diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 4ed2830fed8aa45272dbff4c27fcbba25a61589a..64b48ac8ed51a85e0efab7b20619512f4d3b48c7 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -1,16 +1,11 @@
'''HHblits wrapper.
'''
-import math
import subprocess
import datetime
-import os, re, fcntl
+import os
import shutil
import tempfile
-try:
- import hashlib
-except ImportError:
- import md5 as hashlib
import ost
from ost import settings, seq
@@ -19,31 +14,31 @@ from ost.bindings import utils
class HHblitsHit:
"""
A hit found by HHblits
-
+
.. attribute:: hit_id
-
+
String identifying the hit
-
+
.. attribute:: aln
-
+
Pairwise alignment containing the aligned part between the query and the
target. First sequence is the query, the second sequence the target.
-
+
: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):
+ def __init__(self, hit_id, aln, score, ss_score, evalue, pvalue, prob):
self.hit_id = hit_id
self.aln = aln
self.score = score
@@ -91,48 +86,48 @@ def ParseHHblitsOutput(output):
Parses the HHblits output and returns a tuple of HHblitsHeader and
a list of HHblitsHit instances.
"""
- lines=iter(output)
+ 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()
+ 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()
+ header.match_columns = int(line[value_start_column:].strip())
+
+ line = lines.next()
assert line.startswith('No_of_seqs')
-
- line=lines.next()
+
+ line = lines.next()
assert line.startswith('Neff')
- header.n_eff=float(line[value_start_column:].strip())
-
- line=lines.next()
+ 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()
+ 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()
+ 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
+ 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=[]
+ hits = []
while True:
- line=lines.next()
- if len(line.strip())==0:
+ line = lines.next()
+ if len(line.strip()) == 0:
return hits
hits.append(ParseHeaderLine(line))
return hits
@@ -141,62 +136,65 @@ def ParseHHblitsOutput(output):
entry_index = None
query_str = ''
templ_str = ''
- def _MakeAln(query_id, hit_id, query_string, templ_string,
+ 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
+ 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()
+ line = lines.next()
if len(line.strip()) == 0:
continue
if line.startswith('Done!'):
- if len(query_str)>0:
+ 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]
+ return [h for h, o in hits]
if line.startswith('No '):
- if len(query_str)>0:
- hits[entry_index][0].aln=_MakeAln(\
+ 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=''
+ 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
+ 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]
+ 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]
+ 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
+ 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)
+ hits = _ParseTableOfContents(lines)
return header, _ParseResultBody(header.query, hits, lines)
@@ -262,7 +260,7 @@ def ParseHHM(profile):
profile_dict['msa'] = None
if len(msa_seq):
t = msa_seq[0]
- al=seq.AlignmentList()
+ al = seq.AlignmentList()
for i in range(1, len(msa_seq)):
qs = ''
ts = ''
@@ -275,11 +273,12 @@ def ParseHHM(profile):
qs += t[k]
ts += c
k += 1
- nl=seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
- seq.CreateSequence(msa_head[i], ts))
+ nl = seq.CreateAlignment(seq.CreateSequence(msa_head[0], qs),
+ seq.CreateSequence(msa_head[i], ts))
al.append(nl)
- profile_dict['msa'] = seq.alg.MergePairwiseAlignments(al,
- seq.CreateSequence(msa_head[0], t))
+ profile_dict['msa'] = seq.alg.MergePairwiseAlignments(\
+ al,
+ seq.CreateSequence(msa_head[0], t))
#print profile_dict['msa'].ToString(80)
# Consensus
profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
@@ -299,10 +298,10 @@ class HHblits:
"""
Initialise a new HHblits "search" for the given query. Query may either
be a :class:`ost.seq.SequenceHandle` or a string. In the former case, the
- query is the actual query sequence, in the latter case, the query is the
+ query is the actual query sequence, in the latter case, the query is the
filename to the file containing the query.
- :param query: Query sequence as file or sequence.
+ :param query: Query sequence as file or sequence.
:type query: :class:`ost.seq.SequenceHandle` or :class:`str`
:param hhsuite_root: Path to the top-level directory of your hhsuite
installation.
