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adding test, handling duplicate hits, handling dbxrefs, and calculating aln_span
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azneto
committed by
Wibowo Arindrarto
Wibowo Arindrarto
parent
dce9f54939
commit
d94c47c4c4
@ -1,13 +1,27 @@
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"""Test."""
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"""Bio.SearchIO parser for InterProScan XML output formats."""
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# for more info: https://github.com/ebi-pf-team/interproscan/wiki/OutputFormats
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import sys
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import re
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from Bio.Alphabet import generic_protein
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from Bio.SearchIO._model import QueryResult, Hit, HSP, HSPFragment
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from xml.etree import cElementTree as ElementTree
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# For speed try to use cElementTree rather than ElementTree
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try:
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if (3, 0) <= sys.version_info[:2] <= (3, 1):
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# Workaround for bug in python 3.0 and 3.1,
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# see http://bugs.python.org/issue9257
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from xml.etree import ElementTree as ElementTree
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else:
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from xml.etree import cElementTree as ElementTree
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except ImportError:
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from xml.etree import ElementTree as ElementTree
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# element - hit attribute name mapping
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_ELEM_HIT = {
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'name': ('id', str),
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'ac': ('accession', str),
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'name': ('accession', str),
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'ac': ('id', str),
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'desc': ('description', str),
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'library': ('target', str),
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'version': ('target_version', str),
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@ -44,7 +58,7 @@ class InterproXmlParser(object):
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"""Parse the header for the InterProScan version."""
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event, elem = next(self.xml_iter)
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meta = dict()
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meta['target'] = 'Interpro'
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meta['target'] = 'InterPro'
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meta['program'] = 'InterProScan'
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meta['version'] = elem.attrib['interproscan-version']
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# store the namespace value
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@ -65,8 +79,20 @@ class InterproXmlParser(object):
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query_desc = xref.attrib['name']
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# parse each hit
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hit_list = [hit for hit in self._parse_hit(
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elem.find(self.NS + 'matches'), query_id, query_seq)]
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hit_list = []
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for hit_new in self._parse_hit(
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elem.find(self.NS + 'matches'), query_id, query_seq):
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# interproscan results contain duplicate hits rather than
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# a single hit with multiple hsps. In this case the hsps
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# of a duplicate hit will be appended to the already
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# existing hit
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for hit in hit_list:
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if hit.id == hit_new.id:
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for hsp in hit_new.hsps:
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hit.hsps.append(hsp)
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break
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else:
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hit_list.append(hit_new)
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# create qresult and assing attributes
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qresult = QueryResult(hit_list, query_id)
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@ -86,22 +112,24 @@ class InterproXmlParser(object):
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signature = hit_elem.find(self.NS + 'signature')
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hit_id = signature.attrib['ac']
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# store alt_ids and alt_descs
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alt_ids, alt_descs = self._parse_alt_ids(
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# store xrefs and alt_descs
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xrefs = self._parse_xrefs(
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signature.find(self.NS + 'entry'))
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# parse each hsp
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hsps = [hsp for hsp in self._parse_hsp(
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hit_elem.find(self.NS + 'locations'), query_id, hit_id, query_seq)]
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hit_elem.find(self.NS + 'locations'),
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query_id, hit_id, query_seq)]
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# create hit and assign attributes
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hit = Hit(hsps, hit_id)
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# setattr(hit, '_id_alt', alt_ids)
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setattr(hit, 'dbxrefs', xrefs)
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for key, (attr, caster) in _ELEM_HIT.items():
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value = signature.attrib.get(key)
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if value is not None:
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setattr(hit, attr, caster(value))
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signature_lib = signature.find(self.NS + 'signature-library-release')
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signature_lib = signature.find(
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self.NS + 'signature-library-release')
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for key, (attr, caster) in _ELEM_HIT.items():
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value = signature_lib.attrib.get(key)
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if value is not None:
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@ -127,7 +155,14 @@ class InterproXmlParser(object):
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# start should be 0-based
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if attr.endswith('start'):
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value = caster(value) - 1
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# store query start and end to calculate aln_span
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if attr == 'query_start':
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start = int(value)
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if attr == 'query_end':
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end = int(value)
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setattr(frag, attr, caster(value))
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# calculate aln_span and store
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setattr(frag, 'aln_span', end - start)
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# create hsp and assign attributes
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hsp = HSP([frag])
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@ -139,34 +174,30 @@ class InterproXmlParser(object):
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setattr(hsp, attr, caster(value))
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yield hsp
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def _parse_alt_ids(self, root_entry_elem):
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def _parse_xrefs(self, root_entry_elem):
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"""Parse xrefs."""
