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|
# Copyright 2011 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for the Bio.AlignIO.FastaIO module."""
import unittest
from Bio.AlignIO import FastaIO
class FastaIOTests(unittest.TestCase):
"""Test FastaIO module."""
def test_output001(self):
"""Check output001.m10 file."""
fasta_file = "Fasta/output001.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 4)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 108)
self.assertEqual(
alignments[0][0].seq,
"SGSNT-RRRAISRPVRLTAEED---QE"
"IRKRAAECGKTVSGFLRAAALGKKVNS"
"LTDDRVLKEVM-----RLGALQKKLFI"
"DGKRVGDREYAEVLIAITEYHRALLSR",
)
self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[0][0].annotations["original_length"], 107)
self.assertEqual(
alignments[0][1].seq,
"AGSGAPRRRGSGLASRISEQSEALLQE"
"AAKHAAEFGRS------EVDTEHLLLA"
"LADSDVVKTILGQFKIKVDDLKRQIES"
"EAKR-GDKPF-EGEIGVSPRVKDALSR",
)
self.assertEqual(alignments[0][1].id, "gi|152973457|ref|YP_001338508.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 931)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 64)
self.assertEqual(
alignments[1][0].seq,
"AAECGKTVSGFLRAAALGKKVNSLTDD"
"RVLKEV-MRLGALQKKLFIDGKRVGDR"
"EYAEVLIAIT",
)
self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[1][0].annotations["original_length"], 107)
self.assertEqual(
alignments[1][1].seq,
"ASRQGCTVGG--KMDSVQDKASDKDKE"
"RVMKNINIMWNALSKNRLFDG----NK"
"ELKEFIMTLT",
)
self.assertEqual(alignments[1][1].id, "gi|152973588|ref|YP_001338639.1|")
self.assertEqual(alignments[1][1].annotations["original_length"], 459)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 38)
self.assertEqual(
alignments[2][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE"
)
self.assertEqual(alignments[2][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[2][0].annotations["original_length"], 126)
self.assertEqual(
alignments[2][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ"
)
self.assertEqual(alignments[2][1].id, "gi|152973462|ref|YP_001338513.1|")
self.assertEqual(alignments[2][1].annotations["original_length"], 101)
self.assertEqual(len(alignments[3]), 2)
self.assertEqual(alignments[3].get_alignment_length(), 43)
self.assertEqual(
alignments[3][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEMEDYSTYC"
)
self.assertEqual(alignments[3][0].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[3][0].annotations["original_length"], 346)
self.assertEqual(
alignments[3][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLISSHGEYC"
)
self.assertEqual(alignments[3][1].id, "gi|152973545|ref|YP_001338596.1|")
self.assertEqual(alignments[3][1].annotations["original_length"], 242)
def test_output002(self):
"""Check output002.m10 file."""
fasta_file = "Fasta/output002.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 6)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 88)
self.assertEqual(
alignments[0][0].seq,
"SGSNTRRRAISRPVR--LTAEED"
"QEIRKRAAECG-KTVSGFLRAAA"
"LGKKVNSLTDDRVLKEVMRLGAL"
"QKKLFIDGKRVGDREYAEV",
)
self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[0][0].annotations["original_length"], 107)
self.assertEqual(
alignments[0][1].seq,
"SQRSTRRKPENQPTRVILFNKPY"
"DVLPQFTDEAGRKTLKEFIPVQG"
"VYAAGRLDRDSEGLLVLTNNGAL"
"QARLTQPGKRTGKIYYVQV",
)
self.assertEqual(alignments[0][1].id, "gi|162139799|ref|NP_309634.2|")
self.assertEqual(alignments[0][1].annotations["original_length"], 207)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 53)
self.assertEqual(
alignments[1][0].seq,
"EIRKRAAECGKTVSGFLRAAA-LGKKV----NSLTDDRVLKEVMRLGALQKKL",
)
self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[1][0].annotations["original_length"], 107)
self.assertEqual(
alignments[1][1].seq,
"EIKPRGTSKGEAIAAFMQEAPFIGRTPVFLGDDLTDESGFAVVNRLGGMSVKI",
)
self.assertEqual(alignments[1][1].id, "gi|15831859|ref|NP_310632.1|")
self.assertEqual(alignments[1][1].annotations["original_length"], 266)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 92)
self.assertEqual(
alignments[2][0].seq,
"SEFFSKIESDLKKKKSKGDVFFD"
"LIIPNG-----GKKDRYVYTSFN"
"GEKFSSYTLNKVTKTDEYNDLSE"
"LSASFFKKNFDKINVNLLSKATS",
)
