Re: [GUSDEV] Blast Similarities

[Pablo M. <pa...@ug...>]

Hi Adhemar,
it seems you need the BlastAnal.pm package=20

> Can't locate object method "new" via package "Blast::BlastAnal" =
(perhaps you forgot to=20
> load "Blast::BlastAnal"?) at

It is available in a CBIL tar:
http://www.cbil.upenn.edu/downloads/CBIL/releases/

CBIL/Bio/lib/perl/Blast/BlastAnal.pm

You might want to change/add a "use lib" to =
'parseBlastFilesForSimilarity.pl' or to add the CBIL to your =
"classpath", changing the $PERL5LIB variable.
(http://www.perl.com/doc/manual/html/pod/perlrun.html)


Good luck,
Pablo
  ----- Original Message -----=20
  From: Adhemar Zerlotini Neto=20
  To: gus...@li...=20
  Sent: Wednesday, July 12, 2006 11:31 AM
  Subject: [GUSDEV] Blast Similarities


  I'm trying to upload some blast results following a manual created by =
Pablo, who works at Jessica's Lab. at UGA.

  The problem is that the perl script 'parseBlastFilesForSimilarity.pl' =
isn't working.

  Here is the error:

  perl parseBlastFilesForSimilarity.pl --regex=3D'(\S+)'
  =
--outputFile=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.S=
Jcontigs/SJest.VS.SJcontigs.PARSED =
--dir=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontig=
s/SJest.VS.SJcontigs.RESULTS Opening
  =
/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.=
VS.SJcontigs.PARSED =
/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.=
VS.SJcontigs.PARSED is open
  Cutoff parameters:
  P value: 1e-05
  Length: 10
  Percent Identity: 20


  Analyzing
  opening
  =
/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.=
VS.SJcontigs.PARSED Can't locate object method "new" via package =
"Blast::BlastAnal" (perhaps you forgot to load "Blast::BlastAnal"?) at
  parseBlastFilesForSimilarity.pl line 81.


  I would like to know how to fix this script or to download a new =
version of the blast parse scripts.

  Thanks,

  Ad.





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