diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 7ce8f8d0b9c1f15dc9fe30a6a06f672166672357..98c7d0e4bc9b16e5da09cd5618e5ca9a24807d93 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -26,11 +26,11 @@ class HHblitsHit:
.. attribute:: aln
- Pairwise alignment containing the aligned part between the query and the
+ 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
@@ -208,95 +208,91 @@ def ParseHHblitsOutput(output):
return header, _ParseResultBody(header.query, hits, lines)
-def ParseHHblitsProfile(profile):
- '''
- HHblits does not need profiles, it works on the MSA (a3m) file!
- Do they contain all information?
-
- Parse secondary structure information and the MSA out of an HHM profile.
-
- :param profile: Opened file handle holding the profile.
- :type profile: :class:`file`
-
- :return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
- (:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
- "consensus" (~ost.seq.SequenceHandle).
- '''
- profile_dict = dict()
- state = 'NONE'
- pred_seq_txt = ''
- conf_seq_txt = ''
- consensus_txt = ''
- msa_seq = list()
- msa_head = list()
- for line in profile:
- if len(line.rstrip()) == 0:
- continue
- if line.rstrip() == '>ss_pred PSIPRED predicted secondary structure':
- state = 'sspred'
- continue
- elif line.rstrip() == '>ss_conf PSIPRED confidence values':
- state = 'ssconf'
- continue
- elif line.rstrip() == '>Consensus':
- state = 'consensus'
- continue
- elif line[0] == '>':
- if state == 'consensus' or state == 'msa':
- msa_seq.append('')
- msa_head.append(line[1:].rstrip())
- else:
- raise IOError('Profile file "%s" is missing the "Consensus" section' \
- % profile.name)
- state = 'msa'
- continue
- elif line[0] == '#':
- state = 'NONE'
- continue
-
- if state == 'sspred':
- pred_seq_txt += line.rstrip()
- elif state == 'ssconf':
- conf_seq_txt += line.rstrip()
- elif state == 'msa':
- msa_seq[len(msa_seq)-1] += line.rstrip()
- elif state == 'consensus':
- consensus_txt += line.rstrip()
-
- profile_dict['ss_pred'] = list()
- profile_dict['ss_conf'] = list()
- for i in range(0, len(pred_seq_txt)):
- profile_dict['ss_pred'].append(pred_seq_txt[i])
- profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
-
- # post processing
- # MSA
- profile_dict['msa'] = None
- if len(msa_seq):
- t = msa_seq[0]
- al=seq.AlignmentList()
- for i in range(1, len(msa_seq)):
- qs = ''
- ts = ''
- k = 0
- for c in msa_seq[i]:
- if c.islower():
- qs += '-'
- ts += c.upper()
- else:
- qs += t[k]
- ts += c
- k += 1
- 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,
+def ParseHHM(profile):
+ '''Parse secondary structure information and the MSA out of an HHM profile.
+
+ :param profile: Opened file handle holding the profile.
+ :type profile: :class:`file`
+
+ :return: Dictionary containing "ss_pred" (:class:`list`), "ss_conf"
+ (:class:`list`), "msa" (:class:`~ost.seq.AlignmentHandle`) and
+ "consensus" (~ost.seq.SequenceHandle).
