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Added tabular format indexer and related tests
This commit is contained in:
Samuel Prince
committed by
Wibowo Arindrarto
Wibowo Arindrarto
parent
10e37cecc3
commit
361870aa9d
@ -7,6 +7,7 @@
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from .infernal_tab import InfernalTabParser
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from .infernal_tab import InfernalTabIndexer
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from .infernal_text import InfernalTextParser
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@ -43,3 +43,4 @@ class _BaseInfernalParser:
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setattr(hit, attr, value)
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hit_list.append(hit)
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return hit_list
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@ -17,7 +17,7 @@ from Bio.SearchIO.HmmerIO import Hmmer3TabParser
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from ._base import _BaseInfernalParser
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__all__ = ("InfernalTabParser")
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__all__ = ("InfernalTabParser", "InfernalTabIndexer")
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# tabular format column names
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@ -251,6 +251,97 @@ class InfernalTabParser(_BaseInfernalParser):
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self.line = self.handle.readline()
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class InfernalTabIndexer(SearchIndexer):
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"""Indexer class for Infernal tabular output."""
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_parser = InfernalTabParser
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def __iter__(self):
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"""Iterate over the file handle; yields key, start offset, and length."""
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handle = self._handle
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handle.seek(0)
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qresult_key = None
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query_id_idx = None
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# mark for the comments
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comment_mark = b"#"
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# mark for the row names line
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row_names_mark = b"#target name"
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row_names_mark_fmt_2 = b"#idx"
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split_mark = b" "
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# set line with initial mock value, to emulate header
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line = comment_mark
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# read through header and get the query index position based on the
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# tabular output format
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while line.startswith(comment_mark):
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start_offset = handle.tell()
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line = handle.readline()
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if line.startswith(row_names_mark):
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query_id_idx = 2
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elif line.startswith(row_names_mark_fmt_2):
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query_id_idx = 3
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assert query_id_idx is not None
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# handle empty file
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if not line:
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return
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# index the qresults
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while True:
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# get end offset here since we only know a qresult ends after
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# encountering the next one
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end_offset = handle.tell()
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# process the previous line
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cols = [x for x in line.strip().split(split_mark) if x]
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if qresult_key is None:
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qresult_key = cols[query_id_idx]
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else:
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curr_key = cols[query_id_idx]
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if curr_key != qresult_key:
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adj_end = end_offset - len(line)
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yield (qresult_key.decode(), start_offset, adj_end - start_offset)
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qresult_key = curr_key
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start_offset = adj_end
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line = handle.readline()
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if not line or line.startswith(comment_mark):
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yield (qresult_key.decode(), start_offset, end_offset - start_offset)
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break
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def get_raw(self, offset):
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"""Return the raw bytes string of a QueryResult object from the given offset."""
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handle = self._handle
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handle.seek(offset)
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query_id_idx = 2
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qresult_key = None
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qresult_raw = b""
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split_mark = b" "
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comment_mark = b"#"
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while True:
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line = handle.readline()
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if not line or line.startswith(comment_mark):
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break
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cols = [x for x in line.strip().split(split_mark) if x]
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if qresult_key is None:
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qresult_key = cols[query_id_idx]
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else:
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curr_key = cols[query_id_idx]
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if curr_key != qresult_key:
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break
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qresult_raw += line
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return qresult_raw
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# if not used as a module, run the doctest
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if __name__ == "__main__":
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from Bio._utils import run_doctest
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@ -245,7 +245,6 @@ _INDEXER_MAP = {
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"hmmscan3-domtab": ("HmmerIO", "Hmmer3DomtabHmmhitIndexer"),
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"hmmsearch3-domtab": ("HmmerIO", "Hmmer3DomtabHmmqueryIndexer"),
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"infernal-tab": ("InfernalIO", "InfernalTabIndexer"),
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"infernal-text": ("InfernalIO", "InfernalTextIndexer"),
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"phmmer3-domtab": ("HmmerIO", "Hmmer3DomtabHmmqueryIndexer"),
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}
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@ -18,59 +18,58 @@ from search_tests_common import CheckRaw
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class InfernalTabRawCases(CheckRaw):
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fmt = "infernal-tab"
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def test_infernal_tab_single(self):
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"""Test infernal-tab raw string retrieval, cmsearch, single query (U2_Yeast)."""
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filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast.tbl")
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raw = """#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
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#---------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
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ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 5.9e-20 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
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"""Test infernal-tab raw string retrieval, cmsearch, single query."""
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filename = os.path.join("Infernal", "U2_Yeast-threshold.tbl")
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raw = """ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 5.9e-20 ! TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
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"""
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self.check_raw(filename, "U2", raw)
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def test_infernal_tab_multiple_first(self):
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def test_infernal_tab_multiple(self):
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"""Test infernal-tab raw string retrieval, cmsearch, single query, multiple non-consecutive hits."""
