diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 0eac983c99f8df2671a000dc4e2447e4cd5ce2d9..4ed2830fed8aa45272dbff4c27fcbba25a61589a 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -17,40 +17,40 @@ from ost import settings, seq
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):
- 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
+ """
+ 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):
+ 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):
@@ -62,25 +62,29 @@ class HHblitsHeader:
self.command = ''
def ParseHeaderLine(line):
- # First, we seek the start of the identifier, that is, the first whitespace
- # after the hit number + 1. Since the identifier may contain whitespaces
- # itself, we cannot split the whole line
- for i in range(0, len(line)):
- if line[i].isdigit():
- break
- for i in range(i, len(line)):
- if line[i] == ' ':
- break
- assert len(line)-i >= 31 and line[i+1] != ' '
- hit_id = line[i+1:i+31].strip()
- fields = line[i+32:].split()
- prob = float(fields[0])
- evalue = float(fields[1])
- pvalue = float(fields[2])
- score = float(fields[3])
- ss_score = float(fields[4])
- offsets = (int(fields[6].split('-')[0]), int(fields[7].split('-')[0]))
- return (HHblitsHit(hit_id, None, score, ss_score, evalue, pvalue, prob), offsets)
+ '''Fetch header content.
+
+ First, we seek the start of the identifier, that is, the first whitespace
+ after the hit number + 1. Since the identifier may contain whitespaces
+ itself, we cannot split the whole line
+ '''
+ for i in range(0, len(line)):
+ if line[i].isdigit():
+ break
+ for i in range(i, len(line)):
+ if line[i] == ' ':
+ break
+ assert len(line)-i >= 31 and line[i+1] != ' '
+ hit_id = line[i+1:i+31].strip()
+ fields = line[i+32:].split()
+ prob = float(fields[0])
+ evalue = float(fields[1])
+ pvalue = float(fields[2])
+ score = float(fields[3])
+ ss_score = float(fields[4])
+ offsets = (int(fields[6].split('-')[0]), int(fields[7].split('-')[0]))
+ return (HHblitsHit(hit_id, None, score, ss_score, evalue, pvalue, prob),
+ offsets)
def ParseHHblitsOutput(output):
"""
@@ -444,45 +448,45 @@ class HHblits:
def A3MToCS(self, a3m_file, cs_file=None, options={}):
- """
- Converts the A3M alignment file to a column state sequence file. If
- cs_file is not given, the output file will be set to
- <file-basename>.seq219.
- :param a3m_file: A3M file to be converted.
- :type a3m_file: :class:`str`
- :param cs_file: Output file name (may be omitted)
- :type cs_file: :class:`str`
- :param options: dictionary of options to *cstranslate*, must come with the
- right amount of '-' in front.
- :type options: :class:`dict`
- """
- cstranslate = os.path.join(self.hhlib_dir, 'bin', 'cstranslate')
- if not cs_file:
- 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))
- 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)
- 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()
- #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:
- return cs_file
- ost.LogWarning('Creating column state sequence file (%s) failed' % \
- cs_file)
+ """
+ Converts the A3M alignment file to a column state sequence file. If
+ cs_file is not given, the output file will be set to
+ <file-basename>.seq219.
+ :param a3m_file: A3M file to be converted.
+ :type a3m_file: :class:`str`
+ :param cs_file: Output file name (may be omitted)
+ :type cs_file: :class:`str`
+ :param options: dictionary of options to *cstranslate*, must come with
+ the right amount of '-' in front.
+ :type options: :class:`dict`
+ """
+ cstranslate = os.path.join(self.hhlib_dir, 'bin', 'cstranslate')
+ if not cs_file:
+ 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))
+ 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)
+ 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()
+ #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:
+ return cs_file
+ ost.LogWarning('Creating column state sequence file (%s) failed' % \
+ cs_file)
def CleanupFailed(self):
'''In case something went wrong, call to make sure everything is clean.