SearchIO: Correctly parse empty consensus lines in hmmer2 parser

Hmmer2TextParser.read_next() usually reads over lines only containing
whitespace. The original code to deal with the consensus line would already
turn off the strip() call, so the consensus lines would come out in the
correct length. However, if the consensus line was completely empty,
read_next() would erroneously skip over the consensus line.
This fix disables the empty line skip when whitespace stripping is
turned off.

Signed-off-by: Kai Blin <kai.blin@biotech.uni-tuebingen.de>

Bio/SearchIO/HmmerIO/hmmer2_text.py

@@ -51,7 +51,7 @@ class Hmmer2TextParser(object):
         if len(self.buf) > 0:
             return self.buf.pop()
         self.line = self.handle.readline()
-        while self.line and not self.line.strip():
+        while self.line and rstrip and not self.line.strip():
             self.line = self.handle.readline()
         if self.line:
             if rstrip:

Tests/Hmmer/README.txt

@@ -41,6 +41,7 @@ text_21_hmmpfam_001.out     single query, two matches, bioperl's hmmpfam.out fil
 text_22_hmmpfam_001.out     single query, one match, bioperl's L77119.hmmer file
 text_23_hmmpfam_001.out     single query, multiple matches, bioperl's hmmpfam_cs.out file
 text_23_hmmpfam_002.out     single query, no match
+text_23_hmmpfam_003.out     single query, one match, missing some consensus content
 text_24_hmmpfam_001.out     multiple queries
 text_20_hmmsearch_001.out   single query, multiple matches, bioperl's hmmsearch.out file
 text_22_hmmsearch_001.out   single query, multiple matches, bioperl's cysprot1b.hmmsearch file

Tests/Hmmer/text_23_hmmpfam_003.out

@@ -0,0 +1,34 @@
+hmmpfam - search one or more sequences against HMM database
+HMMER 2.3.2 (Oct 2003)
+Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Freely distributed under the GNU General Public License (GPL)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+HMM file:                 antismash/specific_modules/lantipeptides/ClassIVLanti.hmm
+Sequence file:            -
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query sequence: small_input
+Accession:      [none]
+Description:    [none]
+
+Scores for sequence family classification (score includes all domains):
+Model        Description                                Score    E-value  N
+--------     -----------                                -----    ------- ---
+ClassIVLanti Class-IV                                   -79.3          1   1
+
+Parsed for domains:
+Model        Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
+--------     ------- ----- -----    ----- -----      -----  -------
+ClassIVLanti   1/1       6    20 ..     1    66 []   -79.3        1
+
+Alignments of top-scoring domains:
+ClassIVLanti: domain 1 of 1, from 6 to 20: score -79.3, E = 1
+                   *->msEEqLKAFiAKvqaDtsLqEqLKaEGADvvaiAKAaGFtitteDLn
+                              F+                           G  +t   Ln
+  small_inpu     6    -------CFL---------------------------GCLVTNWVLN 18
+
+                   ahiqakeLsdeeLEgvaGg<-*
+
+  small_inpu    19 RS-----------------    20
+
+//

Tests/test_SearchIO_hmmer2_text.py

@@ -166,6 +166,44 @@ class HmmpfamTests(unittest.TestCase):
         self.assertEqual('SEQ0002', res.id)
         self.assertEqual(0, len(res.hits))
 
+    def test_hmmpfam_23_missing_consensus(self):
+        """Test parsing hmmpfam 2.3 file (text_23_hmmpfam_003.out)"""
+        results = parse(path.join("Hmmer", "text_23_hmmpfam_003.out"), self.fmt)
+        res = results.next()
+
+        self.assertEqual('small_input', res.id)
+        self.assertEqual('[none]', res.description)
+        self.assertEqual('[none]', res.accession)
+        self.assertEqual('hmmpfam', res.program)
+        self.assertEqual('2.3.2', res.version)
+        self.assertEqual('antismash/specific_modules/lantipeptides/ClassIVLanti.hmm', res.target)
+        self.assertEqual(1, len(res))
+
+        hit = res[0]
+        self.assertEqual('ClassIVLanti', hit.id)
+        self.assertEqual('Class-IV', hit.description)
+        self.assertAlmostEqual(-79.3, hit.bitscore)
+        self.assertAlmostEqual(1, hit.evalue)
+        self.assertEqual(1, hit.domain_obs_num)
+        self.assertEqual(1, len(hit))
+
+        hsp = hit[0]
+        self.assertEqual(1, hsp.domain_index)
+        self.assertEqual(0, hsp.hit_start)
+        self.assertEqual(66, hsp.hit_end)
+        self.assertEqual('[]', hsp.hit_endtype)
+        self.assertEqual(5, hsp.query_start)
+        self.assertEqual(20, hsp.query_end)
+        self.assertEqual('..', hsp.query_endtype)
+        self.assertAlmostEqual(-79.3, hsp.bitscore)
+        self.assertAlmostEqual(1, hsp.evalue)
+        self.assertEqual('msEEqLKAFiAKvqaDtsLqEqLKaEGADvvaiAKAaGFtitteDLnahiqakeLsdeeLEgvaGg',
+                         str(hsp.hit.seq))
+        self.assertEqual('        F+                           G  +t   Ln',
+                         str(hsp.aln_annotation['homology']))
+        self.assertEqual('-------CFL---------------------------GCLVTNWVLNRS-----------------',
+                         str(hsp.query.seq))
+
     def test_hmmpfam_24(self):
         """Test parsing hmmpfam 2.4 file (text_24_hmmpfam_001.out)"""
         results = list(parse(path.join("Hmmer", "text_24_hmmpfam_001.out"), self.fmt))