def geneusage_ttests(attr, type, outfile, g2n, name2obj, matched, pcutoff):
# attr: "clones"/"reads"; type=genetype: v, d, j, vj, dj
testtype = statcommon.get_test_type(g2n, matched)
f = open(outfile, 'w')
f.write(("Name\tGroup1_Group2\tt_val\tp_val\tMean1 +/- Std1\t" +
"Mean2 +/- Std2\n"))
genes = get_genes(name2obj.values(), type)
for gene in genes:
pair2tp, group2mean = statcommon.ttest_allpairs(g2n, name2obj, matched,
attr=None, func=get_geneusage,
func_args=(attr, type, gene),
testtype=testtype)
statcommon.ttest_write(f, gene, pair2tp, group2mean, pcutoff)
f.close()
def lendist_ttests(attr, outfile, g2n, name2obj, matched, pcutoff):
testtype = statcommon.get_test_type(g2n, matched)
f = open(outfile, 'w')
# compare median length
f.write(("#Category\tGroup1_Group2\tt_val\tp_val\tMean1 +/- Std1\t" +
"Mean2 +/- Std2\n"))
medattr = "median_" + attr
pair2tp, group2mean = statcommon.ttest_allpairs(g2n, name2obj, matched,
medattr, testtype=testtype)
statcommon.ttest_write(f, medattr, pair2tp, group2mean)
# compare freq of each length
f.write("#Length\n")
lens = get_lens(name2obj.values())
lenattr = "len2" + attr
for l in lens:
pair2tp, group2mean = statcommon.ttest_allpairs(g2n, name2obj,
matched, attr=None,
func=statcommon.obj_dictattr_lookup,
func_args=(lenattr, l), testtype=testtype)
statcommon.ttest_write(f, str(l), pair2tp, group2mean, pcutoff)
f.close()