self.assertEqual(alignments[2][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[2][0].annotations["original_length"], 126)
self.assertEqual(
alignments[2][1].seq,
"TELNSELAKAMKVDAQRG-AFVS"
"QVLPNSSAAKAGIKAGDVITSL"
"NGKPISSFAALRA-QVGTMPVG"
"SKLTLGLLRDG-KQVNVNLELQ"
"QSS",
)
self.assertEqual(alignments[2][1].id, "gi|15829419|ref|NP_308192.1|")
self.assertEqual(alignments[2][1].annotations["original_length"], 474)
self.assertEqual(len(alignments[3]), 2)
self.assertEqual(alignments[3].get_alignment_length(), 73)
self.assertEqual(
alignments[3][0].seq,
"FFDLIIPNGGKKDRYVYTSFNGE"
"KFSSYTLNKVTKTDEYNDLSELS"
"ASFFKKNFDKINVNLLSKATSFA"
"LKKG",
)
self.assertEqual(alignments[3][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[3][0].annotations["original_length"], 126)
self.assertEqual(
alignments[3][1].seq,
"LFDLFLKNDAMHDPMVNESYC-E"
"TFGWVSKENLARMKE---LTYKA"
"NDVLKKLFDDAGLILVDFKLEFG"
"LYKG",
)
self.assertEqual(alignments[3][1].id, "gi|15832592|ref|NP_311365.1|")
self.assertEqual(alignments[3][1].annotations["original_length"], 237)
self.assertEqual(len(alignments[4]), 2)
self.assertEqual(alignments[4].get_alignment_length(), 63)
self.assertEqual(
alignments[4][0].seq,
"VDIKK-ETIESELHSKLPKSIDKIHEDIKKQLSCSLI--MKKID-VEMEDYSTYCFSALRAIE",
)
self.assertEqual(alignments[4][0].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[4][0].annotations["original_length"], 346)
self.assertEqual(
alignments[4][1].seq,
"IDPKKIEQIARQVHESMPKGIREFGEDVEKKIRQTLQAQLTRLDLVSREEFDVQTQVLLRTRE",
)
self.assertEqual(alignments[4][1].id, "gi|38704138|ref|NP_311957.2|")
self.assertEqual(alignments[4][1].annotations["original_length"], 111)
self.assertEqual(len(alignments[5]), 2)
self.assertEqual(alignments[5].get_alignment_length(), 157)
self.assertEqual(
alignments[5][0].seq,
"QYIMTTSNGDRVRAKIYKRGSIQ"
"FQGKYLQIASLINDFMCSILNMK"
"EIVEQKNKEFNVDI---KKETI-"
"ESELHSKLPKSIDKIHEDIKKQL"
"SCSLIMKKIDV-EMEDYSTYCFS"
"ALRA-IEGFIYQILNDVCNPSSS"
"KNLGEYFTENKPKYIIREI",
)
self.assertEqual(alignments[5][0].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[5][0].annotations["original_length"], 346)
self.assertEqual(
alignments[5][1].seq,
"EFIRLLSDHDQFEKDQISELTVA"
"ANALKLEVAK--NNY-----NMK"
"YSFDTQTERRMIELIREQKDLIP"
"EKYLHQSGIKKL-KLHED---EF"
"SSLLVDAERQVLEGSSFVLCCGE"
"KINSTISELLSKKITDLTHPTES"
"FTLSEYFSYDVYEEIFKKV",
)
self.assertEqual(alignments[5][1].id, "gi|15833861|ref|NP_312634.1|")
self.assertEqual(alignments[5][1].annotations["original_length"], 330)
def test_output003(self):
"""Check output003.m10 file."""
fasta_file = "Fasta/output003.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 3)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 55)
self.assertEqual(
alignments[0][0].seq,
"ISISNNKDQYEELQKEQGERDLKTVDQLVRIAAAGGGLRLSASTKTVDQLVRIAA",
)
self.assertEqual(alignments[0][0].id, "gi|152973837|ref|YP_001338874.1|")
self.assertEqual(alignments[0][0].annotations["original_length"], 183)
self.assertEqual(
alignments[0][1].seq,
"VRLTAEEDQ--EIRKRAAECG-KTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGA",
)
self.assertEqual(alignments[0][1].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 107)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 22)
self.assertEqual(alignments[1][0].seq, "DDAEHLFRTLSSR-LDALQDGN")
self.assertEqual(alignments[1][0].id, "gi|152973840|ref|YP_001338877.1|")
self.assertEqual(alignments[1][0].annotations["original_length"], 63)
self.assertEqual(alignments[1][1].seq, "DDRANLFEFLSEEGITITEDNN")
self.assertEqual(alignments[1][1].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[1][1].annotations["original_length"], 346)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 63)
self.assertEqual(
alignments[2][0].seq,
"VFGSFEQPKGEHLSGQVSEQ--RDTAFADQNEQVIRHLKQEIEHLNTLLLSKDSHIDSLKQAM",
)
self.assertEqual(alignments[2][0].id, "gi|152973841|ref|YP_001338878.1|")
self.assertEqual(alignments[2][0].annotations["original_length"], 133)
self.assertEqual(
alignments[2][1].seq,
"VYTSFN---GEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSF-ALKKGI",
)
self.assertEqual(alignments[2][1].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[2][1].annotations["original_length"], 126)
def test_output004(self):
"""Check output004.m10 file."""
