def test_indv_blk(self):
"""tests that indv_block can pull out individual fasta sequences with their identifying line"""
tester = constool.indv_block(
""">OAP01791.1 CDC48A [Arabidopsis thaliana]
MSTPAESSDSKSKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKD
TVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLK"""
)
self.assertTrue(
'>OAP01791.1 CDC48A [Arabidopsis thaliana]' in tester[0])
self.assertTrue(
'SKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQL' in tester[0])
def test_indv_blk_multi(self):
"""tests that indv_block can pull out individual fasta sequences from a string with multiple"""
tester = constool.indv_block(
">PROCA12070 | ENSPCAG00000012030 | HOG:0377891.2a.2a | [Procavia capensis]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEVSAPKVSKQGRGEEISESE\n"
">LOXAF14113 | G3TAL7 | HOG:0377891.2a.2a | [Loxodonta africana]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTA\n"
">ECHTE02547 | ENSETEG00000016682 | HOG:0377891.2a.2a | [Echinops telfairi]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRS")
self.assertEqual(len(tester), 3)
self.assertEqual(tester[1], (
">LOXAF14113 | G3TAL7 | HOG:0377891.2a.2a | [Loxodonta africana]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTA"))
def find_motif(self, msa, motif):
"""
Searches a multiple sequence alignment for the given motif- if found, it returns the index at which the motif
was found. Note: The indexing refers to the consensus sequence, or to each individual protein, as they are all
the same length
Args:
msa (str): the path to the multiple sequence alignment
motif (str): the motif to be located in the msa
Returns:
The index at which the motif can be found
"""
with open(msa, "r") as file:
msa = file.read()
msa_list = constool.indv_block(msa)
index = -1
for prot in msa_list:
prot = constool.seqnwl_strip(prot)
prot = constool.get_fasta_sequence(prot)
index = prot.find(motif)
if not index == -1:
break
return index