Mercurial > repos > davidvanzessen > shm_csr
view baseline/script_imgt.py @ 50:75ee66a691a0 draft
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author | davidvanzessen |
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date | Mon, 15 May 2017 03:13:16 -0400 |
parents | 4c5ba6b5d10d |
children | 8728284105ee |
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#import xlrd #avoid dep import argparse import re parser = argparse.ArgumentParser() parser.add_argument("--input", help="Excel input file containing one or more sheets where column G has the gene annotation, H has the sequence id and J has the sequence") parser.add_argument("--ref", help="Reference file") parser.add_argument("--output", help="Output file") parser.add_argument("--id", help="ID to be used at the '>>>' line in the output") args = parser.parse_args() refdic = dict() with open(args.ref, 'rU') as ref: currentSeq = "" currentId = "" for line in ref: if line[0] is ">": if currentSeq is not "" and currentId is not "": refdic[currentId[1:]] = currentSeq currentId = line.rstrip() currentSeq = "" else: currentSeq += line.rstrip() refdic[currentId[1:]] = currentSeq vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?\*\d{1,2})"]#, # r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)", # r"(IGKV[0-3]D?-[0-9]{1,2})", # r"(IGLV[0-9]-[0-9]{1,2})", # r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)", # r"(TRGV[234589])", # r"(TRDV[1-3])"] #vPattern = re.compile(r"|".join(vPattern)) vPattern = re.compile("|".join(vPattern)) def filterGene(s, pattern): s1 = s[s.find(" ") + 1:] return s1[:s1.find(" ")] """ if type(s) is not str: return None res = pattern.search(s) if res: return res.group(0) return None """ currentSeq = "" currentId = "" first=True with open(args.input, 'r') as i: with open(args.output, 'a') as o: o.write(">>>" + args.id + "\n") outputdic = dict() for line in i: if first: first = False continue linesplt = line.split("\t") ref = filterGene(linesplt[1], vPattern) if not ref or not linesplt[2].rstrip(): continue if ref in outputdic: outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())] else: outputdic[ref] = [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())] #print outputdic for k in outputdic.keys(): if k in refdic: o.write(">>" + k + "\n") o.write(refdic[k] + "\n") for seq in outputdic[k]: #print seq o.write(">" + seq[0] + "\n") o.write(seq[1] + "\n") else: print k + " not in reference, skipping " + k