fasta_file = "Fasta/output004.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 102)
self.assertEqual(
alignments[0][0].seq,
"AAAAAAGATAAAAAATATCAAAT"
"AGAAGCAATAAAAAATAAAGATA"
"AAACTTTATTTATTGTCTATGCT"
"ACTGATATTTATAGCCCGAGCGA"
"ATTTTTCTCA",
)
self.assertEqual(alignments[0][0].id, "ref|NC_002127.1|:c1351-971")
self.assertEqual(alignments[0][0].annotations["original_length"], 381)
self.assertEqual(
alignments[0][1].seq,
"AGAGAAAATAAAACAAGTAATAA"
"AATATTAATGGAAAAAATAAATT"
"CTTGTTTATTTAGACCTGATTCT"
"AATCACTTTTCTTGCCCGGAGTC"
"ATTTTTGACA",
)
self.assertEqual(alignments[0][1].id, "ref|NC_002695.1|:1970775-1971404")
self.assertEqual(alignments[0][1].annotations["original_length"], 630)
def test_output005(self):
"""Check output005.m10 file."""
fasta_file = "Fasta/output005.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 110)
self.assertEqual(
alignments[0][0].seq,
"IKNKDKTLFIVYAT-DIYSPSEF"
"FSKIESDLKKKKSKGDV--FFDL"
"IIPNGGKKD--RYVYTSFNGEKF"
"SSYTLNKVTKTDEYNDL--SELS"
"ASFFKKNFDKINVNLLSK",
)
self.assertEqual(alignments[0][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[0][0].annotations["original_length"], 126)
self.assertEqual(
alignments[0][1].seq,
"IKDELPVAFCSWASLDLECEVKY"
"INDVTSLYAKDWMSGERKWFIDW"
"IAPFGHNMELYKYMRKKYPYELF"
"RAIRLDESSKTGKIAEFHGGGID"
"KKLASKIFRQYHHELMSE",
)
self.assertEqual(alignments[0][1].id, "gi|10955282|ref|NP_052623.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 163)
def test_output006(self):
"""Check output006.m10 file."""
fasta_file = "Fasta/output006.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 131)
self.assertEqual(
alignments[0][0].seq,
"GCAACGCTTCAAGAACTGGAATT"
"AGGAACCGTGACAACGATTAATG"
"AGGAGATTTATGAAGAGGGTTCT"
"TCGATTTTAGGCCAATCGGAAGG"
"AATTATGTAGCAAGTCCATCAGA"
"AAATGGAAGAAGTCAT",
)
self.assertEqual(alignments[0][0].id, "query")
self.assertEqual(alignments[0][0].annotations["original_length"], 131)
self.assertEqual(
alignments[0][1].seq,
"GCAACGCTTCAAGAACTGGAATT"
"AGGAACCGTGACAACGATTAATG"
"AGGAGATTTATGAAGAGGGTTCT"
"TCGATTTTAGGCCAATCGGAAGG"
"AATTATGTAGCAAGTCCATCAGA"
"AAATGGAAGTAGTCAT",
)
self.assertEqual(alignments[0][1].id, "gi|116660610|gb|EG558221.1|EG558221")
self.assertEqual(alignments[0][1].annotations["original_length"], 573)
def test_output007(self):
"""Check output007.m10 file."""
fasta_file = "Fasta/output007.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 9)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 108)
self.assertEqual(
alignments[0][0].seq,
"SGSNT-RRRAISRPVRLTAEED-"
"--QEIRKRAAECGKTVSGFLRAA"
"ALGKKVNSLTDDRVLKEVM----"
"-RLGALQKKLFIDGKRVGDREYA"
"EVLIAITEYHRALLSR",
)
self.assertEqual(alignments[0][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[0][0].annotations["original_length"], 107)
self.assertEqual(
alignments[0][1].seq,
"AGSGAPRRRGSGLASRISEQSEA"
"LLQEAAKHAAEFGRS------EV"
"DTEHLLLALADSDVVKTILGQFK"
"IKVDDLKRQIESEAKR-GDKPF-"
"EGEIGVSPRVKDALSR",
)
self.assertEqual(alignments[0][1].id, "gi|152973457|ref|YP_001338508.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 931)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 64)
self.assertEqual(
alignments[1][0].seq,
"AAECGKTVSGFLRAAALGKKVNS"
"LTDDRVLKEV-MRLGALQKKLFI"
"DGKRVGDREYAEVLIAIT",
)
self.assertEqual(alignments[1][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[1][0].annotations["original_length"], 107)
self.assertEqual(
alignments[1][1].seq,
"ASRQGCTVGG--KMDSVQDKASD"
"KDKERVMKNINIMWNALSKNRLF"
"DG----NKELKEFIMTLT",
)
self.assertEqual(alignments[1][1].id, "gi|152973588|ref|YP_001338639.1|")
self.assertEqual(alignments[1][1].annotations["original_length"], 459)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 45)
self.assertEqual(
alignments[2][0].seq, "EIRKRAAECGKTVSGFLRAAA-----LGKKVNSLTDDRVLKEVMR"
