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| author | Lei Yan | 2014-02-21 17:04:51 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-21 17:04:51 -0600 |
| commit | 1014d09efced9c36274aec0d2486469648569721 (patch) | |
| tree | 152d489c8b56349c6f3680ee7cf5554c95df90c0 | |
| parent | ff6224c23ff0894012297dc569de0bfdbb0da1c3 (diff) | |
| download | genenetwork2-1014d09efced9c36274aec0d2486469648569721.tar.gz | |
On branch master
| -rw-r--r-- | wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini | 8 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/load_genotypes.py | 17 |
2 files changed, 15 insertions, 10 deletions
diff --git a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini index 638c3bd8..1f977cf8 100644 --- a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini +++ b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini @@ -1,4 +1,6 @@ [config] -inbredsetid = 1 -datafile = datasampledir/load_phenotypes/sample_data.txt -metafile = datasampledir/load_phenotypes/sample_meta.txt +genofile = datasampledir/load_genotypes/sample.geno +U = x +H = 0 +B = -1 +D = 1 diff --git a/wqflask/maintenance/dataset/load_genotypes.py b/wqflask/maintenance/dataset/load_genotypes.py index d309a903..204fb926 100644 --- a/wqflask/maintenance/dataset/load_genotypes.py +++ b/wqflask/maintenance/dataset/load_genotypes.py @@ -1,3 +1,8 @@ +import sys +import re + +import utilities + def main(argv): # config config = utilities.get_config(argv[1]) @@ -21,11 +26,10 @@ def main(argv): kv = re.split(':|=', item) metadic[kv[0].strip()] = kv[1].strip() continue - if line.startswith("Chr"): - print "[meta dictionary]" - for k,v in metadic.items(): - print "%s: %s" % (k, v) - print + if line.lower().startswith("chr"): + print "geno meta:" + for k, v in metadic.items(): + print "\t%s: %s" % (k, v) continue cells = line.split() Chr = cells[0] @@ -33,7 +37,6 @@ def main(argv): cM = cells[2] Mb = cells[3] print len(cells) - ? return # open db @@ -183,7 +186,7 @@ def main(argv): file_geno.close() con.close() -# main if __name__ == "__main__": + print "command line arguments:\n\t%s" % sys.argv main(sys.argv) print "exit successfully" |