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alt_ids, alt_descs = [], []
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xrefs = []
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# store entry id and description
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if root_entry_elem is not None:
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alt_ids.append(root_entry_elem.attrib['ac'])
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if (root_entry_elem.attrib['name'] is not None or
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root_entry_elem.attrib['desc'] is not None):
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alt_descs.append('%s %s %s' % (
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root_entry_elem.attrib['ac'],
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root_entry_elem.attrib.get('name'),
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root_entry_elem.attrib.get('desc')))
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xrefs.append('IPR:' + root_entry_elem.attrib['ac'])
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# store go-xrefs and pathway-refs id and description
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if root_entry_elem is not None:
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alt_elem = []
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alt_elem = alt_elem + root_entry_elem.findall(
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xref_elems = []
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xref_elems = xref_elems + root_entry_elem.findall(
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self.NS + 'go-xref')
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alt_elem = alt_elem + root_entry_elem.findall(
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xref_elems = xref_elems + root_entry_elem.findall(
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self.NS + 'pathway-xref')
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for entry in alt_elem:
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if entry.attrib['id'] is not None:
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alt_ids.append(entry.attrib['id'])
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if (entry.attrib['name'] is not None or
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entry.attrib['category'] is not None):
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alt_descs.append('%s %s [%s]' % (
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entry.attrib['id'],
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entry.attrib.get('name'),
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entry.attrib.get('db')))
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return alt_ids, alt_descs
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for entry in xref_elems:
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xref = entry.attrib['id']
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if ':' not in xref:
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xref = entry.attrib['db'] + ':' + xref
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xrefs.append(xref)
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return xrefs
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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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run_doctest()
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@ -124,8 +124,9 @@ class Hit(_BaseSearchObject):
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self._description = None
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self._description_alt = []
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self._query_description = None
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self.target = '<unknown target>'
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self.target_version = '<unknown target version>'
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self.target = None
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self.target_version = None
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self.dbxrefs = []
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# TODO - Move this into the for look below in case
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# hsps is a single use iterator?
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@ -186,7 +187,13 @@ class Hit(_BaseSearchObject):
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lines.append(hid_line)
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# set target line
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lines.append(' Target: %s %s' % (self.target, self.target_version))
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if self.target is not None:
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lines.append(' Target: %s %s' % (self.target, self.target_version))
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# set dbxrefs line
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if self.dbxrefs:
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lines.append("Database cross-references: " +
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", ".join(self.dbxrefs))
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# set hsp line and table
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if not self.hsps:
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@ -92,6 +92,14 @@
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<mobidblite-location start="136" end="158"/>
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</locations>
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</mobidblite-match>
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<mobidblite-match>
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<signature ac="mobidb-lite" desc="consensus disorder prediction" name="disorder_prediction">
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<signature-library-release library="MOBIDB_LITE" version="1.0"/>
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</signature>
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<locations>
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<mobidblite-location start="36" end="58"/>
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</locations>
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</mobidblite-match>
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<superfamilyhmmer3-match evalue="2.48E-35">
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<signature ac="SSF47113" name="Histone-fold">
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<entry ac="IPR009072" desc="Histone-fold" name="Histone-fold" type="HOMOLOGOUS_SUPERFAMILY">
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@ -34,82 +34,41 @@ class BlastnXmlCases(unittest.TestCase):
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qresult = next(qresults)
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counter += 1
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self.assertEqual('2.2.12', qresult.version)
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self.assertEqual(10.0, qresult.param_evalue_threshold)
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self.assertEqual(1, qresult.param_score_match)
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self.assertEqual(-3, qresult.param_score_mismatch)
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self.assertEqual(5, qresult.param_gap_open)
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self.assertEqual(2, qresult.param_gap_extend)
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self.assertEqual('5.26-65.0', qresult.version)
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# test parsed values of qresult
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self.assertEqual('gi|1348916|gb|G26684.1|G26684', qresult.id)
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self.assertEqual('human STS STS_D11570, sequence tagged site',
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self.assertEqual('AT5G23090.4', qresult.id)
