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biopython/Tests/test_SearchIO_infernal_text.py
Samuel Prince 86decf2df1 Fixed docstring
2025-03-22 06:59:36 +01:00

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# Copyright 2024 by Samuel Prince. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tests for SearchIO InfernalIO infernal-text parser."""
import os
import unittest
import itertools
from Bio.SearchIO import parse
# test case files are in the Infernal directory
TEST_DIR = "Infernal"
FMT = "infernal-text"
def get_file(filename):
"""Return the path of a test file."""
return os.path.join(TEST_DIR, filename)
def next_result(qresults, counter):
"""Iterate over the results and counter."""
return next(qresults), next(counter)
class CmscanCases(unittest.TestCase):
"""Test parsing cmsearch output."""
def test_cmscan(self):
"""Test parsing infernal-text, cmscan, multiple queries"""
tab_file = get_file("cmscan_115_IRES_5S_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
# first qresult
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "ENA|BK006935|BK006935.2")
self.assertEqual(qresult.seq_len, 230218)
self.assertEqual(qresult.description, "<unknown description>")
self.assertEqual(qresult.program, "cmscan")
self.assertEqual(qresult.version, "1.1.5")
self.assertEqual(qresult.target, "IRES_5S_U2.cm")
# first hit
hit = qresult[0]
self.assertEqual(len(hit), 2)
self.assertEqual(hit.id, "U2")
self.assertEqual(hit.description, "U2 spliceosomal RNA")
self.assertEqual(hit.query_id, "ENA|BK006935|BK006935.2")
hsp = hit[0]
self.assertEqual(len(hsp), 2)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.44)
self.assertEqual(hsp.evalue, 0.91)
self.assertEqual(hsp.bitscore, 13.5)
self.assertEqual(hsp.bias, 0.0)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 52929)
self.assertEqual(hsp.hit_end, 53083)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.80)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 46)
self.assertEqual(frag.hit_start, 52929)
self.assertEqual(frag.hit_end, 52974)
self.assertEqual(frag.hit_strand, 0)
# second fragment
frag = hsp[1]
self.assertEqual(frag.query_start, 84)
self.assertEqual(frag.query_end, 193)
self.assertEqual(frag.hit_start, 52977)
self.assertEqual(frag.hit_end, 53083)
self.assertEqual(frag.hit_strand, 0)
# second hit
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 196389)
self.assertEqual(hsp.hit_end, 196571)
# second qresult
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "ENA|BK006936|BK006936.2")
# first hit
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "U2")
self.assertEqual(hit.description, "U2 spliceosomal RNA")
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
# third (last) qresult
qresult, count = next_result(qresults, counter)
self.assertEqual(qresult.id, "ENA|BK006937|BK006937.2")
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, count)
class CmsearchCases(unittest.TestCase):
"""Test parsing cmsearch output."""
def test_cmsearch_1q_0m(self):
"""Test parsing infernal-text, cmsearch, one query, no hits (IRES_Yeast)"""
text_file = get_file("cmsearch_114_IRES_Yeast.txt")
qresults = parse(text_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 0)
self.assertEqual(qresult.id, "IRES_HCV")
self.assertEqual(qresult.seq_len, 352)
self.assertEqual(qresult.accession, "RF00061")
self.assertEqual(
qresult.description, "Hepatitis C virus internal ribosome entry site"
)
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, multiple fragments (U2_Yeast)"""
tab_file = get_file("cmsearch_114_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.",
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 2)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.33)
self.assertEqual(hsp.evalue, 5.9e-20)
self.assertEqual(hsp.bitscore, 98.7)
self.assertEqual(hsp.bias, 0.1)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.91)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 112)
self.assertEqual(frag.hit_start, 681763)
self.assertEqual(frag.hit_end, 681858)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq,
"AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaau-uauaUUAaauuaAUUUUUggaacua",
)
self.assertEqual(
frag.hit.seq,
"AUC---UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGA-CCUCAAUGAGGCUCAUUaCCUUUUAAUUUG-------------",
)
self.assertEqual(
frag.aln_annotation["PP"],
"***...************************************************************999.****************86555555555443.............",
