"""Testing facility for conkit.io.A3mIO"""
__author__ = "Felix Simkovic"
__date__ = "11 Sep 2016"
import os
import unittest
from conkit.io.a3m import A3mParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestA3mParser(ParserTestCase):
[docs] def test_read_1(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
>gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]
PPRFLVCTRDDIYEDENGRQWVVAKVETSRSpygsrietcITVHLQHMTTIPQEPTPQQPINNNSL
>gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]
HPDRLWAWEKFVYLDEKQHAWLPLTIEikDRLQLRVLLRREDVVLGRPMTPTQIGPSLL
>gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]
----------GIYEDEHHRVWIAVNVETSHSSHgnrietcvtVHLQHMTTLPQEPTPQQPINNNSL
>gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]
LPVYLVSVRLGIYEDEHHRVWIVANVETshSSHGNRRRTHVTVHLWKLIPQQVIPFNplnydFL
>gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1
-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL
>gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;
-PHILTLRTHGIYEDEHHRLWVVLDLQAShlSFSNRLLIYLTVYLQqgvafplESTPPSPMNLNGL
>gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]
PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPycskietcvtVHLWQMTTLFQEPSPDSLKTFNFL
>gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]
---------PGFYEDEHHRLWMVAKLETCSHSPycnkietcvtVHLWQMTRYPQEPAPYNPMNYNFL
"""
f_name = self.tempfile(content=msa)
with open(f_name, "r") as f_in:
sequence_file = A3mParser().read(f_in, remove_inserts=True)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual("d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}", sequence_entry.id)
self.assertEqual("PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL", sequence_entry.seq)
elif i == 1:
self.assertEqual(
"gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]", sequence_entry.id
)
self.assertEqual("HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL", sequence_entry.seq)
elif i == 2:
self.assertEqual(
"gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual("PPRFLVCTRDDIYEDENGRQWVVAKVETSRSITVHLQHMTTIPQEPTPQQPINNNSL", sequence_entry.seq)
elif i == 3:
self.assertEqual(
"gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
sequence_entry.id,
)
self.assertEqual("HPDRLWAWEKFVYLDEKQHAWLPLTIEDRLQLRVLLRREDVVLGRPMTPTQIGPSLL", sequence_entry.seq)
elif i == 4:
self.assertEqual(
"gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual("----------GIYEDEHHRVWIAVNVETSHSSHVHLQHMTTLPQEPTPQQPINNNSL", sequence_entry.seq)
elif i == 5:
self.assertEqual(
"gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual("LPVYLVSVRLGIYEDEHHRVWIVANVETSSHGNRRRTHVTVHLWKLIPQQVIPFNFL", sequence_entry.seq)
elif i == 6:
self.assertEqual(
"gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
sequence_entry.id,
)
self.assertEqual("-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL", sequence_entry.seq)
elif i == 7:
self.assertEqual(
"gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;", sequence_entry.id
)
self.assertEqual("-PHILTLRTHGIYEDEHHRLWVVLDLQASSFSNRLLIYLTVYLQESTPPSPMNLNGL", sequence_entry.seq)
elif i == 8:
self.assertEqual(
"gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual("PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPVHLWQMTTLFQEPSPDSLKTFNFL", sequence_entry.seq)
elif i == 9:
self.assertEqual(
"gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual("---------PGFYEDEHHRLWMVAKLETCSHSPVHLWQMTRYPQEPAPYNPMNYNFL", sequence_entry.seq)
[docs] def test_read_2(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
>gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]
PPRFLVCTRDDIYEDENGRQWVVAKVETSRSpygsrietcITVHLQHMTTIPQEPTPQQPINNNSL
>gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]
