pvalue = float(sys.argv[4])
# output file
out = sys.argv[5]
# genes to be used as potential targets
filter_targets = []
targets = None
if len(sys.argv) > 6:
targets_file = sys.argv[6]
# reading targets
targets = GeneSet("genes")
targets.read(targets_file)
# starting motif databases
motif_set = MotifSet()
if len(sys.argv) > 7:
motif_set.read_file([sys.argv[7]])
else:
motif_set.read_file([jaspar, uniprobe, internal])
# reading genes
factors = GeneSet("genes")
factors.read(factor_file)
# reading networks
#for f in glob.glob(enrichment_files):
# # use last dir name as name for condition
# condition=os.path.dirname(f)
# condition=condition.split("/")[-1]
motif_set.read_motif_targets_enrichment(enrichment_files, pvalue)
#motif_set.write_enrichment_table(pvalue,out+"/pvalue_table_"+str(pvalue*100)+".txt")
from rgt.MotifSet import MotifSet
from rgt.GeneSet import GeneSet
import sys
jaspar = '/home/ivan/projects/reg-gen/data/motifs/jaspar_vertebrates.mtf'
uniprobe = '/home/ivan/projects/reg-gen/data/motifs/uniprobe_primary.mtf'
internal = '/home/ivan/projects/reg-gen/data/motifs/internal.mtf'
motif_set = MotifSet()
motif_set.read_file([jaspar, uniprobe, internal])
motifs = [(l.strip("\n")).split("\t")[0] for l in open(sys.argv[1])]
geneset_file = sys.argv[2]
search_mode = sys.argv[3]
genes = GeneSet("DC Genes")
genes.read_expression(geneset_file)
filtered = motif_set.filter_by_motifs(motifs)
[filtered_genes, g_m, m_g] = filtered.filter_by_genes(genes,
search=search_mode)
genes_found = []
not_found = []
print "\t\t" + ("\t".join(genes.cond))
for m in motifs:
try:
sel_genes = m_g[m]
from rgt.MotifSet import MotifSet
from rgt.GeneSet import GeneSet
import sys
jaspar='/home/ivan/projects/reg-gen/data/motifs/jaspar_vertebrates.mtf'
uniprobe='/home/ivan/projects/reg-gen/data/motifs/uniprobe_primary.mtf'
internal='/home/ivan/projects/reg-gen/data/motifs/internal.mtf'
motif_set = MotifSet()
motif_set.read_file([jaspar,uniprobe,internal])
motifs=[(l.strip("\n")).split("\t")[0] for l in open(sys.argv[1])]
geneset_file=sys.argv[2]
search_mode=sys.argv[3]
genes=GeneSet("DC Genes")
genes.read_expression(geneset_file)
filtered=motif_set.filter_by_motifs(motifs)
[filtered_genes,g_m,m_g]=filtered.filter_by_genes(genes,search=search_mode)
genes_found=[]
not_found=[]
print "\t\t"+("\t".join(genes.cond))
for m in motifs:
try:
sel_genes=m_g[m]
for g in sel_genes:
# output file
out=sys.argv[5]
# genes to be used as potential targets
filter_targets=[]
targets=None
if len(sys.argv) > 6:
targets_file=sys.argv[6]
# reading targets
targets=GeneSet("genes")
targets.read(targets_file)
# starting motif databases
motif_set = MotifSet()
if len(sys.argv) > 7:
motif_set.read_file([sys.argv[7]])
else:
motif_set.read_file([jaspar,uniprobe,internal])
# reading genes
factors=GeneSet("genes")
factors.read(factor_file)
# reading networks
#for f in glob.glob(enrichment_files):
# # use last dir name as name for condition
# condition=os.path.dirname(f)
# condition=condition.split("/")[-1]
motif_set.read_motif_targets_enrichment(enrichment_files,pvalue)
#motif_set.write_enrichment_table(pvalue,out+"/pvalue_table_"+str(pvalue*100)+".txt")