+ '''
+ profile_dict = dict()
+ state = 'NONE'
+ pred_seq_txt = ''
+ conf_seq_txt = ''
+ consensus_txt = ''
+ msa_seq = list()
+ msa_head = list()
+ for line in profile:
+ if len(line.rstrip()) == 0:
+ continue
+ if line.rstrip() == '>ss_pred PSIPRED predicted secondary structure':
+ state = 'sspred'
+ continue
+ elif line.rstrip() == '>ss_conf PSIPRED confidence values':
+ state = 'ssconf'
+ continue
+ elif line.rstrip() == '>Consensus':
+ state = 'consensus'
+ continue
+ elif line[0] == '>':
+ if state == 'consensus' or state == 'msa':
+ msa_seq.append('')
+ msa_head.append(line[1:].rstrip())
+ else:
+ raise IOError('Profile file "%s" is missing ' % profile.name+
+ 'the "Consensus" section')
+ state = 'msa'
+ continue
+ elif line[0] == '#':
+ state = 'NONE'
+ continue
+
+ if state == 'sspred':
+ pred_seq_txt += line.rstrip()
+ elif state == 'ssconf':
+ conf_seq_txt += line.rstrip()
+ elif state == 'msa':
+ msa_seq[len(msa_seq)-1] += line.rstrip()
+ elif state == 'consensus':
+ consensus_txt += line.rstrip()
+
+ profile_dict['ss_pred'] = list()
+ profile_dict['ss_conf'] = list()
+ for i in range(0, len(pred_seq_txt)):
+ profile_dict['ss_pred'].append(pred_seq_txt[i])
+ profile_dict['ss_conf'].append(int(conf_seq_txt[i]))
+
+ # post processing
+ # MSA
+ profile_dict['msa'] = None
+ if len(msa_seq):
+ t = msa_seq[0]
+ al=seq.AlignmentList()
+ for i in range(1, len(msa_seq)):
+ qs = ''
+ ts = ''
+ k = 0
+ for c in msa_seq[i]:
+ if c.islower():
+ qs += '-'
+ ts += c.upper()
+ else:
+ qs += t[k]
+ ts += c
+ k += 1
+ 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))
- #print profile_dict['msa'].ToString(80)
- # Consensus
- profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
+ #print profile_dict['msa'].ToString(80)
+ # Consensus
+ profile_dict['consensus'] = seq.CreateSequence('Consensus', consensus_txt)
- return profile_dict
+ return profile_dict
def EstimateMemConsumption():
"""
@@ -561,4 +557,4 @@ class HHblits:
__all__= (HHblits)
# LocalWords: HHblits MSA hhblits hhtools PSIPRED addss param nrdb str mact
-# LocalWords: cpu hhm func ParseHHblitsOutput
+# 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 a241d9f15d4515c15a42307b492216c39a7a819c..92276d44b69787c305e9015ca4707c51fba15953 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -264,8 +264,32 @@ class TestHHblitsBindings(unittest.TestCase):
'testfiles/hhblitsdb/hhblitsdb')
self.assertEqual(search_file, None)
-# search:
-# search with non-existing a3m
+ def testParseHHMWorking(self):
+ # get info from an HHM file
+ with open("testfiles/test.hmm") as hhm_fh:
+ prof = hhblits.ParseHHM(hhm_fh)
+ self.assertEqual(''.join([str(x) for x in prof['ss_conf']]),
+ '999999999999998873391557999999998639441123987788888'+
+ '856788999999999998735477789999999887650299989899889'+
+ '999999997536679989999999999999999984329')
+ self.assertEqual(''.join(prof['ss_pred']), 'CCCHHHHHHHHHHHHHHHCCCHHHH'+
+ 'HHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH'+
+ 'HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH'+
+ 'HHHHHHHHHHHHCC')
+ self.assertEqual(str(prof['consensus']), 'xltxxxxxxixxsWxxvxxxxxxxgxx'+
+ 'xxxxlfxxxPxxxxxFxxxxxxxxxxxxxxhxxxvxxxlxxxixxldxxxx'+
+ 'xlxxlxxxHxxxxgvxxxxxxxxxxxlxxxlxxxxgxxxxxxxxxAWxxxx'+
+ 'xxixxxmxxxyx')
+ self.assertEqual(prof['msa'].GetCount(), 7)
+
+ def testParseHHMNotWorking(self):
+ # get info from an HHM file
+ with self.assertRaises(IOError) as ioe:
+ hhblits.ParseHHM(open('testfiles/testali.a3m'))
+ self.assertEqual(ioe.exception.message,
+ 'Profile file "testfiles/testali.a3m" is missing '+
+ 'the "Consensus" section')
+
if __name__ == "__main__":
hhsuite_root_dir = os.getenv('EBROOTHHMINSUITE')