)
self.assertEqual(alignments[2][0].id, "gi|10955263|ref|NP_052604.1|")
self.assertEqual(alignments[2][0].annotations["original_length"], 107)
self.assertEqual(
alignments[2][1].seq, "ELVKLIADMGISVRALLRKNVEPYEELGLEEDKFTDDQLIDFMLQ"
)
self.assertEqual(alignments[2][1].id, "gi|152973480|ref|YP_001338531.1|")
self.assertEqual(alignments[2][1].annotations["original_length"], 141)
self.assertEqual(len(alignments[3]), 2)
self.assertEqual(alignments[3].get_alignment_length(), 38)
self.assertEqual(
alignments[3][0].seq, "MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIE"
)
self.assertEqual(alignments[3][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[3][0].annotations["original_length"], 126)
self.assertEqual(
alignments[3][1].seq, "IKKDLGVSFLKLKNREKTLIVDALKKKYPVAELLSVLQ"
)
self.assertEqual(alignments[3][1].id, "gi|152973462|ref|YP_001338513.1|")
self.assertEqual(alignments[3][1].annotations["original_length"], 101)
self.assertEqual(len(alignments[4]), 2)
self.assertEqual(alignments[4].get_alignment_length(), 11)
self.assertEqual(alignments[4][0].seq, "FFDLIIPNGGK")
self.assertEqual(alignments[4][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[4][0].annotations["original_length"], 126)
self.assertEqual(alignments[4][1].seq, "FFDLVIENPGK")
self.assertEqual(alignments[4][1].id, "gi|152973509|ref|YP_001338560.1|")
self.assertEqual(alignments[4][1].annotations["original_length"], 448)
self.assertEqual(len(alignments[5]), 2)
self.assertEqual(alignments[5].get_alignment_length(), 40)
self.assertEqual(
alignments[5][0].seq, "DKTLFIVYATDIYSPSE-FFSKIESDLKKKKSKGD-VFFD"
)
self.assertEqual(alignments[5][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[5][0].annotations["original_length"], 126)
self.assertEqual(
alignments[5][1].seq, "ESVVFILMAGFAMSVCYLFFSVLEKVINARKSKDESIYHD"
)
self.assertEqual(alignments[5][1].id, "gi|152973581|ref|YP_001338632.1|")
self.assertEqual(alignments[5][1].annotations["original_length"], 84)
self.assertEqual(len(alignments[6]), 2)
self.assertEqual(alignments[6].get_alignment_length(), 30)
self.assertEqual(alignments[6][0].seq, "ASFFKKNFDKINVNLLSKATSFALKKGIPI")
self.assertEqual(alignments[6][0].id, "gi|10955264|ref|NP_052605.1|")
self.assertEqual(alignments[6][0].annotations["original_length"], 126)
self.assertEqual(alignments[6][1].seq, "ASFSKEEQDKVAVDKVAADVAWQERMNKPV")
self.assertEqual(alignments[6][1].id, "gi|152973536|ref|YP_001338587.1|")
self.assertEqual(alignments[6][1].annotations["original_length"], 84)
self.assertEqual(len(alignments[7]), 2)
self.assertEqual(alignments[7].get_alignment_length(), 43)
self.assertEqual(
alignments[7][0].seq, "SELHSKLPKSIDKIHEDIKKQLSC-SLIMKKIDVEMEDYSTYC"
)
self.assertEqual(alignments[7][0].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[7][0].annotations["original_length"], 346)
self.assertEqual(
alignments[7][1].seq, "SRINSDVARRIPGIHRDPKDRLSSLKQVEEALDMLISSHGEYC"
)
self.assertEqual(alignments[7][1].id, "gi|152973545|ref|YP_001338596.1|")
self.assertEqual(alignments[7][1].annotations["original_length"], 242)
self.assertEqual(len(alignments[8]), 2)
self.assertEqual(alignments[8].get_alignment_length(), 64)
self.assertEqual(
alignments[8][0].seq,
"ISGTYKGIDFLIKLMPSGGNTTI"
"GRASGQNNTYFDEIALIIKENCL"
"Y--SDTKNFEYTIPKFSD",
)
self.assertEqual(alignments[8][0].id, "gi|10955265|ref|NP_052606.1|")
self.assertEqual(alignments[8][0].annotations["original_length"], 346)
self.assertEqual(
alignments[8][1].seq,
"IDGVITAFD-LRTGMNISKDKVV"
"AQIQGMDPVW---ISAAVPESIA"
"YLLKDTSQFEISVPAYPD",
)
self.assertEqual(alignments[8][1].id, "gi|152973505|ref|YP_001338556.1|")
self.assertEqual(alignments[8][1].annotations["original_length"], 430)
def test_output008(self):
"""Check output008.m10 file."""
