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| author | Lei Yan | 2014-02-10 15:21:44 -0600 |
|---|---|---|
| committer | Lei Yan | 2014-02-10 15:21:44 -0600 |
| commit | 37e4152e6bbf446c165faefa0220cc722c5e3c54 (patch) | |
| tree | 08408aed36364f48ae843d1b64036f7f0a99dbc7 | |
| parent | a260db93da548ce7511521c5f63c03c3d279bcb1 (diff) | |
| download | genenetwork2-37e4152e6bbf446c165faefa0220cc722c5e3c54.tar.gz | |
On branch master
| -rw-r--r-- | wqflask/maintenance/dataset/specials2.py | 36 |
1 files changed, 33 insertions, 3 deletions
diff --git a/wqflask/maintenance/dataset/specials2.py b/wqflask/maintenance/dataset/specials2.py index 2acfd2ef..2438af43 100644 --- a/wqflask/maintenance/dataset/specials2.py +++ b/wqflask/maintenance/dataset/specials2.py @@ -54,9 +54,9 @@ def bxd_correlations(): probesetfreezes = datastructure.get_probesetfreezes(inbredsetid) print "From DB, get %d probesetfreezes" % (len(probesetfreezes)) for probesetfreeze in probesetfreezes: - correlations(genos, probesetfreeze) + correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze) -def correlations(genos, probesetfreeze): +def correlations(outputdir, genos, probesetfreeze): print probesetfreeze probesetfreezeid = probesetfreeze[0] probesetfreezename = probesetfreeze[1] @@ -106,4 +106,34 @@ def correlations(genos, probesetfreeze): outputfile.write("\n") outputfile.flush() # - outputfile.close()
\ No newline at end of file + outputfile.close() + +""" +For: Ash +Date: 2014-02-10 +Function: + For BXD group, calculate correlations with genotypes and probesets. + given probesetfreezes +""" +def bxd_correlations_givenprobesetfreezes(probesetfreezesfile): + # + inbredsetid = 1 + genofile = "/home/leiyan/gn/web/genotypes/BXD.geno" + outputdir = "/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output" + # + t = genotypes.load_genos(genofile) + genostrains = t[0] + genos = t[1] + print "From geno file, get %d strains" % (len(genostrains)) + print "From geno file, get %d genos" % (len(genos)) + # + file = open(probesetfreezesfile, 'r') + for line in file: + line = line.strip() + cells = line.split() + probesetfreezeid = cells[0] + probesetfreeze = datastructure.get_probesetfreeze(probesetfreezeid) + correlations(outputdir=outputdir, genos=genos, probesetfreeze=probesetfreeze) + file.close() + +bxd_correlations_givenprobesetfreezes('/home/leiyan/gn2/wqflask/maintenance/dataset/datadir/20140205_Ash_correlations/output/probesetfreezes_filter.txt') |