HPDRLWAWEKFVYLDEKQHAWLPLTIEikDRLQLRVLLRREDVVLGRPMTPTQIGPSLL
>gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]
----------GIYEDEHHRVWIAVNVETSHSSHgnrietcvtVHLQHMTTLPQEPTPQQPINNNSL
>gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]
LPVYLVSVRLGIYEDEHHRVWIVANVETshSSHGNRRRTHVTVHLWKLIPQQVIPFNplnydFL
>gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1
-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL
>gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;
-PHILTLRTHGIYEDEHHRLWVVLDLQAShlSFSNRLLIYLTVYLQqgvafplESTPPSPMNLNGL
>gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]
PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPycskietcvtVHLWQMTTLFQEPSPDSLKTFNFL
>gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]
---------PGFYEDEHHRLWMVAKLETCSHSPycnkietcvtVHLWQMTRYPQEPAPYNPMNYNFL
"""
f_name = self.tempfile(content=msa)
with open(f_name, "r") as f_in:
sequence_file = A3mParser().read(f_in, remove_inserts=False)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual("d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}", sequence_entry.id)
self.assertEqual(
"PPDHLWVHQEGIYRDEYQRTWVAVVEE--E--T--SF---------LR----------ARVQQIQVPLG-------DAARPSHLLTS-----QL",
sequence_entry.seq,
)
elif i == 1:
self.assertEqual(
"gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]", sequence_entry.id
)
self.assertEqual(
"HPNRLWIWEKHVYLDEFRRSWLPVVIK--S--N--EK---------FQ----------VILRQEDVTLG-------EAMSPSQLVPY-----EL",
sequence_entry.seq,
)
elif i == 2:
self.assertEqual(
"gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual(
"PPRFLVCTRDDIYEDENGRQWVVAKVE--T--S--RSpygsrietcIT----------VHLQHMTTIPQ-------EPTPQQPINNN-----SL",
sequence_entry.seq,
)
elif i == 3:
self.assertEqual(
"gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
sequence_entry.id,
)
self.assertEqual(
"HPDRLWAWEKFVYLDEKQHAWLPLTIEikD--R--LQ---------LR----------VLLRREDVVLG-------RPMTPTQIGPS-----LL",
sequence_entry.seq,
)
elif i == 4:
self.assertEqual(
"gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual(
"----------GIYEDEHHRVWIAVNVE--T--S--HS---------SHgnrietcvt-VHLQHMTTLPQ-------EPTPQQPINNN-----SL",
sequence_entry.seq,
)
elif i == 5:
self.assertEqual(
"gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual(
"LPVYLVSVRLGIYEDEHHRVWIVANVE--TshS--SH---------GN----------RRRTHVTVHLW-------KLIPQQVIPFNplnydFL",
sequence_entry.seq,
)
elif i == 6:
self.assertEqual(
"gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
sequence_entry.id,
)
self.assertEqual(
"-PDRLWLWEKHVYLDEFRRSWLPIVIK--S--N--GK---------FQ----------VIMRQKDVILG-------DSMTPSQLVPY-----EL",
sequence_entry.seq,
)
elif i == 7:
self.assertEqual(
"gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;", sequence_entry.id
)
self.assertEqual(
"-PHILTLRTHGIYEDEHHRLWVVLDLQ--A--ShlSF---------SN----------RLLIYLTVYLQqgvafplESTPPSPMNLN-----GL",
sequence_entry.seq,
)
elif i == 8:
self.assertEqual(
"gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual(
"PPCFLVCTRDDIYEDEHGRQWVAAKVE--T--S--SH---------SPycskietcvtVHLWQMTTLFQ-------EPSPDSLKTFN-----FL",
sequence_entry.seq,
)
elif i == 9:
self.assertEqual(
"gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
sequence_entry.id,
)
self.assertEqual(
"---------PGFYEDEHHRLWMVAKLE--T--C--SH---------SPycnkietcvtVHLWQMTRYPQ-------EPAPYNPMNYN-----FL",
sequence_entry.seq,
)
[docs] def test_read_3(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}
PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
>gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]
HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL
"""
f_name = self.tempfile(content=msa)
with open(f_name, "r") as f_in:
sequence_file = A3mParser().read(f_in, remove_inserts=False)
