diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 35 |
1 files changed, 21 insertions, 14 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index 012e96b2..2af84477 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -24,33 +24,38 @@ import numpy as np import input usage = """ -python convertlmm.py [--kinship] infile +python convertlmm.py [--kinship kfile] Convert files for runlmm.py processing. Writes to stdout. try --help for more information """ -parser = OptionParser(usage=usage) -# parser.add_option("-f", "--file", dest="input file", -# help="In", metavar="FILE") -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.") -parser.add_option("-q", "--quiet", +# if len(args) == 0: +# print usage +# sys.exit(1) + +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("--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", + help="Output prefix for output file(s)") +option_parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=True, help="don't print status messages to stdout") +option_parser.add_option("-v", "--verbose", + action="store_true", dest="verbose", default=False, + help="Print extra info") -(options, args) = parser.parse_args() - -if len(args) == 0: - print usage - sys.exit(1) +(options, args) = option_parser.parse_args() if options.kinship: is_header = True - assert(len(args)==1) count = 0 - for line in open(args[0],'r'): + sys.stderr.write("Converting "+options.kinship+"\n") + for line in open(options.kinship,'r'): count += 1 if is_header: size = len(line.split()) @@ -64,3 +69,5 @@ if options.kinship: sys.stdout.write("\t") sys.stdout.write("\t".join(line.split())) sys.stdout.write("\n") + +sys.stderr.write("Converting done\n") |