def test_seqnwl_strip_messy(self):
"""Tests that seqnwl_strip removes the newlines from within the fasta string"""
tester = constool.seqnwl_strip(
">PROCA12070 | ENSPCAG00000012030 | HOG:0377891.2a.2a | [Procavia capensis]\n"
"MKTRQNK\nDSMSMRSGRKKEAPGPREEL\nRSRGRASPGGVSTSSSDGKAEKSRQTAK\nKARVEEVSAPKVSKQGRGEEIS\nESE\n"
)
self.assertEqual(
tester,
">PROCA12070 | ENSPCAG00000012030 | HOG:0377891.2a.2a | [Procavia capensis]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEVSAPKVSKQGRGEEISESE"
)
def get_orthologs(self):
"""
Retrieves a fasta file containing the sequences of the orthologous proteins, based on the input parameters
"""
if not self.fasta:
raise SequenceError("Input sequence is empty!")
self.sequence = constool.get_fasta_sequence(fasta=self.fasta)
if self.has_run:
output = self.orthologs
else:
self.retrieve_OMAid()
output = self.ortholog_to_fasta()
output = constool.remove_first_protein(output)
output = constool.seqnwl_strip(self.sequence) + os.linesep + output
self.has_run = True
return output
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