diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 72 |
1 files changed, 62 insertions, 10 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index 2af84477..0604762e 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -38,6 +38,8 @@ python convertlmm.py [--kinship kfile] option_parser = OptionParser(usage=usage) option_parser.add_option("--kinship", dest="kinship", help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program") +option_parser.add_option("--plink", dest="plink", + help="Parse a phenotype file (PLINK style)") # option_parser.add_option("--kinship",action="store_false", dest="kinship", default=True, # help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program.") option_parser.add_option("--prefix", dest="prefix", @@ -51,23 +53,73 @@ option_parser.add_option("-v", "--verbose", (options, args) = option_parser.parse_args() +writer = None + +def msg(s): + sys.stderr.write("INFO: ") + sys.stderr.write(s) + sys.stderr.write("\n") + +def wr(s): + if writer: + writer.write(s) + else: + sys.stdout.write(s) + +def wrln(s): + wr(s) + wr("\n") + if options.kinship: is_header = True count = 0 - sys.stderr.write("Converting "+options.kinship+"\n") + msg("Converting "+options.kinship) + if options.prefix: + writer = open(options.prefix+".kin","w") for line in open(options.kinship,'r'): count += 1 if is_header: size = len(line.split()) - print "# Kinship format version 1.0" - print "# Size=",size + wrln("# Kinship format version 1.0") + wrln("# Size="+str(size)) for i in range(size): - sys.stdout.write("\t"+str(i+1)) - sys.stdout.write("\n") + wr("\t"+str(i+1)) + wr("\n") is_header = False - sys.stdout.write(str(count)) - sys.stdout.write("\t") - sys.stdout.write("\t".join(line.split())) - sys.stdout.write("\n") + wr(str(count)) + wr("\t") + wr("\t".join(line.split())) + wr("\n") + msg(str(count)+" lines written") + +if options.plink: + # Because plink does not track size we need to read the whole thing first + msg("Converting "+options.plink) + phenos = [] + count = 0 + count_pheno = None + for line in open(options.plink,'r'): + count += 1 + list = line.split() + pcount = len(list)-2 + assert(pcount > 0) + if count_pheno == None: + count_pheno = pcount + assert(count_pheno == pcount) + row = [list[0]]+list[2:] + phenos.append(row) -sys.stderr.write("Converting done\n") + if options.prefix: + writer = open(options.prefix+".pheno","w") + wrln("# Phenotype format version 1.0") + wrln("# Individuals = "+str(count)) + wrln("# Phenotypes = "+str(count_pheno)) + for i in range(count_pheno): + wr("\t"+str(i+1)) + wr("\n") + for i in range(count): + wr("\t".join(phenos[i])) + wr("\n") + msg(str(count)+" lines written") + +msg("Converting done") |