[ensembl-dev] R59: -stepSize=5 in blat_gfclient.pm

[volker.weinberger at novartis.com]

Dear Hiram,

absolutely and sorry for the typo in the posting.  I meant -stepSize. It's 
not available in our gfClient.

stepSize would e.g. be an option for gfServer, but not for gfClient.

The available options for our gfClient are:

gfClient v. 34 - A client for the genomic finding program that produces a 
.psl file
usage:
   gfClient host port seqDir in.fa out.psl
where
   host is the name of the machine running the gfServer
   port is the same as you started the gfServer with
   seqDir is the path of the .nib or .2bit files relative to the current 
dir
       (note these are needed by the client as well as the server)
   in.fa is a fasta format file.  May contain multiple records
   out.psl where to put the output
options:
   -t=type     Database type.  Type is one of:
                 dna - DNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
               The default is dna
   -q=type     Query type.  Type is one of:
                 dna - DNA sequence
                 rna - RNA sequence
                 prot - protein sequence
                 dnax - DNA sequence translated in six frames to protein
                 rnax - DNA sequence translated in three frames to protein
   -prot       Synonymous with -d=prot -q=prot
   -dots=N   Output a dot every N query sequences
   -nohead   Suppresses psl five line header
   -minScore=N sets minimum score.  This is twice the matches minus the 
               mismatches minus some sort of gap penalty.  Default is 30
   -minIdentity=N Sets minimum sequence identity (in percent).  Default is
               90 for nucleotide searches, 25 for protein or translated
               protein searches.
   -out=type   Controls output file format.  Type is one of:
                   psl - Default.  Tab separated format without actual 
sequence
                   pslx - Tab separated format with sequence
                   axt - blastz-associated axt format
                   maf - multiz-associated maf format
                   sim4 - similar to sim4 format
                   wublast - similar to wublast format
                   blast - similar to NCBI blast format
                   blast8- NCBI blast tabular format
                   blast9 - NCBI blast tabular format with comments
   -maxIntron=N  Sets maximum intron size. Default is 750000


Best regards,

Volker







Hiram Clawson <hiram at soe.ucsc.edu> 
23.09.2010 18:01

To
volker.weinberger at novartis.com
cc
dev at ensembl.org
Subject
Re: [ensembl-dev] R59: -stepSize=5   in blat_gfclient.pm






The case on the arguments is important.  It is -stepSize

See also:  http://www.kentinformatics.com/contact-us.html

--Hiram

volker.weinberger at novartis.com wrote:
> Hi,
> 
> I'm confused about the option settings for gfClient in 
> modules/Bio/Tools/Run/Search/blat_gfclient.pm :
> 
>     "-out=wublast -stepSize=5 -minScore=20"
> 
> as our internal version of gfClient (from BLAT34) doesn't support the 
> "-stepsize" option.
> 
> Do you use a customized version of BLAT or any version other than 34 ?
> 
> BTW it would be great if the path to the gfClient executable was 
> configurable in one of the configuration files rather than hard-coded.
> 
> Best regards,
> 
> Volker


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