fasta_file = "Fasta/output008.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 12)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 65)
self.assertEqual(
alignments[0][0].seq,
"LQHRHPHQQQQQQQQQQQQQQQQ"
"QQQQQQQQQQQH---HHHHHHHL"
"LQDAYMQQYQHATQQQQML",
)
self.assertEqual(alignments[0][0].id, "sp|Q9NSY1|BMP2K_HUMAN")
self.assertEqual(alignments[0][0].annotations["original_length"], 1161)
self.assertEqual(
alignments[0][1].seq,
"IPHQLPHALRHRPAQEAAHASQL"
"HPAQPGCGQPLHGLWRLHHHPVY"
"LYAWILRLRGHGMQSGGLL",
)
self.assertEqual(alignments[0][1].id, "gi|283855822|gb|GQ290312.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 983)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 201)
self.assertEqual(
alignments[1][0].seq,
"GPEIL---LGQ-GPPQQPPQQHR"
"VLQQLQQGDWRLQQLH-------"
"LQHRHPHQQQQQQQQQQQQQQQQ"
"QQQQQQQQQQQH-----HHHHHH"
"-HLLQDAYMQQYQHATQQQQMLQ"
"QQF-LMHSVYQPQPSASQYPTMM"
"PQYQQAFFQQQMLAQHQPSQQQA"
"SPEYLTSPQEFSPALVSYTSSLP"
"A-QVGTIMDSSYSANRS",
)
self.assertEqual(alignments[1][0].id, "sp|Q9NSY1|BMP2K_HUMAN")
self.assertEqual(alignments[1][0].annotations["original_length"], 1161)
self.assertEqual(
alignments[1][1].seq,
"GPELLRALLQQNGCGTQPLRVPT"
"VLPG*AMAVLHAGRLHVPAHRAW"
"LPHQLPHALRHGPAQEAAHASQL"
"HPAQPGRG*PLHGLRWLHHHPLH"
"/PLCMDTLSLGPQDAIWRASLPH"
"WAVKLPCGLWWSWPLSGTWWCVS"
"P*ATSA------LGRTMP*WASL"
"SPGSWHWPALHPPSLVGPGTSLK"
"ACSVHAGSTTTHSSQKS",
)
self.assertEqual(alignments[1][1].id, "gi|57163782|ref|NM_001009242.1|")
self.assertEqual(alignments[1][1].annotations["original_length"], 1047)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 348)
self.assertEqual(
alignments[2][0].seq,
"MNGTEGPNFYVPFSNATGVVRSP"
"FEYPQYYLAEPWQFSMLAAYMFL"
"LIVLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVLGGFT"
"STLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLAGWSRYIPEGLQ"
"CSCGIDYYTLKPEVNNESFVIYM"
"FVVHFTIPMIIIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWVPYASVAFYIF"
"THQGSNFGPIFMTIPAFFAKSAA"
"IYNPVIYIMMNKQFRNCMLTTIC"
"CGKNPLGDDEASATVSKTETSQV"
"APA",
)
self.assertEqual(alignments[2][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[2][0].annotations["original_length"], 348)
self.assertEqual(
alignments[2][1].seq,
"MNGTEGPNFYVPFSNKTGVVRSP"
"FEYPQYYLAEPWQFSMLAAYMFL"
"LIVLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVFGGFT"
"TTLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLVGWSRYIPEGMQ"
"CSCGIDYYTLKPEVNNESFVIYM"
"FVVHFTIPMIVIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWVPYASVAFYIF"
"THQGSNFGPIFMTLPAFFAKSSS"
"IYNPVIYIMMNKQFRNCMLTTLC"
"CGKNPLGDDEASTTGSKTETSQV"
"APA",
)
self.assertEqual(alignments[2][1].id, "gi|57163782|ref|NM_001009242.1|")
self.assertEqual(alignments[2][1].annotations["original_length"], 1047)
self.assertEqual(len(alignments[3]), 2)
self.assertEqual(alignments[3].get_alignment_length(), 348)
self.assertEqual(
alignments[3][0].seq,
"MNGTEGPNFYVPFSNATGVVRSP"
"FEYPQYYLAEPWQFSMLAAYMFL"
"LIVLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVLGGFT"
"STLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLAGWSRYIPEGLQ"
"CSCGIDYYTLKPEVNNESFVIYM"
"FVVHFTIPMIIIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWVPYASVAFYIF"
"THQGSNFGPIFMTIPAFFAKSAA"
"IYNPVIYIMMNKQFRNCMLTTIC"
"CGKNPLGDDEASATVSKTETSQV"
"APA",
)
self.assertEqual(alignments[3][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[3][0].annotations["original_length"], 348)
self.assertEqual(
alignments[3][1].seq,
"MNGTEGPNFYVPFSNKTGVVRSP"
"FEAPQYYLAEPWQFSMLAAYMFL"
"LIMLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVFGGFT"
"TTLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLVGWSRYIPEGMQ"
"CSCGIDYYTPHEETNNESFVIYM"
"FVVHFIIPLIVIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWLPYAGVAFYIF"
"THQGSDFGPIFMTIPAFFAKTSA"
"VYNPVIYIMMNKQFRNCMVTTLC"
"CGKNPLGDDEASTTVSKTETSQV"
"APA",
)
self.assertEqual(alignments[3][1].id, "gi|18148870|dbj|AB062417.1|")
self.assertEqual(alignments[3][1].annotations["original_length"], 1047)
self.assertEqual(len(alignments[4]), 2)
self.assertEqual(alignments[4].get_alignment_length(), 326)
self.assertEqual(
alignments[4][0].seq,
"VPFSNATGVVRSPFEYPQYYLAE"
"PWQFSMLAAYMFLLIVLGFPINF"
"LTLYVTVQHKKLRTPLNYILLNL"
"AVADLFMVLGGFTSTLYTSLHGY"
"FVFGPTGCNLEGFFATLGGEIAL"
"WSLVVLAIERYVVVCKPMSNFRF"
"GENHAIMGVAFTWVMALACAAPP"
"LAGWSRYIPEGLQCSCGIDYYTL"
"KPEVNNESFVIYMFVVHFTIPMI"
"IIFFCYGQLVFTVKEAAAQQQES"
"ATTQKAEKEVTRMVIIMVIAFLI"
"CWVPYASVAFYIFTHQGSNFGPI"
"FMTIPAFFAKSAAIYNPVIYIMM"
"NKQFRNCMLTTICCGKNPLGDDE"
"ASAT",
)
self.assertEqual(alignments[4][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[4][0].annotations["original_length"], 348)
self.assertEqual(
alignments[4][1].seq,
"VPFSNKTGVVRSPFEYPQYYLAE"
"PWQFSMLAAYMFLLIVLGFPINF"
"LTLYVTVQHKKLRTPLNYILLNL"
"AVANLFMVFGGFTTTLYTSMHGY"
"FVFGATGCNLEGFFATLGGEIAL"
"WSLVVLAIERYVVVCKPMSNFRF"
"GENHAIMGLAFTWVMALACAAPP"
"LAGWSRYIPEGMQCSCGIDYYTL"
"KPEVNNESFVIYMFVVHFTIPMI"
"VIFFCYGQLVFTVKEAAAQQQES"
"ATTQKAEKEVTRMVIIMVVAFLI"
"CWLPYASVAFYIFTHQGSNFGPV"
"FMTIPAFFAKSSSIYNPVIYIMM"
"NKQFRNCMLTTLCCGKNPLGDDE"
"ASTT",
)
self.assertEqual(alignments[4][1].id, "gi|283855822|gb|GQ290312.1|")
self.assertEqual(alignments[4][1].annotations["original_length"], 983)
self.assertEqual(len(alignments[5]), 2)
self.assertEqual(alignments[5].get_alignment_length(), 354)
self.assertEqual(
alignments[5][0].seq,
"MNGTEGPNFYVPFSNATGVVRSP"
"FEYPQYYLAEPWQFSMLAAYMFL"
"LIVLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVLGGFT"
"STLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLAGWSRYIPEGLQ"
"CSCGIDYYTLKPEVNNESFVIYM"
"FVVHFTIPMIIIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWVPYASVAFYIF"
"THQGSNFGPIFMTIPAFFAKSAA"
"IYNPVIYIMMNKQFRNCMLTTIC"
"CGKNPLGDDEAS-ATVSKTE---"
"--TSQVAPA",
)
self.assertEqual(alignments[5][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[5][0].annotations["original_length"], 348)
self.assertEqual(
alignments[5][1].seq,
"MNGTEGPNFYIPMSNKTGVVRSP"
"FEYPQYYLAEPWQYSILCAYMFL"
"LILLGFPINFMTLYVTIQHKKLR"
"TPLNYILLNLAFANHFMVLCGFT"
"VTMYSSMNGYFILGATGCYVEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFSENHAVMGVAFTW"
"IMALSCAVPPLLGWSRYIPEGMQ"
"CSCGVDYYTLKPEVNNESFVIYM"
"FVVHFTIPLIIIFFCYGRLVCTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVVFFLICWVPYASVAFFIF"
"SNQGSEFGPIFMTVPAFFAKSSS"
"IYNPVIYIMLNKQFRNCMITTLC"
"CGKNPFGEDDASSAATSKTEASS"
"VSSSQVSPA",
)
self.assertEqual(alignments[5][1].id, "gi|2734705|gb|U59921.1|BBU59921")
self.assertEqual(alignments[5][1].annotations["original_length"], 1574)
self.assertEqual(len(alignments[6]), 2)
self.assertEqual(alignments[6].get_alignment_length(), 347)
self.assertEqual(
alignments[6][0].seq,
"MNGTEGPNFYVPFSNATGVVRSP"
"FEYPQYYLAEPWQFSMLAAYMFL"
"LIVLGFPINFLTLYVTVQHKKLR"
"TPLNYILLNLAVADLFMVLGGFT"
"STLYTSLHGYFVFGPTGCNLEGF"
"FATLGGEIALWSLVVLAIERYVV"
"VCKPMSNFRFGENHAIMGVAFTW"
"VMALACAAPPLAGWSRYIPEGLQ"
"CSCGIDYYTLKPEVNNESFVIYM"
"FVVHFTIPMIIIFFCYGQLVFTV"
"KEAAAQQQESATTQKAEKEVTRM"
"VIIMVIAFLICWVPYASVAFYIF"
"THQGSNFGPIFMTIPAFFAKSAA"
"IYNPVIYIMMNKQFRNCMLTTIC"
"CGKNPLGD-DEASATVSKTETSQ"
"VA",
)
self.assertEqual(alignments[6][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[6][0].annotations["original_length"], 348)
self.assertEqual(
alignments[6][1].seq,
"MNGTEGPNFYIPMSNATGVVRSP"
"FEYPQYYLAEPWAFSALSAYMFF"
"LIIAGFPINFLTLYVTIEHKKLR"
"TPLNYILLNLAVADLFMVFGGFT"
"TTMYTSMHGYFVFGPTGCNIEGF"
"FATLGGEIALWCLVVLAIERWMV"
"VCKPVTNFRFGESHAIMGVMVTW"
