"""Testing facility for conkit.io.StockholmIO"""
__author__ = "Felix Simkovic"
__date__ = "12 Sep 2016"
import os
import unittest
from conkit.io.stockholm import StockholmParser
from conkit.io.tests.helpers import ParserTestCase
[docs]class TestStockholmParser(ParserTestCase):
[docs] def test_read_1(self):
msa = """# STOCKHOLM 1.0
#=GF ID 1EAZ:A|PDBID|CHAIN|SEQUENCE-i5
#=GS UniRef100_A0A0D2WIY8/647-745 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3
#=GS UniRef100_A0A0D2WIY8/761-857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3
#=GS UniRef100_A0A0D2WIY8/1126-1228 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3
#=GS UniRef100_A0A0D2WIY8/1245-1341 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3
#=GS UniRef100_A0A0D2WIY8/1752-1857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3
1EAZ:A|PDBID|CHAIN|SEQUENCE GSMFTPKPPQDSAVIKAG-YC-V------K-Q-------------------------------------------------G-A------------VM------------------------------------------------------------------------------------------------------
UniRef100_A0A0D2WIY8/647-745 ---------------IEG-YL-S------K-Q-------------------------------------------------G-GV----------NNN------------------------------------------------------------------------------------------------------
#=GR UniRef100_A0A0D2WIY8/647-745 PP ...............79*.**.*......*.*.................................................*.99..........9**......................................................................................................
UniRef100_A0A0D2WIY8/761-857 -----------ANPDKEG-WL-K------K-Q-------------------------------------------------G-N-----------SMA------------------------------------------------------------------------------------------------------
#=GR UniRef100_A0A0D2WIY8/761-857 PP ...........5899***.**.*......*.*.................................................*.9...........9**......................................................................................................
UniRef100_A0A0D2WIY8/1126-1228 ------------AVRKLG-FL-Y------K-Q-------------------------------------------------G-G------------SN------------------------------------------------------------------------------------------------------
#=GR UniRef100_A0A0D2WIY8/1126-1228 PP ............68999*.**.*......*.*.................................................*.*............**......................................................................................................
UniRef100_A0A0D2WIY8/1245-1341 ------------NPARQG-WL-C------K-R-------------------------------------------------G-G------------TY------------------------------------------------------------------------------------------------------
#=GR UniRef100_A0A0D2WIY8/1245-1341 PP ............6789**.**.*......*.*.................................................*.*............**......................................................................................................
UniRef100_A0A0D2WIY8/1752-1857 -------QRATPGFKMKG-WL-H------K-E-------------------------------------------------G-G------------SV------------------------------------------------------------------------------------------------------
#=GR UniRef100_A0A0D2WIY8/1752-1857 PP .......556677889**.**.*......*.*.................................................*.*............**......................................................................................................
#=GC PP_cons .......*....*...................................*.....*..*................*.................*..*....*................................................*****999875555677766776.
#=GC RF .......x....x...................................x.....x..x................x.................x..x....x................................................xxxxxxxxxxxxxxxxxxxxxxxx
1EAZ:A|PDBID|CHAIN|SEQUENCE -------------------K-----------------------NW---------------------------------------------------------------------------------------------K--R-R------------Y----F-QL--------D--E-----------------------
UniRef100_A0A0D2WIY8/647-745 -------------------K-----------------------GW---------------------------------------------------------------------------------------------K--R-R------------Y----C-VL--------E--N-----------------------
#=GR UniRef100_A0A0D2WIY8/647-745 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................
UniRef100_A0A0D2WIY8/761-857 -------------------K-----------------------DW---------------------------------------------------------------------------------------------K--K-R------------Y----I-AI--------K--E-----------------------
#=GR UniRef100_A0A0D2WIY8/761-857 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................
UniRef100_A0A0D2WIY8/1126-1228 -------------------K-----------------------GW---------------------------------------------------------------------------------------------R--K-R------------W----I-VM--------E--H-----------------------
#=GR UniRef100_A0A0D2WIY8/1126-1228 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................