)
self.assertEqual(
frag.aln_annotation["NC"],
" v v ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"AU+ UCU+:GCCUUUUGGC:+AGAUCAAGUGUAGUAUCUGUUCUU:UCAGU+UAA+A+CUGA:AUG: CC:CA+UG:GG+:CA+U U+UUAA+UU ",
)
# second fragment
frag = hsp[1]
self.assertEqual(frag.query_start, 186)
self.assertEqual(frag.query_end, 193)
self.assertEqual(frag.hit_start, 681747)
self.assertEqual(frag.hit_end, 681754)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(frag.query.seq, "Acccuuu")
self.assertEqual(frag.hit.seq, "ACAUUUU")
self.assertEqual(frag.aln_annotation["PP"], "*******")
self.assertEqual(frag.aln_annotation["NC"], " ")
self.assertEqual(frag.aln_annotation["CS"], ":::::::")
self.assertEqual(frag.aln_annotation["similarity"], "AC +UUU")
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h_notextw(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, multiple fragments, notextw (U2_Yeast)"""
tab_file = get_file("cmsearch_114_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.",
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 2)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.33)
self.assertEqual(hsp.evalue, 5.9e-20)
self.assertEqual(hsp.bitscore, 98.7)
self.assertEqual(hsp.bias, 0.1)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.91)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 112)
self.assertEqual(frag.hit_start, 681763)
self.assertEqual(frag.hit_end, 681858)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq,
"AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaau-uauaUUAaauuaAUUUUUggaacua",
)
self.assertEqual(
frag.hit.seq,
"AUC---UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGA-CCUCAAUGAGGCUCAUUaCCUUUUAAUUUG-------------",
)
self.assertEqual(
frag.aln_annotation["PP"],
"***...************************************************************999.****************86555555555443.............",
)
self.assertEqual(
frag.aln_annotation["NC"],
" v v ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"AU+ UCU+:GCCUUUUGGC:+AGAUCAAGUGUAGUAUCUGUUCUU:UCAGU+UAA+A+CUGA:AUG: CC:CA+UG:GG+:CA+U U+UUAA+UU ",
)
# second fragment
frag = hsp[1]
self.assertEqual(frag.query_start, 186)
self.assertEqual(frag.query_end, 193)
self.assertEqual(frag.hit_start, 681747)
self.assertEqual(frag.hit_end, 681754)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(frag.query.seq, "Acccuuu")
self.assertEqual(frag.hit.seq, "ACAUUUU")
self.assertEqual(frag.aln_annotation["PP"], "*******")
self.assertEqual(frag.aln_annotation["NC"], " ")
self.assertEqual(frag.aln_annotation["CS"], ":::::::")
self.assertEqual(frag.aln_annotation["similarity"], "AC +UUU")
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_mm_1h(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple hits, one hsp, multiple fragments (U2_Yeast_full)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 5)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# skip first hit (equivalent to test_cmsearch_1q_1m)
# second hit (3 hsp, reverse strand)
hit = qresult[1]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome XV, complete sequence.",
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 3)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.39)
self.assertEqual(hsp.evalue, 0.49)
self.assertEqual(hsp.bitscore, 19.8)
self.assertEqual(hsp.bias, 0.0)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.96)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 52)
self.assertEqual(frag.hit_start, 737448)
self.assertEqual(frag.hit_end, 737498)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq, "AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAG"
)
self.assertEqual(
frag.hit.seq, "AUCCCAUAUUUGCCAUC-GGCAUAUAUUAAGUAUAUUAGCAGUUCUAAUUAC"
)
self.assertEqual(
frag.aln_annotation["PP"],
"**************999.*******************************996",
)
self.assertEqual(
frag.aln_annotation["NC"],
" ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"AU+CC U U+ GCC U GGC +A AU AAGU UA UA C GUUCU:A::A ",
)
# second fragment
frag = hsp[1]
self.assertEqual(frag.query_start, 60)
self.assertEqual(frag.query_end, 112)
self.assertEqual(frag.hit_start, 737334)
self.assertEqual(frag.hit_end, 737360)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq, "CUGauAuggcccccAuugggggccaauuauaUUAaauuaAUUUUUggaacua"
)
self.assertEqual(
frag.hit.seq, "GUAGUUGGAAGGAUACUAUCCUUUAU--------------------------"
)
self.assertEqual(
