[Bioperl-l] t_cofee tests

[Heikki Lehvaslaiho]

I am going crazy trying to understand what is going on with clustalw!

It is the profile alignment test that fails. If I rewrite the test so that
profile_align() is passed two strings pointing to MSE files the test works.
The current test is passed two Bio::SimpleAlign objects which forces the
module to write both alignments into a temporary file. It is these temp
files (or rather the first one) which clustalw program can not see and
fails. I can not understand why not since I can change permissions of these
files to 777 and list them before and after clustalw call:


.....|/home/heikki/tmp/PFVaKAGjRS|.......
clustal command = /home/heikki/bin/clustalw -profile
-profile1=/home/heikki/tmp/PFVaKAGjRS  -profile2=/home/heikki/tmp
/PGq86fVYZO -output=gcg  -ktuple=2 -matrix=BLOSUM
-outfile=/home/heikki/tmp/33f8uL5v4k



 CLUSTAL W (1.82) Multiple Sequence Alignments




ERROR: Could not open sequence file /home/heikki/tmp/PFVaKAGjRS)

|>ALEU_HORVU/1-362
MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALR
FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN....RKGLPYRLGINRFSDMSWEE
FQATRLG.AAQTCSATLAGNHLMRDAAA..LPETKDWREDG.IVSPVKNQAHCGSCWTFS
TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF........GCNGGLPSQAFEYIKYNG
GIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVID
GFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVEN.....GVPYWLIKNSWGADWGDNGY
FKMEMGKNMCAIATCASYPVVAA
>CATH_HUMAN/1-335
......MWATLPLLCAGAWLLG........VPVCGAAELSVNSLEK............FH
FKSWMSKHRKTYS.TEEYHHRLQTFASNWRKINAHN....NGNHTFKMALNQFSDMSFAE
IKHKYLWSEPQNCSATKS..NYLRGTGP..YPPSVDWRKKGNFVSPVKNQGACGSCWTFS
TTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY........GCQGGLPSQAFEYILYNK
GIMGEDTYPYQGKDGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQ
DFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKN.....GIPYWIVKNSWGPQWGMNGY
FLIERGKNMCGLAACASYPIPLV
>CYS1_DICDI/1-343
.....MKVILLFVLAVFTVFVS...............SRGIPPEEQ............SQ
FLEFQDKFNKKYS.HEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE
FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG.AVTPVKNQGQCGSCWSFS
TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG
GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVE
.WQFYIGGVFDIPCN...PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGY
IYLRRGKNTCGVSNFVSTSII..
|------------- EXCEPTION -------------
|------------- EXCEPTION -------------
MSG: Clustalw call crashed: 0

STACK Bio::Tools::Run::Alignment::Clustalw::_run
/home/heikki/src/bioperl-live/Bio/Tools/Run/Alignment/Clustalw.pm:528
STACK Bio::Tools::Run::Alignment::Clustalw::profile_align
/home/heikki/src/bioperl-live/Bio/Tools/Run/Alignment/Clusta
lw.pm:485
STACK toplevel t/c.t:90

-------------------------------------


There is a chance that clustaw is doing something strange with the -profile1
filenames from commandline and that causes all these probelms. If you look
carefully the error message, the file name contains an additional character.

I've asked the maintainers of clustaw to check this bug, because I can not
trace it down. It occurs only to -profile1 and it is easy to reproduce by
adding a character to filename 'cysprot1a.msf' which is in t/data bioperl
directory.

	-Heikki


Jason Stajich wrote:
> 
> I am having a hard time reproducing the TCoffee bug or Clustalw bugs.
> 
> I have tested on Linux, solaris, and IRIX system w and w/o File::Temp
> (running File::Temp 0.11 and 0.12) on both Clustalw and TCoffee and perl
> 5.6.0 and have all tests running fine.
> 
> Will try on OSF1 on sanger machines and see if I can reproduce the
> problem there.
> 
> --
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________