"TMALACALPPLFGWSRYIPEGLQ"
"CSCGIDYYTRAPGINNESFVIYM"
"FTCHFSIPLAVISFCYGRLVCTV"
"KEAAAQQQESETTQRAEREVTRM"
"VVIMVISFLVCWVPYASVAWYIF"
"THQGSTFGPIFMTIPSFFAKSSA"
"LYNPMIYICMNKQFRHCMITTLC"
"CGKNPFEEEDGASATSSKTEASS"
"VS",
)
self.assertEqual(alignments[6][1].id, "gi|12583664|dbj|AB043817.1|")
self.assertEqual(alignments[6][1].annotations["original_length"], 1344)
self.assertEqual(len(alignments[7]), 2)
self.assertEqual(alignments[7].get_alignment_length(), 111)
self.assertEqual(
alignments[7][0].seq,
"VPFSNATGVVRSPFEYPQYYLAE"
"PWQFSMLAAYMFLLIVLGFPINF"
"LTLYVTVQHKKLRTPLNYILLNL"
"AVADLFMVLGGFTSTLYTSLHGY"
"FVFGPTGCNLEGFFATLGG",
)
self.assertEqual(alignments[7][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[7][0].annotations["original_length"], 348)
self.assertEqual(
alignments[7][1].seq,
"VPFSNKTGVVRSPFEHPQYYLAE"
"PWQFSMLAAYMFLLIVLGFPINF"
"LTLYVTVQHKKLRTPLNYILLNL"
"AVADLFMVFGGFTTTLYTSLHGY"
"FVFGPTGCNLEGFFATLGG",
)
self.assertEqual(alignments[7][1].id, "gi|283855845|gb|GQ290303.1|")
self.assertEqual(alignments[7][1].annotations["original_length"], 4301)
self.assertEqual(len(alignments[8]), 2)
self.assertEqual(alignments[8].get_alignment_length(), 172)
self.assertEqual(
alignments[8][0].seq,
"RYIPEGLQCSCGIDYYTLKPEVN"
"NESFVIYMFVVHFTIPMIIIFFC"
"YGQLVFTVKE-------------"
"-----------------------"
"AAAQQQESATTQKAEKEVTRMVI"
"IMVIAFLICWVPYASVAFYIFTH"
"QGSNFGPIFMTIPAFFAKSAAIY"
"NPVIYIMMNKQ",
)
self.assertEqual(alignments[8][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[8][0].annotations["original_length"], 348)
self.assertEqual(
alignments[8][1].seq,
"RYIPEGMQCSCGIDYYTLKPEVN"
"NESFVIYMFVVHFTIPMIVIFFC"
"YGQLVFTVKEVRSCVGHWGHAH*"
"VNGAQLHSQSCHSLDT*PCVPA\\"
"AAAQQQESATTQKAEKEVTRMVI"
"IMVIAFLICWLPYAGVAFYIFTH"
"QGSNFGPIFMTLPAFFAKSSSIY"
"NPVIYIMMNKQ",
)
self.assertEqual(alignments[8][1].id, "gi|283855845|gb|GQ290303.1|")
self.assertEqual(alignments[8][1].annotations["original_length"], 4301)
self.assertEqual(len(alignments[9]), 2)
self.assertEqual(alignments[9].get_alignment_length(), 73)
self.assertEqual(
alignments[9][0].seq,
"LGGEIALWSLVVLAIERYVVVCK"
"PMSNFRFGENHAIMGVAFTWVMA"
"LACAAPPLAGWSR--YIPEGLQC"
"SCGI",
)
self.assertEqual(alignments[9][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[9][0].annotations["original_length"], 348)
self.assertEqual(
alignments[9][1].seq,
"LAGEIALWSLVVLAIERYVVVCK"
"PMSNFRFGENHAIMGLALTWVMA"
"LACAAPPLVGWSR*WH*TEG-KC"
"L*GL",
)
self.assertEqual(alignments[9][1].id, "gi|283855845|gb|GQ290303.1|")
self.assertEqual(alignments[9][1].annotations["original_length"], 4301)
self.assertEqual(len(alignments[10]), 2)
self.assertEqual(alignments[10].get_alignment_length(), 30)
self.assertEqual(alignments[10][0].seq, "IMMNKQFRNCMLTTICCGKNPLGDDEASAT")
self.assertEqual(alignments[10][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[10][0].annotations["original_length"], 348)
self.assertEqual(alignments[10][1].seq, "MLLAFQFRNCMLTTLCCGKNPLGDDEASTT")
self.assertEqual(alignments[10][1].id, "gi|283855845|gb|GQ290303.1|")
self.assertEqual(alignments[10][1].annotations["original_length"], 4301)
self.assertEqual(len(alignments[11]), 2)
self.assertEqual(alignments[11].get_alignment_length(), 31)
self.assertEqual(alignments[11][0].seq, "AQQQESATTQKAEKEVTRMVIIMVIAFLICW")
self.assertEqual(alignments[11][0].id, "sp|P08100|OPSD_HUMAN")
self.assertEqual(alignments[11][0].annotations["original_length"], 348)
self.assertEqual(alignments[11][1].seq, "SQQIRNATTMMMTMRVTSFSAFWVVADSCCW")
self.assertEqual(alignments[11][1].id, "gi|283855822|gb|GQ290312.1|")
self.assertEqual(alignments[11][1].annotations["original_length"], 983)
def test_output009(self):
"""Check output009.m10 file."""