frag.aln_annotation["PP"],
"69999999999999999999999987..........................",
)
self.assertEqual(
frag.aln_annotation["NC"],
" ",
)
self.assertEqual(
frag.aln_annotation["CS"],
">>>>>>,<<<<<<<___>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,",
)
self.assertEqual(
frag.aln_annotation["similarity"],
" U::U: ::::::A U:::::: A+ ",
)
# third fragment
frag = hsp[2]
self.assertEqual(frag.query_start, 186)
self.assertEqual(frag.query_end, 193)
self.assertEqual(frag.hit_start, 737324)
self.assertEqual(frag.hit_end, 737331)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(frag.query.seq, "Acccuuu")
self.assertEqual(frag.hit.seq, "AUCCCCU")
self.assertEqual(frag.aln_annotation["PP"], "*******")
self.assertEqual(frag.aln_annotation["NC"], " ")
self.assertEqual(frag.aln_annotation["CS"], ":::::::")
self.assertEqual(frag.aln_annotation["similarity"], "A CC++U")
# third hit (2 hsp, forward strand)
hit = qresult[2]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006947|BK006947.3")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.",
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 2)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.39)
self.assertEqual(hsp.evalue, 5.7)
self.assertEqual(hsp.bitscore, 15.3)
self.assertEqual(hsp.bias, 0.0)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 266059)
self.assertEqual(hsp.hit_end, 266208)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.91)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 36)
self.assertEqual(frag.hit_start, 266059)
self.assertEqual(frag.hit_end, 266097)
self.assertEqual(frag.hit_strand, 0)
self.assertEqual(frag.query.seq, "AUacCU-UCu-cgGCcUUUUgGCuaaGAUCAA-GUGUAG")
self.assertEqual(frag.hit.seq, "AUGUUGaUCUaUCGUCAAUUGACCCAGAUGAUaGUGUAG")
self.assertEqual(
frag.aln_annotation["PP"], "*****9****999****************9988999987"
)
self.assertEqual(
frag.aln_annotation["NC"], " v v "
)
self.assertEqual(
frag.aln_annotation["CS"], "::::::.<<<.-<<<<____>>>>->>>,,,,.,,,,,,"
)
self.assertEqual(
frag.aln_annotation["similarity"], "AU UCU + G C UUG C AGAU A GUGUAG"
)
# second fragment
frag = hsp[1]
self.assertEqual(frag.query_start, 84)
self.assertEqual(frag.query_end, 193)
self.assertEqual(frag.hit_start, 266098)
self.assertEqual(frag.hit_end, 266208)
self.assertEqual(frag.hit_strand, 0)
self.assertEqual(
frag.query.seq,
"aauuauaUUAaauuaAUUUUUggaacuaGugggggcauuu-uggGCUUGCccau--ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu",
)
self.assertEqual(
frag.hit.seq,
"-GUUAUAUAGUUUUGAUAUUUUGGCGAAAAGUUGAGAAUAuUGCGCUUGCGUAUauAUUCCAUUUGAGGUGGCACUAGAGCUCGCAUUAU-UACCAGUAGUGGCAGGAUUGC",
)
self.assertEqual(
frag.aln_annotation["PP"],
".3377778888888888888888888888888888888888**************99999******************************.99*******************",
)
self.assertEqual(
frag.aln_annotation["NC"],
" v v v v v v v v v v ",
)
self.assertEqual(
frag.aln_annotation["CS"],
",,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<----.<<<<<__>>>>>-..->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>:::::::",
)
self.assertEqual(
frag.aln_annotation["similarity"],
" UUAUAU +UU AU UUU G +A:: : G::A+U+ U :GCUUGC: AU +::C : :: G: :AC: G U GCA UA+ C :GU+: :C +U +",
)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_mm_1h_shuffled(self):
"""Test parsing infernal-text, cmsearch, one queries, multiple non-consecutive hits, one hsp, multiple fragments (U2_Yeast_full_shuffled)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full_shuffled.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 2)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "BK006936_7-8.fasta")
# first hit (3 hsps at rank 1,3 and 4)
hit = qresult[0]
self.assertEqual(len(hit), 3)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(hit.description, "")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 1)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
# second hsp (rank 3)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1370418)
self.assertEqual(hsp.hit_end, 1370563)
# last hsp (rank 4)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1079243)
self.assertEqual(hsp.hit_end, 1079392)
# second hit
hit = qresult[1]
self.assertEqual(len(hit), 3)
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(hit.description, "")
self.assertEqual(hit.query_id, "U2")
# first hsp (rank 2)
hsp = hit[0]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