@@ -322,15 +321,15 @@ class HHblits:
self.bin_dir = os.path.join(self.hhsuite_root, 'bin')
self.hhblits_bin = os.path.join(self.hhsuite_root, 'bin/hhblits')
else:
- self.hhblits_bin=settings.Locate('hhblits',
- explicit_file_name=hhblits_bin)
+ self.hhblits_bin = settings.Locate('hhblits',
+ explicit_file_name=hhblits_bin)
self.bin_dir = os.path.dirname(self.hhblits_bin)
self.hhlib_dir = os.path.join(self.hhsuite_root, 'lib', 'hh')
if working_dir:
self.needs_cleanup = False
self.working_dir = working_dir
if not os.path.exists(working_dir):
- os.mkdir(working_dir)
+ os.mkdir(working_dir)
if isinstance(query, str):
self.filename = os.path.abspath(os.path.join(
self.working_dir, os.path.basename(query)))
@@ -364,7 +363,7 @@ class HHblits:
def BuildQueryMSA(self, nrdb, iterations=1, mact=None, cpu=1):
"""Builds the MSA for the query sequence
-
+
This function directly uses hhblits of hhtools. While in theory it
would be possible to do this by PSI-blasting on our own, hhblits is
supposed to be faster. Also it is supposed to prevent alignment
@@ -390,14 +389,14 @@ class HHblits:
full_nrdb = os.path.join(os.path.abspath(os.path.split(nrdb)[0]),
os.path.split(nrdb)[1])
# create MSA
- hhblits_cmd='%s -e 0.001 -cpu %d -i %s -oa3m %s -d %s -n %d' % \
- (self.hhblits_bin, cpu, self.filename, a3m_file, full_nrdb,
- iterations)
+ hhblits_cmd = '%s -e 0.001 -cpu %d -i %s -oa3m %s -d %s -n %d' % \
+ (self.hhblits_bin, cpu, self.filename, a3m_file,
+ full_nrdb, iterations)
if mact:
hhblits_cmd += '-mact %f' % mact
job = subprocess.Popen(hhblits_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- sout, serr = job.communicate()
+ sout, _ = job.communicate()
#lines = sout.splitlines()
#for l in lines:
# print l.strip()
@@ -420,12 +419,12 @@ class HHblits:
job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
env=env, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
- sout, serr = job.communicate()
+ sout, _ = job.communicate()
lines = sout.splitlines()
- for l in lines:
- if 'error' in l.lower():
+ for line in lines:
+ if 'error' in line.lower():
ost.LogWarning('Predicting secondary structure for MSA '+
- '(%s) failed, on command: %s' % (a3m_file,l))
+ '(%s) failed, on command: %s' % (a3m_file, line))
return a3m_file
return a3m_file
@@ -436,7 +435,7 @@ class HHblits:
"""
hhmake = os.path.join(self.bin_dir, 'hhmake')
if not hhm_file:
- hhm_file='%s.hhm' % os.path.splitext(a3m_file)[0]
+ hhm_file = '%s.hhm' % os.path.splitext(a3m_file)[0]
if os.path.exists(hhm_file):
return hhm_file
ost.LogVerbose('converting %s to %s' % (a3m_file, hhm_file))
@@ -465,25 +464,25 @@ class HHblits:
cs_file = '%s.seq219' % os.path.splitext(a3m_file)[0]
if os.path.exists(cs_file):
return cs_file
- o = list()
- for k, v in options.iteritems():
- if type(v) == type(True):
- if v == True:
- o.append('%s' % str(k))
+ opt_cmd = list()
+ for k, val in options.iteritems():
+ if type(val) == type(True):
+ if val == True:
+ opt_cmd.append('%s' % str(k))
else:
- o.append('%s %s' % (str(k), str(v)))
- o = ' '.join(o)
- cs_cmd = '%s -i %s -o %s %s' % (cstranslate, a3m_file, cs_file, o)
+ opt_cmd.append('%s %s' % (str(k), str(val)))
+ opt_cmd = ' '.join(opt_cmd)
+ cs_cmd = '%s -i %s -o %s %s' % (cstranslate, a3m_file, cs_file, opt_cmd)
ost.LogVerbose('converting %s to %s' % (a3m_file, cs_file))
job = subprocess.Popen(cs_cmd, shell=True,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- sout, serr = job.communicate()
+ sout, _ = job.communicate()
#lines = serr.splitlines()
#for l in lines:
# print l
lines = sout.splitlines()
- for l in lines:
- if l in 'Wrote abstract state sequence to %s' % cs_file:
+ for line in lines:
+ if line in 'Wrote abstract state sequence to %s' % cs_file:
return cs_file
ost.LogWarning('Creating column state sequence file (%s) failed' % \
cs_file)
@@ -504,49 +503,48 @@ class HHblits:
result file is returned. This file may be parsed with
:func:`ParseHHblitsOutput`.