UniRef100_A0A0D2WIY8/1245-1341 -------------------T-----------------------SW---------------------------------------------------------------------------------------------K--K-R------------W----L-VL--------K--G-----------------------
#=GR UniRef100_A0A0D2WIY8/1245-1341 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................
UniRef100_A0A0D2WIY8/1752-1857 -------------------K-----------------------TW---------------------------------------------------------------------------------------------K--R-R------------W----F-ST--------T--P-----------------------
#=GR UniRef100_A0A0D2WIY8/1752-1857 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................
#=GC PP_cons ...................9.......................**.............................................................................................*..*.*............*....*.**........9..9.......................
#=GC RF ...................x.......................xx.............................................................................................x..x.x............x....x.xx........x..x.......................
//
"""
f_name = self.tempfile(content=msa)
parser = StockholmParser()
with open(f_name, "r") as f_in:
hierarchy = parser.read(f_in)
for i, sequence_entry in enumerate(hierarchy):
if i == 0:
self.assertEqual("1EAZ:A|PDBID|CHAIN|SEQUENCE", sequence_entry.id)
self.assertEqual(
"GSMFTPKPPQDSAVIKAG-YC-V------K-Q-------------------------------------------------G-A-"
"-----------VM------------------------------------------------------------------------"
"-------------------------------------------------K-----------------------NW----------"
"-----------------------------------------------------------------------------------K-"
"-R-R------------Y----F-QL--------D--E-----------------------",
sequence_entry.seq,
)
elif i == 1:
self.assertEqual("UniRef100_A0A0D2WIY8/647-745", sequence_entry.id)
self.assertEqual(
"---------------IEG-YL-S------K-Q-------------------------------------------------G-GV"
"----------NNN------------------------------------------------------------------------"
"-------------------------------------------------K-----------------------GW----------"
"-----------------------------------------------------------------------------------K-"
"-R-R------------Y----C-VL--------E--N-----------------------",
sequence_entry.seq,
)
self.assertEqual(
[
"[subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=C"
"apsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3"
],
sequence_entry.remark,
)
elif i == 2:
self.assertEqual("UniRef100_A0A0D2WIY8/761-857", sequence_entry.id)
self.assertEqual(
"-----------ANPDKEG-WL-K------K-Q-------------------------------------------------G-N-"
"----------SMA------------------------------------------------------------------------"
"-------------------------------------------------K-----------------------DW----------"
"-----------------------------------------------------------------------------------K-"
"-K-R------------Y----I-AI--------K--E-----------------------",
sequence_entry.seq,
)
self.assertEqual(
[
"[subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=C"
"apsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3"
],
sequence_entry.remark,
)
elif i == 3:
self.assertEqual("UniRef100_A0A0D2WIY8/1126-1228", sequence_entry.id)
self.assertEqual(
"------------AVRKLG-FL-Y------K-Q-------------------------------------------------G-G-"
"-----------SN------------------------------------------------------------------------"
"-------------------------------------------------K-----------------------GW----------"
"-----------------------------------------------------------------------------------R-"
"-K-R------------W----I-VM--------E--H-----------------------",
sequence_entry.seq,
)
self.assertEqual(
[
"[subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=C"
"apsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3"
],
sequence_entry.remark,
)
elif i == 4:
self.assertEqual("UniRef100_A0A0D2WIY8/1245-1341", sequence_entry.id)
self.assertEqual(
"------------NPARQG-WL-C------K-R-------------------------------------------------G-G-"
"-----------TY------------------------------------------------------------------------"
"-------------------------------------------------T-----------------------SW----------"
"-----------------------------------------------------------------------------------K-"
"-K-R------------W----L-VL--------K--G-----------------------",
sequence_entry.seq,
)
self.assertEqual(
[
"[subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=C"
"apsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3"
],
sequence_entry.remark,
)
elif i == 5:
self.assertEqual("UniRef100_A0A0D2WIY8/1752-1857", sequence_entry.id)
self.assertEqual(
"-------QRATPGFKMKG-WL-H------K-E-------------------------------------------------G-G-"
