From a79a6debc7e5b10cbb6887120662eb48a2b7e9d3 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 3 Sep 2015 13:18:09 +0200
Subject: [PATCH] Testing ParseHHBlitsOutput
---
modules/bindings/pymod/hhblits.py | 268 ++++++++++++-------------
modules/bindings/tests/test_hhblits.py | 82 ++++++++
2 files changed, 210 insertions(+), 140 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 98c7d0e4b..0eac983c9 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -32,34 +32,34 @@ class HHblitsHit:
:type: :class:`ost.seq.AlignmentHandle`
.. attribute:: evalue
-
+
The E-value of the alignment
-
+
.. attribute:: prob
-
+
The probability of the alignment (between 0 and 100)
-
+
.. attribute:: score
The alignment score
"""
def __init__(self, hit_id, aln, score, ss_score,evalue, pvalue, prob):
- self.hit_id=hit_id
- self.aln=aln
- self.score=score
- self.ss_score=ss_score
- self.evalue=evalue
- self.prob=prob
- self.pvalue=pvalue
+ self.hit_id = hit_id
+ self.aln = aln
+ self.score = score
+ self.ss_score = ss_score
+ self.evalue = evalue
+ self.prob = prob
+ self.pvalue = pvalue
class HHblitsHeader:
- def __init__(self):
- self.query=''
- self.match_columns=0
- self.n_eff=0
- self.searched_hmms=0
- self.date=None
- self.command=''
+ def __init__(self):
+ self.query = ''
+ self.match_columns = 0
+ self.n_eff = 0
+ self.searched_hmms = 0
+ self.date = None
+ self.command = ''
def ParseHeaderLine(line):
# First, we seek the start of the identifier, that is, the first whitespace
@@ -72,7 +72,6 @@ def ParseHeaderLine(line):
if line[i] == ' ':
break
assert len(line)-i >= 31 and line[i+1] != ' '
- #hit_id=line[split_pos+1:35].strip()
hit_id = line[i+1:i+31].strip()
fields = line[i+32:].split()
prob = float(fields[0])
@@ -80,132 +79,121 @@ def ParseHeaderLine(line):
pvalue = float(fields[2])
score = float(fields[3])
ss_score = float(fields[4])
- # cols = int(fields[5])
offsets = (int(fields[6].split('-')[0]), int(fields[7].split('-')[0]))
- #split_pos=line.find(' ', 3)
- #assert split_pos!=-1 and split_pos<34
- #prob=float(line[35:40].strip())
- #evalue=float(line[41:49].strip())
- #pvalue=float(line[48:57].strip())
- #score=float(line[56:64].strip())
- #ss_score=float(line[63:69].strip())
- #offsets=(int(line[76:79].strip()), int(line[86:89].strip()))
return (HHblitsHit(hit_id, None, score, ss_score, evalue, pvalue, prob), offsets)
def ParseHHblitsOutput(output):
- """
- Parses the HHblits output and returns a tuple of HHblitsHeader and
- a list of HHblitsHit instances.
- """
- lines=iter(output)
- def _ParseHeaderSection(lines):
- value_start_column=14
- date_pattern='%a %b %d %H:%M:%S %Y'
- header=HHblitsHeader()
- line=lines.next()
- assert line.startswith('Query')
- header.query=line[value_start_column:].strip()
- line=lines.next()
- assert line.startswith('Match_columns')
- header.match_columns=int(line[value_start_column:].strip())
-
- line=lines.next()
- assert line.startswith('No_of_seqs')
-
- line=lines.next()
- assert line.startswith('Neff')
- header.n_eff=float(line[value_start_column:].strip())
-
- line=lines.next()
- assert line.startswith('Searched_HMMs')
- header.searched_hmms=int(line[value_start_column:].strip())
-
- line=lines.next()
- assert line.startswith('Date')
- value=line[value_start_column:].strip()
- header.date=datetime.datetime.strptime(value, date_pattern)
-
- line=lines.next()
- assert line.startswith('Command')
- header.command=line[value_start_column:].strip()
-
- line=lines.next()
- assert len(line.strip())==0
- return header
-
- def _ParseTableOfContents(lines):
- assert lines.next().startswith(' No Hit')
- hits=[]
- while True:
- line=lines.next()
- if len(line.strip())==0:
- return hits
- hits.append(ParseHeaderLine(line))
- return hits
- def _ParseResultBody(query_id, hits, lines):
- entry_index=None
- query_str=''
- templ_str=''
- def _MakeAln(query_id, hit_id, query_string, templ_string,
- q_offset, t_offset):
- s1=seq.CreateSequence(query_id, query_string)
- s1.offset=q_offset-1
- s2=seq.CreateSequence(hit_id, templ_string)
- s2.offset=t_offset-1
- return seq.CreateAlignment(s1, s2)
- try:
- while True:
+ """
+ Parses the HHblits output and returns a tuple of HHblitsHeader and
+ a list of HHblitsHit instances.