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self.assertEqual('pacid=19665592 transcript=AT5G23090.4 locus=AT5G23090 ID=AT5G23090.4.TAIR10 annot-version=TAIR10',
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qresult.description)
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self.assertEqual(285, qresult.seq_len)
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self.assertEqual(371021, qresult.stat_db_num)
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self.assertEqual(1233631384, qresult.stat_db_len)
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self.assertEqual(0, qresult.stat_eff_space)
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self.assertEqual(0.710603, qresult.stat_kappa)
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self.assertEqual(1.37406, qresult.stat_lambda)
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self.assertEqual(1.30725, qresult.stat_entropy)
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self.assertEqual(2, len(qresult))
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self.assertEqual(4, len(qresult))
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hit = qresult[0]
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self.assertEqual('gi|9950606|gb|AE004854.1|', hit.id)
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self.assertEqual('Pseudomonas aeruginosa PAO1, section 415 of 529 of the complete genome', hit.description)
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self.assertEqual(11884, hit.seq_len)
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self.assertEqual(1, len(hit))
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self.assertRaises(IndexError, hit.__getitem__, 1)
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self.assertEqual('PF00808', hit.id)
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self.assertEqual('Histone-like transcription factor (CBF/NF-Y) and archaeal histone', hit.description)
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self.assertEqual('PFAM', hit.target)
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self.assertEqual('31.0', hit.target_version)
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self.assertEqual(2, len(hit))
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hsp = hit.hsps[0]
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self.assertEqual(38.1576, hsp.bitscore)
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self.assertEqual(19, hsp.bitscore_raw)
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self.assertEqual(1.0598, hsp.evalue)
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self.assertEqual(67, hsp.query_start)
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self.assertEqual(86, hsp.query_end)
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self.assertEqual(6011, hsp.hit_start)
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self.assertEqual(6030, hsp.hit_end)
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self.assertEqual(1, hsp.query_frame)
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self.assertEqual(1, hsp.hit_frame)
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self.assertEqual(19, hsp.ident_num)
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self.assertEqual(19, hsp.pos_num)
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self.assertEqual(0, hsp.gap_num)
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self.assertEqual(19, hsp.aln_span)
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self.assertEqual('CAGGCCAGCGACTTCTGGG', str(hsp.query.seq))
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self.assertEqual('CAGGCCAGCGACTTCTGGG', str(hsp.hit.seq))
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self.assertEqual('|||||||||||||||||||', hsp.aln_annotation['similarity'])
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self.assertRaises(IndexError, hit.__getitem__, 1)
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self.assertEqual(76.7, hsp.bitscore)
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self.assertEqual(1.1e-21, hsp.evalue)
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self.assertEqual(13, hsp.query_start)
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self.assertEqual(79, hsp.query_end)
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self.assertEqual(0, hsp.hit_start)
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self.assertEqual(65, hsp.hit_end)
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self.assertEqual(66, hsp.aln_span)
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self.assertEqual('MDPMDIVGKSKEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEEVYAAYEQHKYETMDTQRSVKWNPGAQMTEEEAAAEQQRMFAEARARMNGGVSVPQPEHPETDQRSPQS', str(hsp.query.seq))
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# parse last hit
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hit = qresult[-1]
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self.assertEqual('gi|15073988|emb|AL591786.1|SME591786', hit.id)
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self.assertEqual('Sinorhizobium meliloti 1021 complete chromosome; segment 5/12', hit.description)
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self.assertEqual(299350, hit.seq_len)
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self.assertEqual('SSF47113', hit.id)
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self.assertEqual(1, len(hit))
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self.assertRaises(IndexError, hit.__getitem__, 1)
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self.assertEqual('IPR:IPR009072', hit.dbxrefs[0])
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self.assertEqual('GO:0046982', hit.dbxrefs[1])
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hsp = hit.hsps[0]
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self.assertEqual(36.1753, hsp.bitscore)
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self.assertEqual(18, hsp.bitscore_raw)
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self.assertEqual(4.18768, hsp.evalue)
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self.assertEqual(203, hsp.query_start)
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self.assertEqual(224, hsp.query_end)
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self.assertEqual(83627, hsp.hit_start)
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self.assertEqual(83648, hsp.hit_end)
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self.assertEqual(1, hsp.query_frame)
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self.assertEqual(-1, hsp.hit_frame)
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self.assertEqual(20, hsp.ident_num)
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self.assertEqual(20, hsp.pos_num)
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self.assertEqual(0, hsp.gap_num)
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self.assertEqual(21, hsp.aln_span)
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self.assertEqual('TGAAAGGAAATNAAAATGGAA', str(hsp.query.seq))
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self.assertEqual('TGAAAGGAAATCAAAATGGAA', str(hsp.hit.seq))
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self.assertEqual('||||||||||| |||||||||', hsp.aln_annotation['similarity'])
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self.assertRaises(IndexError, hit.__getitem__, 1)
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# check if we've finished iteration over qresults
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self.assertRaises(StopIteration, next, qresults)
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self.assertEqual(1, counter)
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self.assertEqual(11, hsp.query_start)
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self.assertEqual(141, hsp.query_end)
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if __name__ == "__main__":
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