[Bioperl-l] clustalw tests
Heikki Lehvaslaiho
heikki@ebi.ac.uk
Fri, 11 Jan 2002 10:11:02 +0000
Jason suggested that I check clustalw 1.81 and he was right: tests work.
So the current situation with clustalw is the following:
* both 1.81 and 1.82 has serious bug in profile alingment.
Be sure to apply the following parches is you need clustalw
profile functionality:
1.81 & 1.82
===========
prfalign.c. The new lines are:
184-185:
alignment[nseqs1][j]=gap_pos1;
alignment[nseqs1][j] = ENDALN;
216-217:
alignment[nseqs1+nseqs2][j]=gap_pos1;
alignment[nseqs1+nseqs2][j] = ENDALN;
v 1.82 only
===========
interface.c Revert line 215 to
params[i]=(char *)ckalloc(strlen(args[i])*sizeof(char));
Let's hope there will be a new bug fix release of clustalw soon.
-Heikki
Heikki Lehvaslaiho wrote:
>
> 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
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> Bioperl-l mailing list
> Bioperl-l@bioperl.org
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--
______ _/ _/_____________________________________________________
_/ _/ 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
___ _/_/_/_/_/________________________________________________________