#! /usr/bin/env python
#
# test_blast_xml.py
#
__author__ = "Kristian Rother"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Micah Hamady"]
__credits__ = ["Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Kristian Rother"
__email__ = "krother@rubor.de"
__status__ = "Prototype"
from cogent.util.unit_test import main, TestCase
from cogent.parse.blast_xml import BlastXMLResult, MinimalBlastParser7,\
get_tag, parse_hsp, parse_hit, parse_header, parse_parameters,\
HSP_XML_FIELDNAMES, HIT_XML_FIELDNAMES
import xml.dom.minidom
class GetTagTests(TestCase):
"""Tests for the auxiliary function evaluating the tag objects."""
def setUp(self):
self.single_tag = xml.dom.minidom.parseString(\
"<outer>bla <inner>content</inner>bla</outer>")
self.double_tag = xml.dom.minidom.parseString(\
"<outer><inner>first content</inner><inner>second content</inner></outer>")
self.empty_tag = xml.dom.minidom.parseString("<outer></outer>")
def test_get_tag_works(self):
self.assertEqual(get_tag(self.single_tag,'inner'),'content')
self.assertEqual(get_tag(self.double_tag,'inner'),'first content')
self.assertEqual(get_tag(self.empty_tag,'inner'),None)
self.assertEqual(get_tag(self.empty_tag,'inner', 'blue elephant'),\
'blue elephant')
self.assertEqual(get_tag(self.single_tag,'non-existing tag'),None)
self.assertEqual(get_tag(self.single_tag,'non-existing tag',\
'pink elephant'),'pink elephant')
self.assertEqual(get_tag(self.single_tag,'inner'),'content')
def test_get_tag_fail(self):
"""Make sure the tag and name parameters are in the proper types."""
self.assertRaises(AttributeError, get_tag,None,"h1")
self.assertRaises(AttributeError, get_tag,\
"<h1>This is not a XML tag object</h1>","h1")
class MinimalBlastParser7Tests(TestCase):
"""Tests for the functions required by the Blast XML parsers."""
def setUp(self):
self.hit1 = xml.dom.minidom.parseString(HIT_WITH_ONE_HSP)
self.hit2 = xml.dom.minidom.parseString(HIT_WITH_TWO_HSPS)
self.hsp1 = xml.dom.minidom.parseString(HSP_ONE)
self.hsp2 = xml.dom.minidom.parseString(HSP_TWO)
self.hsp_gaps = xml.dom.minidom.parseString(HSP_WITH_GAPS)
self.param = xml.dom.minidom.parseString(PARAM_XML)
self.header = xml.dom.minidom.parseString(HEADER_XML)
self.complete = xml.dom.minidom.parseString(HEADER_COMPLETE)
def test_parse_header(self):
"""Fields from XML header tag should be available as dict."""
data = parse_header(self.header)
self.assertEqual(data.get('application'), 'my Grandma')
self.assertEqual(data.get('version'), 'has')
self.assertEqual(data.get('reference'), 'furry')
self.assertEqual(data.get('query_letters'), 27)
self.assertEqual(data.get('database'), 'Cats')
def test_parse_parameters(self):
"""Fields from XML parameter tag should be available as dict."""
data = parse_parameters(self.param)
self.assertEqual(data.get('matrix'), 'BLOSUM62')
self.assertEqual(data.get('expect'), '10')
self.assertEqual(data.get('gap_open_penalty'), 11.1)
self.assertEqual(data.get('gap_extend_penalty'), 22.2)
self.assertEqual(data.get('filter'), 'F')
def test_parse_header_complete(self):
"""Fields from header+param tag should be available as dict."""