"""
- full_db = os.path.join(os.path.abspath(os.path.split(database)[0]),
- os.path.split(database)[1])
- full_a3m = os.path.abspath(a3m_file)
opts = {'cpu' : 1, # no. of cpus used
'n' : 1} # no. of iterations
opts.update(options)
- o = []
- f = []
- for k, v in opts.iteritems():
- if type(v) == type(True):
- if v == True:
- o.append('-%s' % str(k))
- f.append(str(k))
+ opt_cmd = []
+ opt_str = []
+ for k, val in opts.iteritems():
+ if type(val) == type(True):
+ if val == True:
+ opt_cmd.append('-%s' % str(k))
+ opt_str.append(str(k))
else:
- o.append('-%s %s' % (str(k), str(v)))
- f.append('%s%s' % (str(k), str(v)))
- o = ' '.join(o)
- f = '_'.join(f)
+ opt_cmd.append('-%s %s' % (str(k), str(val)))
+ opt_str.append('%s%s' % (str(k), str(val)))
+ opt_cmd = ' '.join(opt_cmd)
+ opt_str = '_'.join(opt_str)
base = os.path.basename(os.path.splitext(a3m_file)[0])
- hhr_file = '%s%s_%s.hhr' % (prefix, base, f)
+ hhr_file = '%s%s_%s.hhr' % (prefix, base, opt_str)
hhr_file = os.path.join(self.working_dir, hhr_file)
- search_cmd='%s %s -e 0.001 -Z 10000 -B 10000 -i %s -o %s -d %s'%(
- self.hhblits_bin,
- o, full_a3m,
+ search_cmd = '%s %s -e 0.001 -Z 10000 -B 10000 -i %s -o %s -d %s'%(
+ self.hhblits_bin,
+ opt_cmd, os.path.abspath(a3m_file),
hhr_file,
- full_db)
+ os.path.join(os.path.abspath(os.path.split(database)[0]),
+ os.path.split(database)[1]))
ost.LogInfo('searching %s' % database)
ost.LogVerbose(search_cmd)
job = subprocess.Popen(search_cmd, shell=True, cwd=self.working_dir,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
sout, serr = job.communicate()
- if job.returncode !=0:
+ if job.returncode != 0:
lines = sout.splitlines()
- for l in lines:
- print l.strip()
+ for line in lines:
+ print line.strip()
lines = serr.splitlines()
- for l in lines:
- print l.strip()
+ for line in lines:
+ print line.strip()
return None
return hhr_file
-__all__= (HHblits)
+__all__ = ['HHblits', 'HHblitsHit', 'HHblitsHeader', 'ParseHeaderLine',
+ 'ParseHHblitsOutput', 'ParseHHM', 'EstimateMemConsumption']
# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str mact
# LocalWords: cpu hhm func ParseHHblitsOutput ss pred conf msa
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index 61c4ac0de23f95fcb74aeb3be13d18db39696524..1df19fdd8449ce01642b20313860a753df35478b 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -367,9 +367,9 @@ class TestHHblitsBindings(unittest.TestCase):
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')
+ self.assertEqual(str(hits[3].aln),
+ 'Test VDPVNFKLLSHCLLVTLAAHL\ne69e1ac0'+
+ 'a4b2554d... ATPEQAQLVHKEIRKIVKDTC\n')
# ParseHHblitsOutput