Exemplo n.º 1
0
 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)
Exemplo n.º 2
0
 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)
Exemplo n.º 3
0
 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,[])
Exemplo n.º 4
0
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) ??