def test_cmsearch_from_file(self):
"""cmsearch_from_file should work as expected
"""
exp_search_res = [['a', 5, 23, 1, 19, 12.85, '-', 37],\
['b', 1, 19, 1, 19, 14.359999999999999, '-', 47]]
search_res = cmsearch_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs2_unaligned,moltype=RNA)
self.assertEqual(search_res,exp_search_res)
def test_cmsearch_from_file(self):
"""cmsearch_from_file should work as expected
"""
exp_search_res = [['a', 5, 23, 1, 19, 12.85, '-', 37],\
['b', 1, 19, 1, 19, 14.359999999999999, '-', 47]]
search_res = cmsearch_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs2_unaligned,moltype=RNA)
self.assertEqual(search_res, exp_search_res)
def test_cmsearch_from_file_no_hits(self):
"""cmsearch_from_file should work as expected
"""
search_res = cmsearch_from_file(cm_file_path=self.cmfile,\
seqs=self.seqs1_unaligned,moltype=RNA)
self.assertEqual(search_res,[])
if __name__ == "__main__":
from cogent.app.infernal import cmsearch_from_file
from cogent import LoadSeqs, RNA
from math import log
from os import mkdir
from os.path import isdir
for i in range(1,4):
print "making folder structural/Construct" + str(i)
if not isdir("structural/Construct" + str(i)):
mkdir("structural/Construct" + str(i))
for j in range(1,8):
print "Loading R"+ str(j) + "_CleanedStrippedUnique.fas"
seqs = LoadSeqs("R" + str(j) + "_CleanedStrippedUnique.fas", \
moltype=RNA, aligned=False, format='fasta', label_to_name=lambda x: x.split()[0])
print "Running Infernal for structural/Construct" + str(i) + "/R" + str(j) + "_tabfile.txt"
cmsearch_result = cmsearch_from_file("structural/Construct" + str(i) + ".cm", seqs, RNA, \
params={"--tabfile": "structural/Construct" + str(i) + "/R" + str(j) + "_tabfile.txt"})
print "result: " + str(cmsearch_result)
#cutoff=log(len(seqs),2) ??