Mercurial > repos > davidvanzessen > mutation_analysis
diff mutation_analysis.py @ 49:5c6b9e99d576 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 18 Nov 2015 05:55:04 -0500 |
| parents | 4b1bab1a9ad2 |
| children | 7290a88ea202 |
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--- a/mutation_analysis.py Thu Nov 12 09:46:37 2015 -0500 +++ b/mutation_analysis.py Wed Nov 18 05:55:04 2015 -0500 @@ -1,9 +1,10 @@ +from collections import defaultdict import re import argparse parser = argparse.ArgumentParser() parser.add_argument("--input", - help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation") + help="The '7_V-REGION-mutation-and-AA-change-table' and '10_V-REGION-mutation-hotspots' merged together, with an added 'best_match' annotation") parser.add_argument("--genes", help="The genes available in the 'best_match' column") parser.add_argument("--includefr1", help="The genes available in the 'best_match' column") parser.add_argument("--output", help="Output file") @@ -33,6 +34,8 @@ IDlist = [] mutationList = [] mutationListByID = {} +cdr1LengthDic = {} +cdr2LengthDic = {} with open(infile, 'r') as i: for line in i: @@ -45,6 +48,8 @@ fr2Index = linesplt.index("FR2.IMGT") cdr2Index = linesplt.index("CDR2.IMGT") fr3Index = linesplt.index("FR3.IMGT") + cdr1LengthIndex = linesplt.index("CDR1.IMGT.Nb.of.nucleotides") + cdr2LengthIndex = linesplt.index("CDR2.IMGT.Nb.of.nucleotides") first = False continue linecount += 1 @@ -62,9 +67,17 @@ mutationList += mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] mutationListByID[ID] = mutationdic[ID + "_FR1"] + mutationdic[ID + "_CDR1"] + mutationdic[ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] + cdr1Length = linesplt[cdr1LengthIndex] + cdr2Length = linesplt[cdr2LengthIndex] + + cdr1LengthDic[ID] = int(cdr1Length) / 3 + cdr2LengthDic[ID] = int(cdr2Length) / 3 + IDlist += [ID] -AA_mutation = [0] * (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent +AALength = (int(max(mutationList, key=lambda i: int(i[4]) if i[4] else 0)[4]) + 1) # [4] is the position of the AA mutation, None if silent + +AA_mutation = [0] * AALength AA_mutation_empty = AA_mutation[:] aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt" @@ -75,28 +88,74 @@ if mutation[4]: AA_mutation[int(mutation[4])] += 1 AA_mutation_for_ID[int(mutation[4])] += 1 - o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID]) + "\n") + o.write(ID + "\t" + "\t".join([str(x) for x in AA_mutation_for_ID[1:]]) + "\n") -#for mutation in mutationList: -# if mutation[4]: # if non silent mutation -# AA_mutation[int(mutation[4])] += 1 +#absent AA stuff +absentAACDR1Dic = defaultdict(list) +absentAACDR1Dic[5] = range(29,36) +absentAACDR1Dic[6] = range(29,35) +absentAACDR1Dic[7] = range(30,35) +absentAACDR1Dic[8] = range(30,34) +absentAACDR1Dic[9] = range(31,34) +absentAACDR1Dic[10] = range(31,33) +absentAACDR1Dic[11] = [32] + +absentAACDR2Dic = defaultdict(list) +absentAACDR2Dic[0] = range(55,65) +absentAACDR2Dic[1] = range(56,65) +absentAACDR2Dic[2] = range(56,64) +absentAACDR2Dic[3] = range(57,64) +absentAACDR2Dic[4] = range(57,63) +absentAACDR2Dic[5] = range(58,63) +absentAACDR2Dic[6] = range(58,62) +absentAACDR2Dic[7] = range(59,62) +absentAACDR2Dic[8] = range(59,61) +absentAACDR2Dic[9] = [60] + +absentAA = [len(IDlist)] * (AALength-1) +for k, cdr1Length in cdr1LengthDic.iteritems(): + for c in absentAACDR1Dic[cdr1Length]: + absentAA[c] -= 1 + +for k, cdr2Length in cdr2LengthDic.iteritems(): + for c in absentAACDR2Dic[cdr2Length]: + absentAA[c] -= 1 + + +aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/absent_aa_id.txt" +with open(aa_mutations_by_id_file, 'w') as o: + o.write("ID\tcdr1length\tcdr2length\t" + "\t".join([str(x) for x in range(1,AALength-1)]) + "\n") + for ID in IDlist: + absentAAbyID = [1] * (AALength-1) + cdr1Length = cdr1LengthDic[ID] + for c in absentAACDR1Dic[cdr1Length]: + absentAAbyID[c] -= 1 + + cdr2Length = cdr2LengthDic[ID] + for c in absentAACDR2Dic[cdr2Length]: + absentAAbyID[c] -= 1 + o.write(ID + "\t" + str(cdr1Length) + "\t" + str(cdr2Length) + "\t" + "\t".join([str(x) for x in absentAAbyID]) + "\n") + + aa_mutations_file = outfile[:outfile.rindex("/")] + "/aa_mutations.txt" with open(aa_mutations_file, 'w') as o: - o.write(",".join([str(x) for x in AA_mutation]) + "\n") + o.write("row.name\t" + "\t".join([str(x) for x in range(1, AALength-1)]) + "\n") + o.write("mutations.at.position\t" + "\t".join([str(x) for x in AA_mutation[1:]]) + "\n") + o.write("AA.at.position\t" + "\t".join([str(x) for x in absentAA]) + "\n") if linecount == 0: - print "No data, exiting" - with open(outfile, 'w') as o: - o.write("RGYW (%)," + ("0,0,0\n" * len(genes))) - o.write("WRCY (%)," + ("0,0,0\n" * len(genes))) - o.write("WA (%)," + ("0,0,0\n" * len(genes))) - o.write("TW (%)," + ("0,0,0\n" * len(genes))) - import sys + print "No data, exiting" + with open(outfile, 'w') as o: + o.write("RGYW (%)," + ("0,0,0\n" * len(genes))) + o.write("WRCY (%)," + ("0,0,0\n" * len(genes))) + o.write("WA (%)," + ("0,0,0\n" * len(genes))) + o.write("TW (%)," + ("0,0,0\n" * len(genes))) + import sys - sys.exit() + sys.exit() hotspotMatcher = re.compile("[actg]+,(\d+)-(\d+)\((.*)\)") RGYWCount = {g: 0 for g in genes} @@ -111,80 +170,80 @@ atagcctIndex = 0 first = True with open(infile, 'r') as i: - for line in i: - if first: - linesplt = line.split("\t") - ataIndex = linesplt.index("X.a.t.a") - tatIndex = linesplt.index("t.a.t.") - aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.") - atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.") - first = False - continue - linesplt = line.split("\t") - gene = linesplt[best_matchIndex] - ID = linesplt[IDIndex] - RGYW = [(int(x), int(y), z) for (x, y, z) in - [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]] - WRCY = [(int(x), int(y), z) for (x, y, z) in - [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]] - WA = [(int(x), int(y), z) for (x, y, z) in - [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]] - TW = [(int(x), int(y), z) for (x, y, z) in - [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]] - RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0 + for line in i: + if first: + linesplt = line.split("\t") + ataIndex = linesplt.index("X.a.t.a") + tatIndex = linesplt.index("t.a.t.") + aggctatIndex = linesplt.index("X.a.g.g.c.t..a.t.") + atagcctIndex = linesplt.index("X.a.t..a.g.c.c.t.") + first = False + continue + linesplt = line.split("\t") + gene = linesplt[best_matchIndex] + ID = linesplt[IDIndex] + RGYW = [(int(x), int(y), z) for (x, y, z) in + [hotspotMatcher.match(x).groups() for x in linesplt[aggctatIndex].split("|") if x]] + WRCY = [(int(x), int(y), z) for (x, y, z) in + [hotspotMatcher.match(x).groups() for x in linesplt[atagcctIndex].split("|") if x]] + WA = [(int(x), int(y), z) for (x, y, z) in + [hotspotMatcher.match(x).groups() for x in linesplt[ataIndex].split("|") if x]] + TW = [(int(x), int(y), z) for (x, y, z) in + [hotspotMatcher.match(x).groups() for x in linesplt[tatIndex].split("|") if x]] + RGYWCount[ID], WRCYCount[ID], WACount[ID], TWCount[ID] = 0, 0, 0, 0 - mutationList = (mutationdic[ID + "_FR1"] if include_fr1 else []) + mutationdic[ID + "_CDR1"] + mutationdic[ - ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] - for mutation in mutationList: - frm, where, to, AAfrm, AAwhere, AAto, junk = mutation - mutation_in_RGYW = any([(start <= int(where) <= end) for (start, end, region) in RGYW]) - mutation_in_WRCY = any([(start <= int(where) <= end) for (start, end, region) in WRCY]) - mutation_in_WA = any([(start <= int(where) <= end) for (start, end, region) in WA]) - mutation_in_TW = any([(start <= int(where) <= end) for (start, end, region) in TW]) + mutationList = (mutationdic[ID + "_FR1"] if include_fr1 else []) + mutationdic[ID + "_CDR1"] + mutationdic[ + ID + "_FR2"] + mutationdic[ID + "_CDR2"] + mutationdic[ID + "_FR3"] + for mutation in mutationList: + frm, where, to, AAfrm, AAwhere, AAto, junk = mutation + mutation_in_RGYW = any([(start <= int(where) <= end) for (start, end, region) in RGYW]) + mutation_in_WRCY = any([(start <= int(where) <= end) for (start, end, region) in WRCY]) + mutation_in_WA = any([(start <= int(where) <= end) for (start, end, region) in WA]) + mutation_in_TW = any([(start <= int(where) <= end) for (start, end, region) in TW]) - in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW]) + in_how_many_motifs = sum([mutation_in_RGYW, mutation_in_WRCY, mutation_in_WA, mutation_in_TW]) - if in_how_many_motifs > 0: - RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs - WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs - WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs - TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs + if in_how_many_motifs > 0: + RGYWCount[ID] += (1.0 * int(mutation_in_RGYW)) / in_how_many_motifs + WRCYCount[ID] += (1.0 * int(mutation_in_WRCY)) / in_how_many_motifs + WACount[ID] += (1.0 * int(mutation_in_WA)) / in_how_many_motifs + TWCount[ID] += (1.0 * int(mutation_in_TW)) / in_how_many_motifs directory = outfile[:outfile.rfind("/") + 1] value = 0 valuedic = dict() for gene in genes: - with open(directory + gene + "_value.txt", 'r') as v: - valuedic[gene] = int(v.readlines()[0].rstrip()) + with open(directory + gene + "_value.txt", 'r') as v: + valuedic[gene] = int(v.readlines()[0].rstrip()) with open(directory + "total_value.txt", 'r') as v: - valuedic["total"] = int(v.readlines()[0].rstrip()) + valuedic["total"] = int(v.readlines()[0].rstrip()) dic = {"RGYW": RGYWCount, "WRCY": WRCYCount, "WA": WACount, "TW": TWCount} arr = ["RGYW", "WRCY", "WA", "TW"] with open(outfile, 'w') as o: - for typ in arr: - o.write(typ + " (%)") - curr = dic[typ] - for gene in genes: - geneMatcher = re.compile(".*" + gene + ".*") - if valuedic[gene] is 0: - o.write(",0,0,0") - else: - x = int(round(sum([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]]))) - y = valuedic[gene] - z = str(round(x / float(valuedic[gene]) * 100, 1)) - o.write("," + str(x) + "," + str(y) + "," + z) - # for total - x = int(round(sum([y for x, y in curr.iteritems()]))) - y = valuedic["total"] - z = str(round(x / float(valuedic["total"]) * 100, 1)) - o.write("," + str(x) + "," + str(y) + "," + z + "\n") + for typ in arr: + o.write(typ + " (%)") + curr = dic[typ] + for gene in genes: + geneMatcher = re.compile(".*" + gene + ".*") + if valuedic[gene] is 0: + o.write(",0,0,0") + else: + x = int(round(sum([curr[x] for x in [y for y, z in genedic.iteritems() if geneMatcher.match(z)]]))) + y = valuedic[gene] + z = str(round(x / float(valuedic[gene]) * 100, 1)) + o.write("," + str(x) + "," + str(y) + "," + z) + # for total + x = int(round(sum([y for x, y in curr.iteritems()]))) + y = valuedic["total"] + z = str(round(x / float(valuedic["total"]) * 100, 1)) + o.write("," + str(x) + "," + str(y) + "," + z + "\n") # for testing seq_motif_file = outfile[:outfile.rindex("/")] + "/motif_per_seq.txt" with open(seq_motif_file, 'w') as o: - o.write("ID\tRGYWC\tWRCY\tWA\tTW\n") - for ID in IDlist: - o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str( - round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n") + o.write("ID\tRGYWC\tWRCY\tWA\tTW\n") + for ID in IDlist: + o.write(ID + "\t" + str(round(RGYWCount[ID], 2)) + "\t" + str(round(WRCYCount[ID], 2)) + "\t" + str( + round(WACount[ID], 2)) + "\t" + str(round(TWCount[ID], 2)) + "\n")