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filename = os.path.join("Infernal", "U2_Yeast-shuf.tbl")
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raw = """ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.3e-20 ! -
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ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 737498 737324 - no 1 0.39 0.0 19.8 0.11 ? -
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ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 1370418 1370563 + no 1 0.34 0.1 15.6 1.1 ? -
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ENA|BK006936|BK006936.2 - U2 RF00004 cm 1 193 1079243 1079392 + no 1 0.39 0.0 15.3 1.3 ? -
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ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 425490 425693 + no 1 0.34 0.9 13.7 3.1 ? -
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ENA|BK006948|BK006948.2 - U2 RF00004 cm 1 193 1073786 1073950 + no 1 0.33 0.5 11.9 8.3 ? -
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"""
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self.check_raw(filename, "U2", raw)
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def test_infernal_tab_single_first(self):
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"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, first."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
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raw = """#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
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#------------------- --------- ----------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
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U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 52929 53083 + no 1 0.44 0.0 13.5 0.91 ? U2 spliceosomal RNA
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filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
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raw = """U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 52929 53083 + no 1 0.44 0.0 13.5 0.91 ? U2 spliceosomal RNA
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U2 RF00004 ENA|BK006935|BK006935.2 - cm 1 193 196571 196389 - no 1 0.33 5.3 12.8 1.3 ? U2 spliceosomal RNA
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"""
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self.check_raw(filename, "ENA|BK006935|BK006935.2", raw)
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def test_infernal_tab_multiple_middle(self):
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"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, middle."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
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raw = """#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
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#------------------- --------- ----------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
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U2 RF00004 ENA|BK006936|BK006936.2 - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! U2 spliceosomal RNA
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filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
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raw = """U2 RF00004 ENA|BK006936|BK006936.2 - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! U2 spliceosomal RNA
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"""
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self.check_raw(filename, "ENA|BK006936|BK006936.2", raw)
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def test_infernal_tab_multiple_last(self):
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"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, last."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
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raw = """#target name accession query name accession mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc description of target
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#------------------- --------- ----------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
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5S_rRNA RF00001 ENA|BK006937|BK006937.2 - cm 1 119 761 644 - no 1 0.41 0.3 14.1 2.4 ? 5S ribosomal RNA
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filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
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raw = """5S_rRNA RF00001 ENA|BK006937|BK006937.2 - cm 1 119 761 644 - no 1 0.41 0.3 14.1 2.4 ? 5S ribosomal RNA
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U2 RF00004 ENA|BK006937|BK006937.2 - cm 1 193 229986 229885 - no 1 0.32 0.1 11.1 4.7 ? U2 spliceosomal RNA
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"""
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self.check_raw(filename, "ENA|BK006937|BK006937.2", raw)
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def test_infernal_tab_multiple_fmt_2(self):
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"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, fmt 2."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast_fmt_2.tbl")
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raw = """#idx target name accession query name accession clan name mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc olp anyidx afrct1 afrct2 winidx wfrct1 wfrct2 mdl len seq len description of target
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#--- -------------------- --------- ----------------------- --------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- --- ------ ------ ------ ------ ------ ------ ------- ------- ---------------------
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1 U2 RF00004 ENA|BK006936|BK006936.2 - - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! * - - - - - - 193 813184 U2 spliceosomal RNA
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"""
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self.check_raw(filename, "ENA|BK006936|BK006936.2", raw, fmt=2)
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def test_infernal_tab_multiple_fmt_2_infer(self):
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"""Test infernal-tab raw string retrieval, cmsearch, multiple queries, fmt 2, inferred."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast_fmt_2.tbl")
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raw = """#idx target name accession query name accession clan name mdl mdl from mdl to seq from seq to strand trunc pass gc bias score E-value inc olp anyidx afrct1 afrct2 winidx wfrct1 wfrct2 mdl len seq len description of target
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#--- -------------------- --------- ----------------------- --------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- --- ------ ------ ------ ------ ------ ------ ------- ------- ---------------------
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1 U2 RF00004 ENA|BK006936|BK006936.2 - - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! * - - - - - - 193 813184 U2 spliceosomal RNA
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filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan-fmt_2.tbl")
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raw = """1 U2 RF00004 ENA|BK006936|BK006936.2 - - cm 1 193 681858 681747 - no 1 0.33 0.1 98.7 1.2e-20 ! * - - - - - - 193 813184 U2 spliceosomal RNA
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"""
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self.check_raw(filename, "ENA|BK006936|BK006936.2", raw)
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@ -78,24 +77,28 @@ U2 RF00004 ENA|BK006937|BK006937.2 - cm 1
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class InfernalTabIndexCases(CheckIndex):
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fmt = "infernal-tab"
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def test_infernal_tab_1q(self):
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"""Test infernal-tab indexing, cmsearch, one query, one hit."""
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filename = os.path.join("Infernal", "cmsearch_114_U2_Yeast.tbl")
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def test_infernal_tab_single(self):
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"""Test infernal-tab indexing, cmsearch, single query."""
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filename = os.path.join("Infernal", "U2_Yeast-threshold.tbl")
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self.check_index(filename, self.fmt)
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def test_infernal_tab_1q_0m(self):
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"""Test infernal-tab indexing, cmsearch, single query, no hits."""
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filename = os.path.join("Infernal", "cmsearch_114_IRES_Yeast.tbl")
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def test_infernal_tab_single_no_hit(self):
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"""Test infernal-tab indexing, cmsearch, single query."""
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filename = os.path.join("Infernal", "IRES_Yeast.tbl")
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self.check_index(filename, self.fmt)
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def test_infernal_tab_1q_mm(self):
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"""Test infernal-tab indexing, cmsearch, single query, multiple hits."""
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filename = os.path.join("Infernal", "cmsearch_114_5S_Yeast.tbl")
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def test_infernal_tab_single_multiple_hit(self):
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"""Test infernal-tab indexing, cmsearch, single query."""
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filename = os.path.join("Infernal", "5S_Yeast.tbl")
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self.check_index(filename, self.fmt)
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def test_infernal_tab_mq_mm(self):
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"""Test infernal-tab indexing, cmscan, multiple query, multiple matches."""
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filename = os.path.join("Infernal", "cmscan_115_IRES_5S_U2_Yeast.tbl")
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def test_infernal_tab_multiple_multiple_hit(self):
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"""Test infernal-tab indexing, cmscan, multiple query."""
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filename = os.path.join("Infernal", "IRES_5S_U2_Yeast-cmscan.tbl")
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self.check_index(filename, self.fmt)
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