biopython SearchIO with hmmearch 2 error

Question

[MAK]

I want to parse the output file of hmmsearch from hmmer2 with biopython SearchIO

for qresult in SearchIO.read('test2.out', 'hmmer2-text'): 
    print qresult

I get this error:

Traceback (most recent call last):
  File "file.py", line 3285, in <module>
    for qresult in SearchIO.read('test2.out', 'hmmer2-text'):
  File "/usr/lib/python2.7/site-packages/Bio/SearchIO/__init__.py", line 359, in read
    first = next(generator)
  File "/usr/lib/python2.7/site-packages/Bio/SearchIO/__init__.py", line 316, in parse
    for qresult in generator:
  File "/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py", line 45, in __iter__
    for qresult in self.parse_qresult():
  File "/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py", line 126, in parse_qresult
    self.parse_hsp_alignments()
  File "/usr/lib/python2.7/site-packages/Bio/SearchIO/HmmerIO/hmmer2_text.py", line 286, in parse_hsp_alignments
    otherseq += self.line[19:].split()[0].strip()
IndexError: list index out of range

The h2.out file:

hmmsearch - search a sequence database with a profile HMM
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:                   ../../RefSeq/outputdir/GM-refseq63/NC_020772/1244200_cox1.hm [1244200_cox1]
Sequence database:          ../data/trees_and_data/fasta_files-all/219678_cox1.fas
per-sequence score cutoff:  [none]
per-domain score cutoff:    [none]
per-sequence Eval cutoff:   <= 10        
per-domain Eval cutoff:     [none]
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query HMM:   1244200_cox1
Accession:   [none]
Description: [none]
  [HMM has been calibrated; E-values are empirical estimates]

Scores for complete sequences (score includes all domains):
Sequence    Description                                 Score    E-value  N 
--------    -----------                                 -----    ------- ---
219678_cox1                                            1120.6          0   1

Parsed for domains:
Sequence    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
--------    ------- ----- -----    ----- -----      -----  -------
219678_cox1   1/1       3   513 ..     1   511 []  1120.6        0

Alignments of top-scoring domains:
219678_cox1: domain 1 of 1, from 3 to 513: score 1120.6, E = 0
                   *->mnKWLFstnHKDiGtLYFmFGmWsGmvGssmsWiiRiELGqPGAFiG
                      + +W FstnHKDiGtLY +FG W+GmvG ++s +iR EL qPG  +G
  219678_cox     3    ITRWFFSTNHKDIGTLYLVFGAWAGMVGTALSLLIRAELSQPGSLLG 49   

                   nDqiYnvvvtAHAFimiFFmvmPimiGGFGnWLvPLmiGAPDmAFPRmnn
                    DqiYnv+vtAHAF+miFFmvmPi+iGGFGnWLvPLmiGAPDmAFPRmnn
  219678_cox    50 DDQIYNVIVTAHAFVMIFFMVMPILIGGFGNWLVPLMIGAPDMAFPRMNN 99   

                   msFWLLPPsLtLLmAssFiEmGAGtGWtvYPPLsnsLFHsGPsvDLAiFs
                   msFWLLPPs  LL+Ass +E GAGtGWtvYPPL+  L H+G svDL iFs
  219678_cox   100 MSFWLLPPSFLLLLASSGVEAGAGTGWTVYPPLAGNLAHAGASVDLTIFS 149  

                   LHLAGvssiLGAinFistiinmRPtGmiPERiPLFvWsvGitALLLLLsL
                   LHLAGvssiLGA+nFi tiinm+P        PLFvWsv +tA+LLLLsL
  219678_cox   150 LHLAGVSSILGAVNFITTIINMKPPATSQYQTPLFVWSVLVTAVLLLLSL 199  

                   PvLAGAitmLLtDRnFntsFFnPtGGGDPiLYqHLFWFFGHPEvYiLiLP
                   PvLA  itmLLtDRn nt FF P GGGDPiLYqHLFWFFGHPEvYiLiLP
  219678_cox   200 PVLAAGITMLLTDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILP 249  

                   GFGLisHiisqEsGKnEtFGvLGmiYAmmAiGLLGFivWAHHmFtvGmDv
                   GFG+isH+++  sGK E FG +Gm++AmmAiGLLGFivWAHHmFtvGmDv
  219678_cox   250 GFGIISHVVAYYSGKKEPFGYMGMVWAMMAIGLLGFIVWAHHMFTVGMDV 299  

                   DtRAYFtsAtmiiAvPtGiKiFsWLAtLHGvHvKYtPsmLWALGFvFLFt
                   DtRAYFtsAtmiiA+PtG+K+FsWLAtLHG  +K+   mLWALGF+FLFt
  219678_cox   300 DTRAYFTSATMIIAIPTGVKVFSWLATLHGGSIKWETPMLWALGFIFLFT 349  

                   iGGLtGviLAnssiDivLHDtYYvvAHFHYvLsmGAvFAimGsFiqWYPL
                   +GGLtG++LAnss+DivLHDtYYvvAHFHYvLsmGAvFAim +F+ W+PL
  219678_cox   350 VGGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMAAFVHWFPL 399  

                   FtGmtmKnKWLKiqFGLmFiGvnmtFFPqHFLGLsGmPRRYsDYPDCYtt
                   F G t+   W Ki FG+mFiGvn+tFFPqHFLGL+GmPRRYsDYPD Yt 
  219678_cox   400 FSGYTLNDTWTKIHFGVMFIGVNLTFFPQHFLGLAGMPRRYSDYPDAYTL 449  

                   WniistiGstLsmLsiFmFimiLWEsmisKRmmLFssnmtssiEWLqKtP
                   Wn +s iGs +s++++ mF+ iLWE+  +KR +      t  +EWL   P
  219678_cox   450 WNTVSSIGSLISLVAVIMFLFILWEAFAAKREVSSVELTTTNVEWLHGCP 499  

                   PAEHsYCELPmLns<-*
                   P  H + E   +     
  219678_cox   500 PPYHTFEEPAFVQV    513  

Histogram of all scores:
score    obs    exp  (one = represents 1 sequences)
-----    ---    ---
 1120      1      0|=                                                          

% Statistical details of theoretical EVD fit:
              mu =  -346.4556
          lambda =     0.0755
chi-sq statistic =     0.0000
  P(chi-square)  =          0

Total sequences searched: 1

Whole sequence top hits:
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         16K

Domain top hits:
tophits_s report:
     Total hits:           1
     Satisfying E cutoff:  1
     Total memory:         17K

Any idea what's wrong?

[Peter]

Which version of Biopython are you using?

P.S. I modified the question formatting to mark the exception and file as "code" to display more clearly.