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual("d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}", sequence_entry.id)
self.assertEqual("PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL", sequence_entry.seq)
elif i == 1:
self.assertEqual(
"gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
sequence_entry.id[:80],
)
self.assertEqual(79, len(sequence_entry.id))
self.assertEqual("HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL", sequence_entry.seq)
elif i == 1:
self.assertEqual(
"gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
sequence_entry.id[:80],
)
self.assertGreater(79, len(sequence_entry.id))
self.assertEqual("HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL", sequence_entry.seq)
elif i == 1:
self.assertEqual(
"gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
sequence_entry.id[:80],
)
self.assertGreater(79, len(sequence_entry.id))
self.assertEqual("HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL", sequence_entry.seq)
[docs] def test_write_1(self):
msa = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}",
"PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL",
">gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
"HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL",
">gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
"PPRFLVCTRDDIYEDENGRQWVVAKVETSRSpygsrietcITVHLQHMTTIPQEPTPQQPINNNSL",
">gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
"HPDRLWAWEKFVYLDEKQHAWLPLTIEikDRLQLRVLLRREDVVLGRPMTPTQIGPSLL",
">gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
"----------GIYEDEHHRVWIAVNVETSHSSHgnrietcvtVHLQHMTTLPQEPTPQQPINNNSL",
">gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
"LPVYLVSVRLGIYEDEHHRVWIVANVETshSSHGNRRRTHVTVHLWKLIPQQVIPFNplnydFL",
">gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
"-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL",
">gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;",
"-PHILTLRTHGIYEDEHHRLWVVLDLQAShlSFSNRLLIYLTVYLQqgvafplESTPPSPMNLNGL",
">gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
"PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPycskietcvtVHLWQMTTLFQEPSPDSLKTFNFL",
">gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
"---------PGFYEDEHHRLWMVAKLETCSHSPycnkietcvtVHLWQMTRYPQEPAPYNPMNYNFL",
]
f_name_in = self.tempfile(content='\n'.join(msa))
f_name_out = self.tempfile()
parser = A3mParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in, remove_inserts=True)
parser.write(f_out, sequence_file)
ref = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}",
"PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL",
">gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
"HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL",
">gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
"PPRFLVCTRDDIYEDENGRQWVVAKVETSRSITVHLQHMTTIPQEPTPQQPINNNSL",
">gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
"HPDRLWAWEKFVYLDEKQHAWLPLTIEDRLQLRVLLRREDVVLGRPMTPTQIGPSLL",
">gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
"----------GIYEDEHHRVWIAVNVETSHSSHVHLQHMTTLPQEPTPQQPINNNSL",
">gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
"LPVYLVSVRLGIYEDEHHRVWIVANVETSSHGNRRRTHVTVHLWKLIPQQVIPFNFL",
">gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
"-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL",
">gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;",
"-PHILTLRTHGIYEDEHHRLWVVLDLQASSFSNRLLIYLTVYLQESTPPSPMNLNGL",
">gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
"PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPVHLWQMTTLFQEPSPDSLKTFNFL",
">gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
