def test_write_2(self):
msa = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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 = create_tmp_f(content=os.linesep.join(msa))
f_name_out = create_tmp_f()
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_insert=False)
parser.write(f_out, sequence_file)
ref = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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",
"",
]
ref = os.linesep.join(ref)
with open(f_name_out, 'r') as f_in:
output = "".join(f_in.readlines())
self.assertEqual(ref, output)
os.unlink(f_name_in)
os.unlink(f_name_out)
def test_write_1(self):
msa = [
">d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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 (H**o 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 [H**o 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)
def test_read_3(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 (H**o 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)
def test_read_3(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 = create_tmp_f(content=msa)
parser = A3mParser()
with open(f_name, 'r') as f_in:
sequence_file = parser.read(f_in,
remove_insert=False) # <------------
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual(
'd1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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)
os.unlink(f_name)
def test_read_1(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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 (H**o 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 [H**o 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)
def test_read_2(self):
msa = """>d1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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 = create_tmp_f(content=msa)
parser = A3mParser()
with open(f_name, 'r') as f_in:
sequence_file = parser.read(f_in,
remove_insert=False) # <------------
for i, sequence_entry in enumerate(sequence_file):
if i == 0:
self.assertEqual(
'd1a1x__ b.63.1.1 (-) p13-MTCP1 {Human (H**o 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 [H**o 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)
os.unlink(f_name)