def test_remove_protein(self):
"""tests that remove_protein can accurately remove a protein with the given id"""
tester = constool.remove_protein(
">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", "LOXAF14113")
self.assertEqual(
tester,
">PROCA12070 | ENSPCAG00000012030 | HOG:0377891.2a.2a | [Procavia capensis]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRSRGRASPGGVSTSSSDGKAEKSRQTAKKARVEEVSAPKVSKQGRGEEISESE\n"
">ECHTE02547 | ENSETEG00000016682 | HOG:0377891.2a.2a | [Echinops telfairi]\n"
"MKTRQNKDSMSMRSGRKKEAPGPREELRS")
def test_remove_protein_nothing(self):
"""Tests that remove protein deosnt remove anythign if the entry ID is not in string"""
tester = constool.remove_protein(
">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", "PROXY90210")
self.assertEqual(
tester,
">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")
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