# second hsp (rank 5)
hsp = hit[1]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 425490)
self.assertEqual(hsp.hit_end, 425693)
# last hsp (rank 6)
hsp = hit[2]
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 193)
self.assertEqual(hsp.hit_start, 1073786)
self.assertEqual(hsp.hit_end, 1073950)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_mm_mh(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, one fragment (5S_Yeast)"""
tab_file = get_file("cmsearch_114_5S_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "5S_rRNA")
self.assertEqual(qresult.seq_len, 119)
self.assertEqual(qresult.accession, "RF00001")
self.assertEqual(qresult.description, "5S ribosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 6)
self.assertEqual(hit.id, "ENA|BK006945|BK006945.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.",
)
self.assertEqual(hit.query_id, "5S_rRNA")
# first hit
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.52)
self.assertEqual(hsp.evalue, 1.6e-18)
self.assertEqual(hsp.bitscore, 88.8)
self.assertEqual(hsp.bias, 0.0)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 119)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 459676)
self.assertEqual(hsp.hit_end, 459796)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.99)
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 119)
self.assertEqual(frag.hit_start, 459676)
self.assertEqual(frag.hit_end, 459796)
self.assertEqual(frag.hit_strand, 0)
self.assertEqual(
frag.query.seq,
"gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc-gAAguUAAGcgcgcUugggCcagggUA-GUAcuagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc",
)
self.assertEqual(
frag.hit.seq,
"GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU",
)
self.assertEqual(
frag.aln_annotation["PP"],
"***********************************************99***********************8756***************************9*****************",
)
self.assertEqual(
frag.aln_annotation["NC"],
" vv vv ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-<<-----<<____>>----->>->-->>->>>))))))))):",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA + +UGGGUGACC+ G AA :CAGGUGC:GCA::C+",
)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h_noali(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, noali (U2_Yeast_noali)"""
tab_file = get_file("cmsearch_114_U2_Yeast_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(
hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome II,"
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.33)
self.assertEqual(hsp.evalue, 5.9e-20)
self.assertEqual(hsp.bitscore, 98.7)
self.assertEqual(hsp.bias, 0.1)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
# first fragment
frag = hsp[0]
self.assertEqual(frag.hit_start, 681747)
self.assertEqual(frag.hit_end, 681858)
self.assertEqual(frag.hit_strand, -1)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_mh_noali(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali (5S_Yeast_noali)"""
tab_file = get_file("cmsearch_114_5S_Yeast_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "5S_rRNA")
self.assertEqual(qresult.seq_len, 119)
self.assertEqual(qresult.accession, "RF00001")
self.assertEqual(qresult.description, "5S ribosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 6)
self.assertEqual(hit.id, "ENA|BK006945|BK006945.2")
self.assertEqual(
hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome XII"
)
self.assertEqual(hit.query_id, "5S_rRNA")
# first hsp
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.52)
self.assertEqual(hsp.evalue, 1.6e-18)
self.assertEqual(hsp.bitscore, 88.8)
self.assertEqual(hsp.bias, 0.0)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.hit_start, 459676)
self.assertEqual(hsp.hit_end, 459796)
frag = hsp[0]
self.assertEqual(frag.hit_start, 459676)
self.assertEqual(frag.hit_end, 459796)
self.assertEqual(frag.hit_strand, 0)
# last hsp
hsp = hit[-1]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.53)
self.assertEqual(hsp.evalue, 4.4e-17)
self.assertEqual(hsp.bitscore, 83.2)
self.assertEqual(hsp.bias, 0.0)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.hit_start, 485697)
self.assertEqual(hsp.hit_end, 485817)
frag = hsp[0]
self.assertEqual(frag.hit_start, 485697)
self.assertEqual(frag.hit_end, 485817)
self.assertEqual(frag.hit_strand, 0)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_mh_noali_inc(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, multiple hsp, noali, inclusion threshold (U2_Yeast_full_noali)"""