"-----------SV------------------------------------------------------------------------"
"-------------------------------------------------K-----------------------TW----------"
"-----------------------------------------------------------------------------------K-"
"-R-R------------W----F-ST--------T--P-----------------------",
sequence_entry.seq,
)
self.assertEqual(
[
"[subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=C"
"apsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3"
],
sequence_entry.remark,
)
[docs] def test_write_1(self):
msa = [
"# STOCKHOLM 1.0",
"#=GF ID 1EAZ:A|PDBID|CHAIN|SEQUENCE-i5",
"",
"#=GS UniRef100_A0A0D2WIY8/647-745 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/761-857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1126-1228 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1245-1341 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1752-1857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"",
"1EAZ:A|PDBID|CHAIN|SEQUENCE GSMFTPKPPQDSAVIKAG-YC-V------K-Q-------------------------------------------------G-A------------VM------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/647-745 ---------------IEG-YL-S------K-Q-------------------------------------------------G-GV----------NNN------------------------------------------------------------------------------------------------------",
"#=GR UniRef100_A0A0D2WIY8/647-745 PP ...............79*.**.*......*.*.................................................*.99..........9**......................................................................................................",
"UniRef100_A0A0D2WIY8/761-857 -----------ANPDKEG-WL-K------K-Q-------------------------------------------------G-N-----------SMA------------------------------------------------------------------------------------------------------",
"#=GR UniRef100_A0A0D2WIY8/761-857 PP ...........5899***.**.*......*.*.................................................*.9...........9**......................................................................................................",
"UniRef100_A0A0D2WIY8/1126-1228 ------------AVRKLG-FL-Y------K-Q-------------------------------------------------G-G------------SN------------------------------------------------------------------------------------------------------",
"#=GR UniRef100_A0A0D2WIY8/1126-1228 PP ............68999*.**.*......*.*.................................................*.*............**......................................................................................................",
"UniRef100_A0A0D2WIY8/1245-1341 ------------NPARQG-WL-C------K-R-------------------------------------------------G-G------------TY------------------------------------------------------------------------------------------------------",
"#=GR UniRef100_A0A0D2WIY8/1245-1341 PP ............6789**.**.*......*.*.................................................*.*............**......................................................................................................",
"UniRef100_A0A0D2WIY8/1752-1857 -------QRATPGFKMKG-WL-H------K-E-------------------------------------------------G-G------------SV------------------------------------------------------------------------------------------------------",
"#=GR UniRef100_A0A0D2WIY8/1752-1857 PP .......556677889**.**.*......*.*.................................................*.*............**......................................................................................................",
"#=GC PP_cons .......*....*...................................*.....*..*................*.................*..*....*................................................*****999875555677766776.",
"#=GC RF .......x....x...................................x.....x..x................x.................x..x....x................................................xxxxxxxxxxxxxxxxxxxxxxxx",
"",
"1EAZ:A|PDBID|CHAIN|SEQUENCE -------------------K-----------------------NW---------------------------------------------------------------------------------------------K--R-R------------Y----F-QL--------D--E-----------------------",
"UniRef100_A0A0D2WIY8/647-745 -------------------K-----------------------GW---------------------------------------------------------------------------------------------K--R-R------------Y----C-VL--------E--N-----------------------",
"#=GR UniRef100_A0A0D2WIY8/647-745 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................",
"UniRef100_A0A0D2WIY8/761-857 -------------------K-----------------------DW---------------------------------------------------------------------------------------------K--K-R------------Y----I-AI--------K--E-----------------------",
"#=GR UniRef100_A0A0D2WIY8/761-857 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................",