"---------PGFYEDEHHRLWMVAKLETCSHSPVHLWQMTRYPQEPAPYNPMNYNFL",
]
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(ref, output)
[docs] def test_write_2(self):
msa = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}",
"PPDHLWVHQEGIYRDEYQRTWVAVVEEETSFLRARVQQIQVPLGDAARPSHLLTSQL",
">gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
"HPNRLWIWEKHVYLDEFRRSWLPVVIKSNEKFQVILRQEDVTLGEAMSPSQLVPYEL",
">gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
"PPRFLVCTRDDIYEDENGRQWVVAKVETSRSpygsrietcITVHLQHMTTIPQEPTPQQPINNNSL",
">gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
"HPDRLWAWEKFVYLDEKQHAWLPLTIEikDRLQLRVLLRREDVVLGRPMTPTQIGPSLL",
">gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
"----------GIYEDEHHRVWIAVNVETSHSSHgnrietcvtVHLQHMTTLPQEPTPQQPINNNSL",
">gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
"LPVYLVSVRLGIYEDEHHRVWIVANVETshSSHGNRRRTHVTVHLWKLIPQQVIPFNplnydFL",
">gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
"-PDRLWLWEKHVYLDEFRRSWLPIVIKSNGKFQVIMRQKDVILGDSMTPSQLVPYEL",
">gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;",
"-PHILTLRTHGIYEDEHHRLWVVLDLQAShlSFSNRLLIYLTVYLQqgvafplESTPPSPMNLNGL",
">gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
"PPCFLVCTRDDIYEDEHGRQWVAAKVETSSHSPycskietcvtVHLWQMTTLFQEPSPDSLKTFNFL",
">gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
"---------PGFYEDEHHRLWMVAKLETCSHSPycnkietcvtVHLWQMTRYPQEPAPYNPMNYNFL",
]
f_name_in = self.tempfile(content="\n".join(msa))
f_name_out = self.tempfile()
parser = A3mParser()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
sequence_file = parser.read(f_in, remove_inserts=False)
parser.write(f_out, sequence_file)
ref = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (Homo sapiens)}",
"PPDHLWVHQEGIYRDEYQRTWVAVVEE--E--T--SF---------LR----------ARVQQIQVPLG-------DAARPSHLLTS-----QL",
">gi|6678257|ref|NP_033363.1|:(7-103) T-cell lymphoma breakpoint 1 [Mus musculus]",
"HPNRLWIWEKHVYLDEFRRSWLPVVIK--S--N--EK---------FQ----------VILRQEDVTLG-------EAMSPSQLVPY-----EL",
">gi|7305557|ref|NP_038800.1|:(8-103) T-cell leukemia/lymphoma 1B, 3 [Mus musculus]",
"PPRFLVCTRDDIYEDENGRQWVVAKVE--T--S--RSpygsrietcIT----------VHLQHMTTIPQ-------EPTPQQPINNN-----SL",
">gi|11415028|ref|NP_068801.1|:(2-106) T-cell lymphoma-1; T-cell lymphoma-1A [Homo sapiens]",
"HPDRLWAWEKFVYLDEKQHAWLPLTIEikD--R--LQ---------LR----------VLLRREDVVLG-------RPMTPTQIGPS-----LL",
">gi|7305561|ref|NP_038804.1|:(7-103) T-cell leukemia/lymphoma 1B, 5 [Mus musculus]",
"----------GIYEDEHHRVWIAVNVE--T--S--HS---------SHgnrietcvt-VHLQHMTTLPQ-------EPTPQQPINNN-----SL",
">gi|7305553|ref|NP_038801.1|:(5-103) T-cell leukemia/lymphoma 1B, 1 [Mus musculus]",
"LPVYLVSVRLGIYEDEHHRVWIVANVE--TshS--SH---------GN----------RRRTHVTVHLW-------KLIPQQVIPFNplnydFL",
">gi|27668591|ref|XP_234504.1|:(7-103) similar to Chain A, Crystal Structure Of Murine Tcl1",
"-PDRLWLWEKHVYLDEFRRSWLPIVIK--S--N--GK---------FQ----------VIMRQKDVILG-------DSMTPSQLVPY-----EL",
">gi|27668589|ref|XP_234503.1|:(9-91) similar to T-cell leukemia/lymphoma 1B, 5;",
"-PHILTLRTHGIYEDEHHRLWVVLDLQ--A--ShlSF---------SN----------RLLIYLTVYLQqgvafplESTPPSPMNLN-----GL",
">gi|7305559|ref|NP_038802.1|:(8-102) T-cell leukemia/lymphoma 1B, 4 [Mus musculus]",
"PPCFLVCTRDDIYEDEHGRQWVAAKVE--T--S--SH---------SPycskietcvtVHLWQMTTLFQ-------EPSPDSLKTFN-----FL",
">gi|7305555|ref|NP_038803.1|:(9-102) T-cell leukemia/lymphoma 1B, 2 [Mus musculus]",
"---------PGFYEDEHHRLWMVAKLE--T--C--SH---------SPycnkietcvtVHLWQMTRYPQ-------EPAPYNPMNYN-----FL",
]
with open(f_name_out, "r") as f_in:
output = f_in.read().splitlines()
self.assertEqual(ref, output)
if __name__ == "__main__":
unittest.main(verbosity=2)