tab_file = get_file("cmsearch_114_U2_Yeast_full_noali.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 5)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# first hit
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(
hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome II,"
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.33)
self.assertEqual(hsp.evalue, 5.9e-20)
self.assertEqual(hsp.bitscore, 98.7)
self.assertEqual(hsp.bias, 0.1)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.hit_start, 681747)
self.assertEqual(hsp.hit_end, 681858)
frag = hsp[0]
self.assertEqual(frag.hit_start, 681747)
self.assertEqual(frag.hit_end, 681858)
self.assertEqual(frag.hit_strand, -1)
# second hit
hit = qresult[1]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006948|BK006948.2")
self.assertEqual(
hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome XV,"
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.39)
self.assertEqual(hsp.evalue, 0.49)
self.assertEqual(hsp.bitscore, 19.8)
self.assertEqual(hsp.bias, 0.0)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.hit_start, 737324)
self.assertEqual(hsp.hit_end, 737498)
frag = hsp[0]
self.assertEqual(frag.hit_start, 737324)
self.assertEqual(frag.hit_end, 737498)
self.assertEqual(frag.hit_strand, -1)
# last hit
hit = qresult[-1]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006939|BK006939.2")
self.assertEqual(
hit.description, "TPA_inf: Saccharomyces cerevisiae S288C chromosome V,"
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.41)
self.assertEqual(hsp.evalue, 7.1)
self.assertEqual(hsp.bitscore, 14.9)
self.assertEqual(hsp.bias, 0.0)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.hit_start, 190882)
self.assertEqual(hsp.hit_end, 191043)
frag = hsp[0]
self.assertEqual(frag.hit_start, 190882)
self.assertEqual(frag.hit_end, 191043)
self.assertEqual(frag.hit_strand, 0)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_1q_1m_1h_hmmonly(self):
"""Test parsing infernal-text, cmsearch, one queries, one hit, one hsp, one fragments, hmmonly (U2_Yeast_hmmonly)"""
tab_file = get_file("cmsearch_114_U2_Yeast_hmmonly.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 1)
self.assertEqual(qresult.id, "U2")
self.assertEqual(qresult.seq_len, 193)
self.assertEqual(qresult.accession, "RF00004")
self.assertEqual(qresult.description, "U2 spliceosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
hit = qresult[0]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006936|BK006936.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.",
)
self.assertEqual(hit.query_id, "U2")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "hmm")
self.assertEqual(hsp.truncated, "-")
self.assertEqual(hsp.gc, 0.35)
self.assertEqual(hsp.evalue, 1.5e-19)
self.assertEqual(hsp.bitscore, 73.1)
self.assertEqual(hsp.bias, 2.7)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.query_start, 7)
self.assertEqual(hsp.query_end, 100)
self.assertEqual(hsp.query_endtype, "..")
self.assertEqual(hsp.hit_start, 681762)
self.assertEqual(hsp.hit_end, 681855)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.74)
# first fragment
frag = hsp[0]
self.assertEqual(frag.query_start, 7)
self.assertEqual(frag.query_end, 100)
self.assertEqual(frag.hit_start, 681762)
self.assertEqual(frag.hit_end, 681855)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq,
"UCucgGCcUUUUGGCUaaGAUCAAGUGUAGUAUCUGUUCUUuuCAGUuUAAuAuCUGauAuugucucuAuugggggccaau-uauaUUAaauuaA",
)
self.assertEqual(
frag.hit.seq,
"UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGACCUCAAU-GAGGCUCAUUaCCUUUUAAUUUGU",
)
self.assertEqual(
frag.aln_annotation["PP"],
"999*********************************************************7777666666.777776666544444444433221",
)
self.assertEqual(
frag.aln_annotation["CS"],
"<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,,,.,,,,,,,,,,,,,",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"UCu+ GCcUUUUGGCU+aGAUCAAGUGUAGUAUCUGUUCUUuuCAGU+UAA+A+CUGa+Au+ +cuc Au g+gg ca+u u+UUAa+uu ",
)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(1, count)
def test_cmsearch_mq(self):
"""Test parsing infernal-text, cmsearch, multiple queries"""
tab_file = get_file("cmsearch_114_IRES_5S_U2_Yeast.txt")
qresults = parse(tab_file, FMT)
counter = itertools.count(start=1)