+ """
+ lines=iter(output)
+ def _ParseHeaderSection(lines):
+ value_start_column = 14
+ date_pattern = '%a %b %d %H:%M:%S %Y'
+ header = HHblitsHeader()
+ line = lines.next()
+ assert line.startswith('Query')
+ header.query=line[value_start_column:].strip()
+ line=lines.next()
+ assert line.startswith('Match_columns')
+ header.match_columns=int(line[value_start_column:].strip())
+
+ line=lines.next()
+ assert line.startswith('No_of_seqs')
+
+ line=lines.next()
+ assert line.startswith('Neff')
+ header.n_eff=float(line[value_start_column:].strip())
+
line=lines.next()
- if len(line.strip())==0:
- continue
- if line.startswith('Done!'):
- if len(query_str)>0:
- hits[entry_index][0].aln=_MakeAln(query_id, hits[entry_index][0].hit_id,
- query_str, templ_str,
- *hits[entry_index][1])
- return [h for h,o in hits]
- if line.startswith('No '):
- if len(query_str)>0:
- hits[entry_index][0].aln=_MakeAln(query_id,
- hits[entry_index][0].hit_id,
- query_str, templ_str,
- *hits[entry_index][1])
- entry_index=int(line[3:].strip())-1
- hits[entry_index][0].hit_id=lines.next()[1:].strip()
- query_str=''
- templ_str=''
- # skip the next line. It doesn't contain information we don't
- # already know
- lines.next()
- continue
- assert entry_index!=None
- if line[1:].startswith(' Consensus'): continue
- if line[1:].startswith(' ss_pred'): continue
- if line[1:].startswith(' ss_conf'): continue
- if line.startswith('T '):
-
- end_pos=line.find(' ', 22)
- assert end_pos!=-1
- templ_str+=line[22:end_pos]
- if line.startswith('Q '):
- end_pos=line.find(' ', 22)
- assert end_pos!=-1
- query_str+=line[22:end_pos]
-
- #hit.aln=seq.CreateAlignment(query_seq, templ_seq)
- except StopIteration:
- if len(query_str)>0:
- hits[entry_index][0].aln=_MakeAln(query_id, hits[entry_index][0].hit_id,
- query_str, templ_str,
- *hits[entry_index][1])
- return [h for h,o in hits]
- header=_ParseHeaderSection(lines)
- # parse the table of contents. This is neccessary as some of the properties
- # (i.e. start of alignment) we need are only given there. From the TOC we
- # create a list of hits that is then further filled with data when we parse
- # the actual result body
- hits=_ParseTableOfContents(lines)
- return header, _ParseResultBody(header.query, hits, lines)
+ assert line.startswith('Searched_HMMs')
+ header.searched_hmms=int(line[value_start_column:].strip())
+
+ line=lines.next()
+ assert line.startswith('Date')
+ value=line[value_start_column:].strip()
+ header.date=datetime.datetime.strptime(value, date_pattern)
+
+ line=lines.next()
+ assert line.startswith('Command')
+ header.command=line[value_start_column:].strip()
+
+ line=lines.next()
+ assert len(line.strip())==0
+ return header
+
+ def _ParseTableOfContents(lines):
+ assert lines.next().startswith(' No Hit')
+ hits=[]
+ while True:
+ line=lines.next()
+ if len(line.strip())==0:
+ return hits
+ hits.append(ParseHeaderLine(line))
+ return hits
+
+ def _ParseResultBody(query_id, hits, lines):
+ entry_index = None
+ query_str = ''
+ templ_str = ''
+ def _MakeAln(query_id, hit_id, query_string, templ_string,
+ q_offset, t_offset):