# try to process header with parameters etc in the XML
data = parse_header(self.complete)
self.assertEqual(data.get('database'), 'Cats')
self.assertEqual(data.get('matrix'), 'BLOSUM62')
def test_parse_hit(self):
"""Should return a list with all values for a hit+hsp."""
data = parse_hit(self.hit1)
self.assertEqual(len(data),1)
d = dict(zip(HIT_XML_FIELDNAMES,data[0]))
self.assertEqual(d['SUBJECT_ID'],"gi|148670104|gb|EDL02051.1|")
self.assertEqual(d['HIT_DEF'],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]")
self.assertEqual(d['HIT_ACCESSION'],"2001")
self.assertEqual(int(d['HIT_LENGTH']),707)
# check hit with more HSPs
data = parse_hit(self.hit2)
self.assertEqual(len(data),2)
self.assertNotEqual(data[0],data[1])
def test_parse_hsp(self):
"""Should return list with all values for a hsp."""
data = parse_hsp(self.hsp1)
d = dict(zip(HSP_XML_FIELDNAMES,data))
self.assertEqual(float(d['BIT_SCORE']),1023.46)
self.assertEqual(float(d['SCORE']),2645)
self.assertEqual(float(d['E_VALUE']),0.333)
self.assertEqual(int(d['QUERY_START']),4)
self.assertEqual(int(d['QUERY_END']),18)
self.assertEqual(int(d['SUBJECT_START']),5)
self.assertEqual(int(d['SUBJECT_END']),19)
self.assertEqual(int(d['GAP_OPENINGS']),0)
self.assertEqual(int(d['ALIGNMENT_LENGTH']),14)
self.assertEqual(d['QUERY_ALIGN'],'ELEPHANTTHISISAHITTIGER')
self.assertEqual(d['MIDLINE_ALIGN'],'ORCA-WHALE')
self.assertEqual(d['SUBJECT_ALIGN'],'SEALSTHIS---HIT--GER')
class BlastXmlResultTests(TestCase):
"""Tests parsing of output of Blast with output mode 7 (XML)."""
def setUp(self):
self.result = BlastXMLResult(COMPLETE_XML,xml=True)
def test_options(self):
"""Constructor should take parser as an option."""
result = BlastXMLResult(COMPLETE_XML,parser=MinimalBlastParser7)
self.assertEqual(len(result.keys()),1)
# make sure whether normal Blast parser still works upon code merge!
def test_parsed_query_sequence(self):
"""The result dict should have one query sequence as a key."""
# The full query sequence is not given in the XML file.
# Thus it is not checked explicitly, only whether there is
# exactly one found.
self.assertEqual(len(self.result.keys()),1)
def test_parsed_iterations(self):
"""The result should have the right number of iterations."""
n_iter = 0
for query_id,hits in self.result.iterHitsByQuery():
n_iter += 1
self.assertEqual(n_iter,1)
def test_parsed_hsps(self):
"""The result should have the right number of hsps."""
n_hsps = 0
for query_id,hsps in self.result.iterHitsByQuery():
n_hsps += len(hsps)
self.assertEqual(n_hsps,3)
def test_parse_hit_details(self):
"""The result should have data from hit fields."""
for query in self.result:
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['SUBJECT_ID'],
"gi|148670104|gb|EDL02051.1|")
self.assertEqual(first_hsp['HIT_DEF'],
"insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]")
self.assertEqual(first_hsp['HIT_ACCESSION'],"2001")
self.assertEqual(first_hsp['HIT_LENGTH'],707)
def test_parse_hsp_details(self):
"""The result should have data from hsp fields."""
for query in self.result:
# should check integers in next version.
first_hsp = self.result[query][0][0]
self.assertEqual(first_hsp['QUERY ID'],1)
self.assertEqual(first_hsp['BIT_SCORE'],'1023.46')
self.assertEqual(first_hsp['SCORE'],'2645')
self.assertEqual(first_hsp['E_VALUE'],'0.333')
self.assertEqual(first_hsp['QUERY_START'],'4')
self.assertEqual(first_hsp['QUERY_END'],'18')
self.assertEqual(first_hsp['QUERY_ALIGN'],'ELEPHANTTHISISAHITTIGER')
self.assertEqual(first_hsp['MIDLINE_ALIGN'],'ORCA-WHALE')
self.assertEqual(first_hsp['SUBJECT_ALIGN'],'SEALSTHIS---HIT--GER')
self.assertEqual(first_hsp['SUBJECT_START'],'5')
self.assertEqual(first_hsp['SUBJECT_END'],'19')
self.assertEqual(first_hsp['PERCENT_IDENTITY'],'55')
self.assertEqual(first_hsp['POSITIVE'],'555')
self.assertEqual(first_hsp['GAP_OPENINGS'],0)
self.assertEqual(first_hsp['ALIGNMENT_LENGTH'],'14')
gap_hsp = self.result[query][0][1]
self.assertEqual(gap_hsp['GAP_OPENINGS'],'33')
HSP_XML = """
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>1023.46</Hsp_bit-score>
<Hsp_score>2645</Hsp_score>
<Hsp_evalue>0.333</Hsp_evalue>
<Hsp_query-from>4</Hsp_query-from>
<Hsp_query-to>18</Hsp_query-to>
<Hsp_hit-from>5</Hsp_hit-from>
<Hsp_hit-to>19</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
%s
<Hsp_positive>555</Hsp_positive>
<Hsp_align-len>14</Hsp_align-len>
<Hsp_qseq>ELEPHANTTHISISAHITTIGER</Hsp_qseq>
<Hsp_hseq>SEALSTHIS---HIT--GER</Hsp_hseq>
<Hsp_midline>ORCA-WHALE</Hsp_midline>
</Hsp>
"""
HSP_ONE = HSP_XML%''
HSP_WITH_GAPS = HSP_XML%'<Hsp_gaps>33</Hsp_gaps>'
HSP_TWO = """
<Hsp>
<Hsp_num>2</Hsp_num>
<Hsp_bit-score>1023.46</Hsp_bit-score>
<Hsp_score>2645</Hsp_score>
<Hsp_evalue>0.333</Hsp_evalue>
<Hsp_query-from>6</Hsp_query-from>
<Hsp_query-to>22</Hsp_query-to>
<Hsp_hit-from>5</Hsp_hit-from>
<Hsp_hit-to>23</Hsp_hit-to>
<Hsp_query-frame>1</Hsp_query-frame>
<Hsp_hit-frame>1</Hsp_hit-frame>
<Hsp_identity>55</Hsp_identity>
%s
<Hsp_positive>555</Hsp_positive>
<Hsp_align-len>18</Hsp_align-len>
<Hsp_qseq>EPHANT---THISISAHIT-TIGER</Hsp_qseq>
<Hsp_hseq>ALSWWWTHIS---HITW--GER</Hsp_hseq>
<Hsp_midline>ORCA-WHALE</Hsp_midline>
</Hsp>
"""
HIT_XML = """
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|148670104|gb|EDL02051.1|</Hit_id>
<Hit_def>insulin-like growth factor 2 receptor, isoform CRA_c [Mus musculus]</Hit_def>
<Hit_accession>2001</Hit_accession>
<Hit_len>707</Hit_len>
<Hit_hsps>
%s
</Hit_hsps>
</Hit>
"""
HIT_WITH_ONE_HSP = HIT_XML%HSP_ONE
HIT_WITH_TWO_HSPS = HIT_XML%(HSP_WITH_GAPS+HSP_TWO)
PARAM_XML = """
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11.1</Parameters_gap-open>
<Parameters_gap-extend>22.2</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
"""
HEADER_XML = """
<BlastOutput>
<BlastOutput_program>my Grandma</BlastOutput_program>
<BlastOutput_version>has</BlastOutput_version>
<BlastOutput_db>Cats</BlastOutput_db>
<BlastOutput_reference>furry</BlastOutput_reference>
<BlastOutput_query-len>27</BlastOutput_query-len>
%s
</BlastOutput>
"""
HIT_PREFIX = """
<BlastOutput_iterations>
<Iteration>
<Iteration_hits>
"""
HIT_SUFFIX = """
</Iteration_hits>
</Iteration>
</BlastOutput_iterations>
"""
HEADER_COMPLETE=HEADER_XML%(PARAM_XML+HIT_PREFIX+HIT_WITH_ONE_HSP+\
HIT_WITH_TWO_HSPS+HIT_SUFFIX)
COMPLETE_XML = """<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
"""+HEADER_COMPLETE
if __name__ == '__main__':
main()
