def test_get_fasta_seq(self):
"""Tests that get_fasta_seq only gets the sequence of the fasta string, not the identifying line"""
tester = constool.get_fasta_sequence(
""">OAP01791.1 CDC48A [Arabidopsis thaliana]
MSTPAESSDSKSKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQLFRGDTILIKGKKRKD
TVCIALADETCEEPKIRMNKVVRSNLRVRLGDVISVHQCPDVKYGKRVHILPVDDTVEGVTGNLFDAYLK"""
)
self.assertFalse('>OAP01791.1 CDC48A [Arabidopsis thaliana]' in tester)
self.assertTrue(
'SKKDFSTAILERKKSPNRLVVDEAINDDNSVVSLHPATMEKLQL' in tester)
def test_get_fasta_multi(self):
"""tests that get_fasta returns a list of sequences given a fasta file"""
tester = constool.get_fasta_sequence(
""">PROCA12070 | ENSPCAG00000012030 | HOG:0377891.2a.2a | [Procavia capensis]
MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEVSAPKVSKQGRGEEISESE
>LOXAF14113 | G3TAL7 | HOG:0377891.2a.2a | [Loxodonta africana]
MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEASTPKVSKQGRSEEISESE
>ECHTE02547 | ENSETEG00000016682 | HOG:0377891.2a.2a | [Echinops telfairi]
MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQSAKKARVEEASTPKVNKQSRSEXETSAP""",
index=1)
self.assertFalse("[Loxodonta africana]" in tester)
self.assertFalse(">PROCA12070 | ENSPCAG00000012030" in tester)
self.assertEqual(
tester,
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEASTPKVSKQGRSEEISESE"
)
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 get_HOGs(self):
"""
Retrieves a fasta file containing the sequences of the proteins in the HOG to the input protein, 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_hogs:
output = self.HOGs
else:
self.retrieve_OMAid()
self.retrieve_HOG_level()
output = self.HOG_to_fasta()
output = constool.remove_protein(output, self.id)
self.has_run_hogs = 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