+ s1=seq.CreateSequence(query_id, query_string)
+ s1.offset=q_offset-1
+ s2=seq.CreateSequence(hit_id, templ_string)
+ s2.offset=t_offset-1
+ return seq.CreateAlignment(s1, s2)
+ try:
+ while True:
+ line=lines.next()
+ if len(line.strip()) == 0:
+ continue
+ if line.startswith('Done!'):
+ if len(query_str)>0:
+ hits[entry_index][0].aln = _MakeAln(\
+ query_id, hits[entry_index][0].hit_id,
+ query_str, templ_str, *hits[entry_index][1])
+ return [h for h,o in hits]
+ if line.startswith('No '):
+ if len(query_str)>0:
+ hits[entry_index][0].aln=_MakeAln(\
+ query_id, hits[entry_index][0].hit_id,
+ query_str, templ_str, *hits[entry_index][1])
+ entry_index=int(line[3:].strip())-1
+ hits[entry_index][0].hit_id=lines.next()[1:].strip()
+ query_str=''
+ templ_str=''
+ # skip the next line. It doesn't contain information we
+ # don't already know
+ lines.next()
+ continue
+ assert entry_index!=None
+ if line[1:].startswith(' Consensus'): continue
+ if line[1:].startswith(' ss_pred'): continue
+ if line[1:].startswith(' ss_conf'): continue
+ if line.startswith('T '):
+ end_pos=line.find(' ', 22)
+ assert end_pos!=-1
+ templ_str+=line[22:end_pos]
+ if line.startswith('Q '):
+ end_pos=line.find(' ', 22)
+ assert end_pos!=-1
+ query_str+=line[22:end_pos]
+ except StopIteration:
+ if len(query_str)>0:
+ hits[entry_index][0].aln=_MakeAln(query_id,
+ hits[entry_index][0].hit_id,
+ query_str, templ_str,
+ *hits[entry_index][1])
+ return [h for h,o in hits]
+ header=_ParseHeaderSection(lines)
+ # parse the table of contents. This is neccessary as some of the properties
+ # (i.e. start of alignment) we need are only given there. From the TOC we
+ # create a list of hits that is then further filled with data when we parse
+ # the actual result body
+ hits=_ParseTableOfContents(lines)
+ return header, _ParseResultBody(header.query, hits, lines)
def ParseHHM(profile):
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 92276d44b..61c4ac0de 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -7,6 +7,7 @@ import sys
import tempfile
import shutil
import filecmp
+import datetime
import ost
from ost import seq
@@ -290,6 +291,87 @@ class TestHHblitsBindings(unittest.TestCase):
'Profile file "testfiles/testali.a3m" is missing '+
'the "Consensus" section')
+ def testParseHHblitsOutput(self):
+ header, hits = hhblits.ParseHHblitsOutput(open("testfiles/test.hhr"))
+ self.assertEqual(header.query, 'Test')
+ self.assertEqual(header.match_columns, 141)
+ self.assertEqual(header.n_eff, 9.4)
+ self.assertEqual(header.searched_hmms, 5)
+ self.assertEqual(header.date,
+ datetime.datetime.strptime('Mon Aug 31 16:45:45 2015',
+ '%a %b %d %H:%M:%S %Y'))
+ self.assertEqual(header.command, '/import/bc2/apps/HH-suite/2.0.16-go'+
+ 'olf-1.4.10/bin/hhblits -cpu 1 -n 1 -e 0.001 -Z 1000'+
+ '0 -B 10000 -i /import/bc2/home/schwede/bienert/git/'+
+ 'ost_newenv.git/modules/bindings/tests/testfiles/tes'+
+ 'tali.a3m -o /scratch/tmp9E5dor/testali_cpu1_n1.hhr '+
+ '-d /import/bc2/home/schwede/bienert/git/ost_newenv.'+
+ 'git/modules/bindings/tests/testfiles/hhblitsdb/hhbl'+
+ 'itsdb')
+ self.assertEqual(len(hits), 4)
