def test_filter_annotations_1(self):
bacteriocins = [blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin1",
query="ACGTACGTTT",
query_start = 250,
query_end = 260,
sbjct_id = "gi|123|gb|NC_12345.1",
sbjct="ACGTACGTTT",
sbjct_start = 250,
sbjct_end = 260,
strand = "-"),
blast.XMLRecord(description="",
expected_value=0.00001,
score = 0,
query_id = "bacteriocin2",
query="ACGTACGTTT",
query_start = 450,
query_end = 460,
sbjct_id = "gi|123|gb|NC_12345.1",
sbjct="ACGTACGTTT",
sbjct_start = 450,
sbjct_end = 460,
strand = "-")]
radius = 100
annots = [A for A in annotation.AnnotatedGenes(self.out_file)]
filtered,hoods = interval_filter.annotatedGenes(annots,bacteriocins,radius)
self.assertEquals(1,len(filtered))
self.assertEquals(1,len(hoods))
self.assertTrue(bacteriocins[0] in hoods)
def main(genome_files,
bacteriocin_file,
intergene_file,
annotations_file,
bacteriocinsOut,
annotationsOut,
intermediate,
bac_evalue,
num_threads,
formatdb,
bacteriocin_radius,
verbose,
keep_tmp):
for gnome in genome_files:
bacthr = BacteriocinHandler(gnome,
intermediate,
bac_evalue,
num_threads,
verbose,
keep_tmp)
bacteriocins = bacthr.getAlignedBacteriocins(bacteriocin_file,
bac_evalue,
num_threads,
formatdb)
if verbose and bacteriocins == None: print "No bacteriocins found"
if bacteriocins == None: continue
if verbose: print "Bacteriocins found\n","\n".join(map(str,bacteriocins))
if verbose: print "Number of original bacteriocins",len(bacteriocins)
intergeneDict = identifyIntergenic(bacteriocins,intergene_file)
writeBacteriocins(bacteriocins,intergeneDict,bacteriocinsOut)
annots = [annot for annot in annotation.AnnotatedGenes(annotations_file)]
annots,bacteriocinNeighborhoods = interval_filter.annotatedGenes(annots,bacteriocins,bacteriocin_radius)
annot_bact_pairs = zip(annots,bacteriocinNeighborhoods)
writeAnnotatedGenes(annot_bact_pairs, annotationsOut)
