide[3] + pepchrom = peptide[0] + pepposA = int(peptide[1]) + pepposB = int(peptide[2]) + if genchrom == pepchrom and pepposA <= genpos and genpos <= pepposB: + strand = row[vad_headers.index('Strand')] + transcript_strand = row[vad_headers.index('S.O. transcript strand')] + + # Calculates the position of the variant amino acid(s) on peptide + if transcript_strand == strand: + aa_peppos = int(math.ceil((genpos - pepposA)/3.0) - 1) + if strand == '-' or transcript_strand == '-' or aa_peppos >= len(pepseq): + aa_peppos = int(math.floor((pepposB - genpos)/3.0)) + if pepseq in pep_muts: + if aa_change not in pep_muts[pepseq]: + pep_muts[pepseq][aa_change] = [aa_peppos] + else: + if aa_peppos not in pep_muts[pepseq][aa_change]: + pep_muts[pepseq][aa_change].append(aa_peppos) + else: + pep_muts[pepseq] = {aa_change : [aa_peppos]} + # Stores the intersect information by mapping Input Line (CRAVAT output) to peptide sequence. + if input_line in pep_map: + if pepseq not in pep_map[input_line]: + pep_map[input_line].append(pepseq) + else: + pep_map[input_line] = [pepseq] + +with open(file_1) as tsvin_1, open(file_2) as tsvin_2, open(output_filename, 'wb') as tsvout: + tsvreader_1 = csv.reader(tsvin_1, delimiter='\t') + tsvreader_2 = csv.reader(tsvin_2, delimiter='\t') + tsvout = csv.writer(tsvout, delimiter='\t') + + headers = [] + + #loops through each row in the Variant Additional Details (VAD) file + for row in tsvreader_2: + + #sets row_2 equal to the same row in Variant Result (VR) file + row_2 = tsvreader_1.next() + #checks if row is empty or if the first term contains '#' + if row == [] or row[0][0] == '#': + tsvout.writerow(row) + else: + if row[0] == 'Input line': + #Goes through each value in the headers list in VAD + for value in row: + #Adds each value into headers + headers.append(value) + #Loops through the Keys in VR + for i,value in enumerate(row_2): + #Checks if the value is already in headers + if value in headers: + duplicate_indices.append(i) + continue + #else adds the header to headers + else: + headers.append(value) + #Adds appropriate headers when proteomic input is supplied + if (probed_filename != 'None'): + headers.insert(n, 'Variant peptide') + headers.insert(n, 'Reference peptide') + tsvout.writerow(headers) + else: + cells = [] + #Goes through each value in the next list + for value in row: + #adds it to cells + cells.append(value) + #Goes through each value from the VR file after position 11 (After it is done repeating from VAD file) + for i,value in enumerate(row_2): + #adds in the rest of the values to cells + if i not in duplicate_indices: + # Skips the initial 11 columns and the VEST p-value (already in VR file) + cells.append(value) + + # Verifies the peptides intersected previously through sequences obtained from Ensembl's API + if (probed_filename != 'None'): + cells.insert(n,'') + cells.insert(n,'') + input_line = cells[headers.index('Input line')] + if input_line in pep_map: + pepseq = pep_map[input_line][0] + aa_changes = pep_muts[pepseq] + transcript_id = cells[headers.index('S.O. transcript')] + ref_fullseq = getSequence(transcript_id) + # Checks the other S.O. transcripts if the primary S.O. transcript has no sequence available + if not ref_fullseq: + transcripts = cells[headers.index('S.O. all transcripts')] + for transcript in transcripts.split(','): + if transcript: + mat = SOtranscripts.search(transcript) + ref_fullseq = getSequence(mat.group(1)) + if ref_fullseq: + aa_changes = {mat.group(2): [aa_changes.values()[0][0]]} + break + # Resubmits the previous transcripts without extensions if all S.O. transcripts fail to provide a sequence + if not ref_fullseq: + transcripts = cells[headers.index('S.O. all transcripts')] + for transcript in transcripts.split(','): + if transcript: + mat = SOtranscripts.search(transcript) + ref_fullseq = getSequence(mat.group(1).split('.')[0]) + if ref_fullseq: + aa_changes = {mat.group(2): [aa_changes.values()[0][0]]} + break + if ref_fullseq: + # Sorts the amino acid changes + positions = {} + for aa_change in aa_changes: + m = reg_seq_change.search(aa_change) + aa_protpos = int(m.group(2)) + aa_peppos = aa_changes[aa_change][0] + aa_startpos = aa_protpos - aa_peppos - 1 + if aa_startpos in positions: + positions[aa_startpos].append(aa_change) + else: + positions[aa_startpos] = [aa_change] + # Goes through the sorted categories to mutate the Ensembl peptide (uses proBED peptide as a reference) + for pep_protpos in positions: + ref_seq = ref_fullseq[pep_protpos:pep_protpos+len(pepseq)] + muts = positions[pep_protpos] + options = [] + mut_seq = ref_seq + for mut in muts: + m = reg_seq_change.search(mut) + ref_aa = m.group(1) + mut_pos = int(m.group(2)) + alt_aa = m.group(3) + pep_mutpos = mut_pos - pep_protpos - 1 + if ref_seq[pep_mutpos] == ref_aa and (pepseq[pep_mutpos] == alt_aa or pepseq[pep_mutpos] == ref_aa): + if pepseq[pep_mutpos] == ref_aa: + mut_seq = mut_seq[:pep_mutpos] + ref_aa + mut_seq[pep_mutpos+1:] + else: + mut_seq = mut_seq[:pep_mutpos] + alt_aa + mut_seq[pep_mutpos+1:] + else: + break + # Adds the mutated peptide and reference peptide if mutated correctly + if pepseq == mut_seq: + cells[n+1] = pepseq + cells[n] = ref_seq + #print cells + tsvout.writerow(cells) + + + + + + +#a = 'col1\tcol2\tcol3' +#header_list = a.split('\t') + +#loop through the two results, when you first hit header you print out the headers in tabular form +#Print out each header only once +#Combine both headers into one output file +#loop through the rest of the data and assign each value to its assigned header +#combine this all into one output file + + + + +