+ # hit 1
+ self.assertEqual(hits[0].hit_id, '3e7b90809bd446a538f9eb1a1ca0e551')
+ self.assertEqual(hits[0].score, float('222.3'))
+ self.assertEqual(hits[0].ss_score, float('16.4'))
+ self.assertEqual(hits[0].evalue, float('2.7e-42'))
+ self.assertEqual(hits[0].pvalue, float('6.9E-45'))
+ self.assertEqual(hits[0].prob, float('100.0'))
+ self.assertEqual(str(hits[0].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHF-DL-S----HGSAQ\n3e7b90809bd446a5... '+
+ 'VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT'+
+ 'EAEMKASED\n\nTest VKGHGKKVADALTNAVAH'+
+ 'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n3e7b908'+
+ '09bd446a5... LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHA-TKH'+
+ 'KIPIKYLEFISEAIIHVLHSRH\n\nTest PAEFT'+
+ 'PAVHASLDKFLASVSTVLTSKYR\n3e7b90809bd446a5... PGDFGA'+
+ 'DAQGAMNKALELFRKDIAAKYK\n')
+ # hit 2
+ self.assertEqual(hits[1].hit_id, 'af828e69a5f2d0fd42a2a213e09eb64f')
+ self.assertEqual(hits[1].score, float('215.7'))
+ self.assertEqual(hits[1].ss_score, float('17.2'))
+ self.assertEqual(hits[1].evalue, float('1.5e-41'))
+ self.assertEqual(hits[1].pvalue, float('3.9E-44'))
+ self.assertEqual(hits[1].prob, float('100.0'))
+ self.assertEqual(str(hits[1].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHFDLSHGSAQVKGHGK\naf828e69a5f2d0fd... '+
+ 'VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHG'+
+ 'SAQVKGHGK\n\nTest KVADALTNAVAHVDDMPN'+
+ 'ALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA\naf828e6'+
+ '9a5f2d0fd... KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNF'+
+ 'KLLSHCLLVTLAAHLPAEFTPA\n\nTest VHASL'+
+ 'DKFLASVSTVLTSKYR\naf828e69a5f2d0fd... VHASLDKFLASVS'+
+ 'TVLTSKYR\n')
+ # hit 3
+ self.assertEqual(hits[2].hit_id, '9287755aa6aa27583da6be3b2408bfcc')
+ self.assertEqual(hits[2].score, float('215.1'))
+ self.assertEqual(hits[2].ss_score, float('16.5'))
+ self.assertEqual(hits[2].evalue, float('3.8e-41'))
+ self.assertEqual(hits[2].pvalue, float('9.7E-44'))
+ self.assertEqual(hits[2].prob, float('100.0'))
+ self.assertEqual(str(hits[2].aln),
+ 'Test VLSPADKTNVKAAWGKVGAHAGEYGAEALER'+
+ 'MFLSFPTTKTYFPHF-DLS-----HGSAQ\n9287755aa6aa2758... '+
+ 'HLTPEEKSAVTALWGKVN--VDEVGGEALGRLLVVYPWTQRFFESFGDLST'+
+ 'PDAVMGNPK\n\nTest VKGHGKKVADALTNAVAH'+
+ 'VDDMPNALSALSDLHAHK-LRVDPVNFKLLSHCLLVTLAAHL\n9287755'+
+ 'aa6aa2758... VKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHC-DKL'+
+ 'HVDPENFRLLGNVLVCVLAHHF\n\nTest PAEFT'+
+ 'PAVHASLDKFLASVSTVLTSKYR\n9287755aa6aa2758... GKEFTP'+
+ 'PVQAAYQKVVAGVANALAHKYH\n')
+ # hit 4
+ self.assertEqual(hits[3].hit_id, 'e69e1ac0a4b2554df25f2c2183b0fba0')
+ self.assertEqual(hits[3].score, float('12.6'))
+ self.assertEqual(hits[3].ss_score, float('2.6'))
+ self.assertEqual(hits[3].evalue, float('64.0'))
+ self.assertEqual(hits[3].pvalue, float('0.16'))
+ self.assertEqual(hits[3].prob, float('0.6'))
+ self.assertEqual(str(hits[3].aln), 'Test VDPVNFKLLSHCL'+
+ 'LVTLAAHL\ne69e1ac0a4b2554d... ATPEQAQLVHKEIRKIVKDTC'+
+ '\n')
+
+# ParseHHblitsOutput
if __name__ == "__main__":
hhsuite_root_dir = os.getenv('EBROOTHHMINSUITE')
--
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