# First qresult (empty)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 0)
# Second qresult (5S, multiple hits)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 3)
self.assertEqual(qresult.id, "5S_rRNA")
self.assertEqual(qresult.seq_len, 119)
self.assertEqual(qresult.accession, "RF00001")
self.assertEqual(qresult.description, "5S ribosomal RNA")
self.assertEqual(qresult.program, "cmsearch")
self.assertEqual(qresult.version, "1.1.4")
self.assertEqual(qresult.target, "GCA_000146045.2.fasta")
# first hit
hit = qresult[0]
self.assertEqual(len(hit), 6)
self.assertEqual(hit.id, "ENA|BK006945|BK006945.2")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence.",
)
self.assertEqual(hit.query_id, "5S_rRNA")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.52)
self.assertEqual(hsp.evalue, 1.6e-18)
self.assertEqual(hsp.bitscore, 88.8)
self.assertEqual(hsp.bias, 0.0)
self.assertTrue(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 119)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 459676)
self.assertEqual(hsp.hit_end, 459796)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.99)
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 119)
self.assertEqual(frag.hit_start, 459676)
self.assertEqual(frag.hit_end, 459796)
self.assertEqual(frag.hit_strand, 0)
self.assertEqual(
frag.query.seq,
"gccuGcggcCAUAccagcgcgaAagcACcgGauCCCAUCcGaACuCc-gAAguUAAGcgcgcUugggCcagggUA-GUAcuagGaUGgGuGAcCuCcUGggAAgaccagGugccgCaggcc",
)
self.assertEqual(
frag.hit.seq,
"GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACuGUAGUUAAGCUGGUAAGAGCCUGACCGaGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU",
)
self.assertEqual(
frag.aln_annotation["PP"],
"***********************************************99***********************8756***************************9*****************",
)
self.assertEqual(
frag.aln_annotation["NC"],
" vv vv ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"(((((((((,,,,<<-<<<<<---<<--<<<<<<______>>-->>>.>-->>---->>>>>-->><<<-<<---.-<-<<-----<<____>>----->>->-->>->>>))))))))):",
)
self.assertEqual(
frag.aln_annotation["similarity"],
"G::UGC:GCCAUA:C :C::GAAAGCACCG :UCCC+UCCGA C: C G AGUUAAGC::G: +G:GCC G: GUA + +UGGGUGACC+ G AA :CAGGUGC:GCA::C+",
)
# last hit
hsp = hit[-1]
hit = qresult[-1]
self.assertEqual(len(hit), 1)
self.assertEqual(hit.id, "ENA|BK006947|BK006947.3")
self.assertEqual(
hit.description,
"TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.",
)
self.assertEqual(hit.query_id, "5S_rRNA")
hsp = hit[0]
self.assertEqual(len(hsp), 1)
self.assertEqual(hsp.model, "cm")
self.assertEqual(hsp.truncated, "no")
self.assertEqual(hsp.gc, 0.41)
self.assertEqual(hsp.evalue, 6.6)
self.assertEqual(hsp.bitscore, 16.7)
self.assertEqual(hsp.bias, 0.3)
self.assertFalse(hsp.is_included)
self.assertEqual(hsp.query_start, 1)
self.assertEqual(hsp.query_end, 119)
self.assertEqual(hsp.query_endtype, "[]")
self.assertEqual(hsp.hit_start, 6968)
self.assertEqual(hsp.hit_end, 7085)
self.assertEqual(hsp.hit_endtype, "..")
self.assertEqual(hsp.avg_acc, 0.91)
frag = hsp[0]
self.assertEqual(frag.query_start, 1)
self.assertEqual(frag.query_end, 119)
self.assertEqual(frag.hit_start, 6968)
self.assertEqual(frag.hit_end, 7085)
self.assertEqual(frag.hit_strand, -1)
self.assertEqual(
frag.query.seq,
"gccuGcggcCAUAccagc-gcg-aAagcACcgGa-uCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGaUGgGuGAcCuCcUGggAAgaccagGu-gccgCaggcc",
)
self.assertEqual(
frag.hit.seq,
"GAGAUGGUAUAUACUGUAgCAUcCGUGUACGUAUgACCGAUCAGA--AUACAAGUGAAGGUGAGUAUGGCAUGUG--GUAGUGGGAUUAGAG-UGGUAGGGUAAGUAUAUGUgUAUUAUUUAC",
)
self.assertEqual(
frag.aln_annotation["PP"],
"**************976325541459999****989999999999..89**********9999999*********..**********99988.689999************************",
)
self.assertEqual(
frag.aln_annotation["NC"],
"v v v v v v v v ",
)
self.assertEqual(
frag.aln_annotation["CS"],
"(((((((((,,,,<<-<<.<<<.---<<--<<<<.<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<-----<<____>>----->>->-->>->>>.))))))))):",
)
self.assertEqual(
frag.aln_annotation["similarity"],
" : :: ::: AUAC + :: G:AC:::: CC AUC+G ::::AA:U AAG :: U+ GGC: :G GUA U+GGAU :G G : GG AAG+: A:GU ::: :: : C",
)
# third qresult (U2, multiple hits)
qresult, count = next_result(qresults, counter)
self.assertEqual(len(qresult), 5)
# test if we've properly finished iteration
self.assertRaises(StopIteration, next, qresults)
self.assertEqual(3, count)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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