# pvalue cutoff for definition of active factors
pvalue = float(sys.argv[4])
# output file
out = sys.argv[5]
# genes to be used as potential 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
if len(sys.argv) > 7:
motif_set = MotifSet(preload_motifs=False)
motif_set.read_mtf([sys.argv[7]])
else:
motif_set = MotifSet(preload_motifs=True)
# reading genes
factors = GeneSet("genes")
factors.read(factor_file)
# we only want a subset of the motif set
motif_set = motif_set.filter(factors.genes,
key_type="gene_names",
search=search_mode)
motif_set.read_enrichment(enrichment_files, pvalue)
motif_set.write_network(targets, out, pvalue)
class MotifSetTest(unittest.TestCase):
def setUp(self):
dirname = os.path.dirname(__file__)
mtf_file = os.path.join(dirname, "../data/motifs/hocomoco.mtf")
# we must enforce the use hocomoco as database
self.motif_set = MotifSet(preload_motifs=False)
self.motif_set.read_mtf(mtf_file)
def test_create_default(self):
ms = MotifSet()
self.assertEqual(
len(ms.motifs_map),
0,
msg="motif dictionary must be empty by default (no preload)")
def test_create_empty(self):
ms = MotifSet(preload_motifs=False)
self.assertEqual(len(ms.motifs_map),
0,
msg="motif dictionary must be empty")
def test_create_non_empty(self):
ms = MotifSet(preload_motifs=True)
self.assertGreater(len(ms.motifs_map),
0,
msg="motif dictionary must be non empty")
def test_filter_keys_not_list(self):
with self.assertRaises(ValueError):
self.motif_set.filter("test")
def test_filter_wrong_key_type(self):
with self.assertRaises(ValueError):
self.motif_set.filter([], key_type="test")
def test_filter_names(self):
ms2 = self.motif_set.filter(["ALX1_HUMAN.H11MO.0.B"],
key_type="name",
search="exact")
self.assertEqual(len(ms2.motifs_map), 1)
ms2 = self.motif_set.filter(["ALX1"], key_type="name", search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
ms2 = self.motif_set.filter(["ALX1_HUMAN.H11MO.0.B"],
key_type="name",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 1)
ms2 = self.motif_set.filter(["ALX1"],
key_type="name",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 1)
ms2 = self.motif_set.filter(["ALX"], key_type="name", search="inexact")
self.assertEqual(len(ms2.motifs_map), 3)
ms2 = self.motif_set.filter(["ALX1_HUMAN.H11MO.0.B"],
key_type="name",
search="regex")
self.assertEqual(len(ms2.motifs_map), 1)
ms2 = self.motif_set.filter(["ALX1.*"],
key_type="name",
search="regex")
self.assertEqual(len(ms2.motifs_map), 1)
ms2 = self.motif_set.filter(["ALX[134]_.*"],
key_type="name",
search="regex")
self.assertEqual(len(ms2.motifs_map), 3)
def test_filter_genes(self):
ms2 = self.motif_set.filter(["ALX1_HUMAN.H11MO.0.B"],
key_type="gene_names",
search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 0)
self.assertEqual(len(k2m), 0)
ms2 = self.motif_set.filter(["ALX1"],
key_type="gene_names",
search="exact")
self.assertEqual(len(ms2.motifs_map), 1)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 1)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["ALX"],
key_type="gene_names",
search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 0)
self.assertEqual(len(k2m), 0)
ms2 = self.motif_set.filter(["ALX1"],
key_type="gene_names",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 1)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 1)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["ALX"],
key_type="gene_names",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 3)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 3)
self.assertEqual(len(k2m), 3)
ms2 = self.motif_set.filter(["ALX1.*"],
key_type="gene_names",
search="regex")
self.assertEqual(len(ms2.motifs_map), 1)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 1)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["ALX[134]"],
key_type="gene_names",
search="regex")
self.assertEqual(len(ms2.motifs_map), 3)
m2k, k2m = ms2.get_mappings(key_type="gene_names")
self.assertEqual(len(m2k), 3)
self.assertEqual(len(k2m), 3)
def test_filter_family(self):
ms2 = self.motif_set.filter(["Paired-related HD factors"],
key_type="family",
search="exact")
self.assertEqual(len(ms2.motifs_map), 35)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 35)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["factors"],
key_type="family",
search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 0)
self.assertEqual(len(k2m), 0)
ms2 = self.motif_set.filter(["Paired-related HD factors"],
