def run_all(gbfile, groupfile, transfile, tagFiles):
# does this filter out replicates that appear in every tag?
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
gsd = analyze.map_snps(snps, al, dna)
# Count nonsyn vs. syn. sites for each gene
site_counts = genes_sites_dict(annodb)
# Count nonsyn vs. syn. snps for each gene
snp_counts = analyze.get_gene_na_ns(gsd)
genes = annodb.keys()
functional_groups = load_func_assoc(groupfile, transfile)
#binomial_tests(snp_counts, site_counts)
#main(site_counts, snp_counts, genes, functional_groups, test_func=binomial_test)
for name, test_func in [("Fisher test", fisher_test),
("Binomial Test", binomial_test)]:
print name
run_tests(site_counts,
snp_counts,
genes,
functional_groups,
test_func=test_func)
print
def pathways_cmd(gbfile, groupfile, transfile, tagFiles):
pathway_dict = load_func_assoc(groupfile, transfile)
for k, v in pathway_dict.items():
pathway_dict[k] = v[1] # only keep the gene list
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
results = analyze.analyze_nonsyn_groups(pathway_dict, snps, annodb, al,
dna)
for k, v in results:
print "%s,%s,%s" % (k, v, " ".join(pathway_dict[v]))
def pathways_cmd(gbfile, groupfile, transfile, tagFiles):
pathway_dict = load_func_assoc(groupfile, transfile)
for k,v in pathway_dict.items():
pathway_dict[k] = v[1] # only keep the gene list
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
results = analyze.analyze_nonsyn_groups(pathway_dict, snps, annodb,
al, dna)
for k, v in results:
print "%s,%s,%s" % (k, v, " ".join(pathway_dict[v]))
def run_all(gbfile, groupfile, transfile, tagFiles):
# does this filter out replicates that appear in every tag?
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
gsd = analyze.map_snps(snps, al, dna)
# Count nonsyn vs. syn. sites for each gene
site_counts = genes_sites_dict(annodb)
# Count nonsyn vs. syn. snps for each gene
snp_counts = analyze.get_gene_na_ns(gsd)
genes = annodb.keys()
functional_groups = load_func_assoc(groupfile, transfile)
#binomial_tests(snp_counts, site_counts)
#main(site_counts, snp_counts, genes, functional_groups, test_func=binomial_test)
for name, test_func in [("Fisher test", fisher_test), ("Binomial Test", binomial_test)]:
print name
run_tests(site_counts, snp_counts, genes, functional_groups,
test_func=test_func)
print
def phenoseq_top_genes(gbfile, tagFiles):
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
results = analyze.analyze_nonsyn(snps, annodb, al, dna)
return results
def phenoseq_top_genes(gbfile, tagFiles):
annodb, al, dna = analyze.read_genbank_annots(gbfile)
snps = analyze.read_tag_files(tagFiles)
results = analyze.analyze_nonsyn(snps, annodb, al, dna)
return results