"UniRef100_A0A0D2WIY8/1126-1228 -------------------K-----------------------GW---------------------------------------------------------------------------------------------R--K-R------------W----I-VM--------E--H-----------------------",
"#=GR UniRef100_A0A0D2WIY8/1126-1228 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................",
"UniRef100_A0A0D2WIY8/1245-1341 -------------------T-----------------------SW---------------------------------------------------------------------------------------------K--K-R------------W----L-VL--------K--G-----------------------",
"#=GR UniRef100_A0A0D2WIY8/1245-1341 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................",
"UniRef100_A0A0D2WIY8/1752-1857 -------------------K-----------------------TW---------------------------------------------------------------------------------------------K--R-R------------W----F-ST--------T--P-----------------------",
"#=GR UniRef100_A0A0D2WIY8/1752-1857 PP ...................*.......................**.............................................................................................*..*.*............*....*.**........*..*.......................",
"#=GC PP_cons ...................9.......................**.............................................................................................*..*.*............*....*.**........9..9.......................",
"#=GC RF ...................x.......................xx.............................................................................................x..x.x............x....x.xx........x..x.......................",
"//",
]
parser = StockholmParser()
f_name_in = self.tempfile(content="\n".join(msa))
f_name_out = self.tempfile()
with open(f_name_in, "r") as f_in, open(f_name_out, "w") as f_out:
hierarchy = parser.read(f_in)
parser.write(f_out, hierarchy)
ref = [
"# STOCKHOLM 1.0",
"#=GF ID 1EAZ:A|PDBID|CHAIN|SEQUENCE",
"",
"#=GS UniRef100_A0A0D2WIY8/647-745 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/761-857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1126-1228 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1245-1341 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"#=GS UniRef100_A0A0D2WIY8/1752-1857 DE [subseq from] Stromal membrane-associated GTPase-activating protein 2 n=1 Tax=Capsaspora owczarzaki (strain ATCC 30864) RepID=A0A0D2WIY8_CAPO3",
"",
"1EAZ:A|PDBID|CHAIN|SEQUENCE GSMFTPKPPQDSAVIKAG-YC-V------K-Q-------------------------------------------------G-A------------VM------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/647-745 ---------------IEG-YL-S------K-Q-------------------------------------------------G-GV----------NNN------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/761-857 -----------ANPDKEG-WL-K------K-Q-------------------------------------------------G-N-----------SMA------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/1126-1228 ------------AVRKLG-FL-Y------K-Q-------------------------------------------------G-G------------SN------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/1245-1341 ------------NPARQG-WL-C------K-R-------------------------------------------------G-G------------TY------------------------------------------------------------------------------------------------------",
"UniRef100_A0A0D2WIY8/1752-1857 -------QRATPGFKMKG-WL-H------K-E-------------------------------------------------G-G------------SV------------------------------------------------------------------------------------------------------",
"",
"1EAZ:A|PDBID|CHAIN|SEQUENCE -------------------K-----------------------NW---------------------------------------------------------------------------------------------K--R-R------------Y----F-QL--------D--E-----------------------",
"UniRef100_A0A0D2WIY8/647-745 -------------------K-----------------------GW---------------------------------------------------------------------------------------------K--R-R------------Y----C-VL--------E--N-----------------------",
"UniRef100_A0A0D2WIY8/761-857 -------------------K-----------------------DW---------------------------------------------------------------------------------------------K--K-R------------Y----I-AI--------K--E-----------------------",
"UniRef100_A0A0D2WIY8/1126-1228 -------------------K-----------------------GW---------------------------------------------------------------------------------------------R--K-R------------W----I-VM--------E--H-----------------------",
"UniRef100_A0A0D2WIY8/1245-1341 -------------------T-----------------------SW---------------------------------------------------------------------------------------------K--K-R------------W----L-VL--------K--G-----------------------",
"UniRef100_A0A0D2WIY8/1752-1857 -------------------K-----------------------TW---------------------------------------------------------------------------------------------K--R-R------------W----F-ST--------T--P-----------------------",
"//",
]
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)