key_type="family",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 35)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 35)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["Paired-related HD"],
key_type="family",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 35)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 35)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["factors"],
key_type="family",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 676)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 676)
self.assertEqual(len(k2m), 59)
ms2 = self.motif_set.filter(["Paired.*factors"],
key_type="family",
search="regex")
self.assertEqual(len(ms2.motifs_map), 35)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 35)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["Paired-related.*"],
key_type="family",
search="regex")
self.assertEqual(len(ms2.motifs_map), 35)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 35)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter([".*factors"],
key_type="family",
search="regex")
self.assertEqual(len(ms2.motifs_map), 676)
m2k, k2m = ms2.get_mappings(key_type="family")
self.assertEqual(len(m2k), 676)
self.assertEqual(len(k2m), 59)
def test_filter_uniprot(self):
ms2 = self.motif_set.filter(["Q9H3D4"],
key_type="uniprot_ids",
search="exact")
self.assertEqual(len(ms2.motifs_map), 2)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 2)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["Q9H"],
key_type="uniprot_ids",
search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 0)
self.assertEqual(len(k2m), 0)
ms2 = self.motif_set.filter(["Q9H3D4"],
key_type="uniprot_ids",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 2)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 2)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["Q9H"],
key_type="uniprot_ids",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 20)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 20)
self.assertEqual(len(k2m), 16)
ms2 = self.motif_set.filter(["Q9H3D4"],
key_type="uniprot_ids",
search="regex")
self.assertEqual(len(ms2.motifs_map), 2)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 2)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["Q9H.*"],
key_type="uniprot_ids",
search="regex")
self.assertEqual(len(ms2.motifs_map), 20)
m2k, k2m = ms2.get_mappings(key_type="uniprot_ids")
self.assertEqual(len(m2k), 20)
self.assertEqual(len(k2m), 16)
def test_filter_data_source(self):
# implicitly, we are also testing the case insensitiveness of the string matching of all three types
ms2 = self.motif_set.filter(["chip-seq"],
key_type="data_source",
search="exact")
self.assertEqual(len(ms2.motifs_map), 433)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 433)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["chip"],
key_type="data_source",
search="exact")
self.assertEqual(len(ms2.motifs_map), 0)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 0)
self.assertEqual(len(k2m), 0)
ms2 = self.motif_set.filter(["chip-seq"],
key_type="data_source",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 433)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 433)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["chip"],
key_type="data_source",
search="inexact")
self.assertEqual(len(ms2.motifs_map), 433)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 433)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["chip-seq"],
key_type="data_source",
search="regex")
self.assertEqual(len(ms2.motifs_map), 433)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 433)
self.assertEqual(len(k2m), 1)
ms2 = self.motif_set.filter(["(chip|selex)"],
key_type="data_source",
search="regex")
self.assertEqual(len(ms2.motifs_map), 591)
m2k, k2m = ms2.get_mappings(key_type="data_source")
self.assertEqual(len(m2k), 591)
self.assertEqual(len(k2m), 2)
# search mode to map factors to motifs (exact or inexact)
search_mode = sys.argv[3]
# pvalue cutoff for definition of active factors
pvalue = float(sys.argv[4])
# output file
out = sys.argv[5]
# genes to be used as potential 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
if len(sys.argv) > 7:
motif_set = MotifSet(preload_motifs=False)
motif_set.read_mtf([sys.argv[7]])
else:
motif_set = MotifSet(preload_motifs=True)
# reading genes
factors = GeneSet("genes")
factors.read(factor_file)
# we only want a subset of the motif set
motif_set = motif_set.filter(factors.genes, key_type="gene_names", search=search_mode)
motif_set.read_enrichment(enrichment_files, pvalue)
motif_set.write_network(targets, out, pvalue)