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| author | Lei Yan | 2014-02-22 21:41:31 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-22 21:41:31 -0600 |
| commit | 30889320c00673660d194fc03b912d1832e5a6ed (patch) | |
| tree | 1f505fe0e73782c2b7249341d30dac63a89bc070 | |
| parent | 1014d09efced9c36274aec0d2486469648569721 (diff) | |
| download | genenetwork2-30889320c00673660d194fc03b912d1832e5a6ed.tar.gz | |
On branch master
| -rw-r--r-- | wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini | 1 | ||||
| -rw-r--r-- | wqflask/maintenance/dataset/load_genotypes.py | 9 |
2 files changed, 9 insertions, 1 deletions
diff --git a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini index 1f977cf8..6f2adbd2 100644 --- a/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini +++ b/wqflask/maintenance/dataset/datasampledir/load_genotypes/config.ini @@ -1,4 +1,5 @@ [config] +speciesid = 1 genofile = datasampledir/load_genotypes/sample.geno U = x H = 0 diff --git a/wqflask/maintenance/dataset/load_genotypes.py b/wqflask/maintenance/dataset/load_genotypes.py index 204fb926..0ae2c5cd 100644 --- a/wqflask/maintenance/dataset/load_genotypes.py +++ b/wqflask/maintenance/dataset/load_genotypes.py @@ -2,6 +2,7 @@ import sys import re import utilities +import datastructure def main(argv): # config @@ -10,6 +11,7 @@ def main(argv): for item in config.items('config'): print "\t%s" % (str(item)) # variables + speciesid = config.get('config', 'speciesid') genofile = open(config.get('config', 'genofile'), 'r') metadic = {} # parse genofile @@ -27,9 +29,14 @@ def main(argv): metadic[kv[0].strip()] = kv[1].strip() continue if line.lower().startswith("chr"): - print "geno meta:" + # + print "geno file meta:" for k, v in metadic.items(): print "\t%s: %s" % (k, v) + # + print "geno file head:\n\t%s" % line + strainnames = line.split()[4:] + strains = datastructure.get_strains_bynames(speciesid, strainnames) continue cells = line.split() Chr = cells[0] |