fasta_file = "Fasta/output009.m10"
with open(fasta_file) as handle:
alignments = list(FastaIO.FastaM10Iterator(handle))
self.assertEqual(len(alignments), 7)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(alignments[0].get_alignment_length(), 22)
self.assertEqual(alignments[0][0].seq, "TGATGTTCTGTTTCTAAAACAG")
self.assertEqual(alignments[0][0].id, "gi|255708421:1-99")
self.assertEqual(alignments[0][0].annotations["original_length"], 99)
self.assertEqual(alignments[0][1].seq, "TGATTTTTTTTGTCTAAAACAG")
self.assertEqual(alignments[0][1].id, "gi|23308614|ref|NM_152952.1|")
self.assertEqual(alignments[0][1].annotations["original_length"], 5188)
self.assertEqual(len(alignments[1]), 2)
self.assertEqual(alignments[1].get_alignment_length(), 14)
self.assertEqual(alignments[1][0].seq, "AGAAGGAAAAAAAA")
self.assertEqual(alignments[1][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[1][0].annotations["original_length"], 16)
self.assertEqual(alignments[1][1].seq, "AGAACTAAAAAAAA")
self.assertEqual(alignments[1][1].id, "gi|47271416|ref|NM_131257.2|")
self.assertEqual(alignments[1][1].annotations["original_length"], 597)
self.assertEqual(len(alignments[2]), 2)
self.assertEqual(alignments[2].get_alignment_length(), 14)
self.assertEqual(alignments[2][0].seq, "AGAAGGAAAAAAAA")
self.assertEqual(alignments[2][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[2][0].annotations["original_length"], 16)
self.assertEqual(alignments[2][1].seq, "AGAAGGTATAAAAA")
self.assertEqual(alignments[2][1].id, "gi|332859474|ref|XM_001156938.2|")
self.assertEqual(alignments[2][1].annotations["original_length"], 762)
self.assertEqual(len(alignments[3]), 2)
self.assertEqual(alignments[3].get_alignment_length(), 14)
self.assertEqual(alignments[3][0].seq, "TTTTTTTCCTTCTT")
self.assertEqual(alignments[3][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[3][0].annotations["original_length"], 16)
self.assertEqual(alignments[3][1].seq, "TTTTTTTACATCTT")
self.assertEqual(alignments[3][1].id, "gi|332211534|ref|XM_003254825.1|")
self.assertEqual(alignments[3][1].annotations["original_length"], 805)
self.assertEqual(len(alignments[4]), 2)
self.assertEqual(alignments[4].get_alignment_length(), 14)
self.assertEqual(alignments[4][0].seq, "AAGAAGGAAAAAAA")
self.assertEqual(alignments[4][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[4][0].annotations["original_length"], 16)
self.assertEqual(alignments[4][1].seq, "AATAAGTAAAAAAA")
self.assertEqual(alignments[4][1].id, "gi|23308614|ref|NM_152952.1|")
self.assertEqual(alignments[4][1].annotations["original_length"], 5188)
self.assertEqual(len(alignments[5]), 2)
self.assertEqual(alignments[5].get_alignment_length(), 14)
self.assertEqual(alignments[5][0].seq, "TTTTTTTCCTTCTT")
self.assertEqual(alignments[5][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[5][0].annotations["original_length"], 16)
self.assertEqual(alignments[5][1].seq, "TTTTTTTACATCTT")
self.assertEqual(alignments[5][1].id, "gi|297689475|ref|XM_002822130.1|")
self.assertEqual(alignments[5][1].annotations["original_length"], 1158)
self.assertEqual(len(alignments[6]), 2)
self.assertEqual(alignments[6].get_alignment_length(), 14)
self.assertEqual(alignments[6][0].seq, "AAGAAGGAAAAAAA")
self.assertEqual(alignments[6][0].id, "gi|156718121:2361-2376")
self.assertEqual(alignments[6][0].annotations["original_length"], 16)
self.assertEqual(alignments[6][1].seq, "AAGAAGGTAAAAGA")
self.assertEqual(alignments[6][1].id, "gi|297689475|ref|XM_002822130.1|")
self.assertEqual(alignments[6][1].annotations["original_length"], 1158)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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