<br><font size=2 face="sans-serif">Dear Hiram,</font>
<br>
<br><font size=2 face="sans-serif">absolutely and sorry for the typo in
the posting. I meant -stepSize. It's not available in our gfClient.</font>
<br>
<br><font size=2 face="sans-serif">stepSize would e.g. be an option for
gfServer, but not for gfClient.</font>
<br>
<br><font size=2 face="sans-serif">The available options for our gfClient
are:</font>
<br>
<br><font size=2 face="Courier New">gfClient v. 34 - A client for the genomic
finding program that produces a .psl file</font>
<br><font size=2 face="Courier New">usage:</font>
<br><font size=2 face="Courier New"> gfClient host port seqDir
in.fa out.psl</font>
<br><font size=2 face="Courier New">where</font>
<br><font size=2 face="Courier New"> host is the name of the
machine running the gfServer</font>
<br><font size=2 face="Courier New"> port is the same as you
started the gfServer with</font>
<br><font size=2 face="Courier New"> seqDir is the path of
the .nib or .2bit files relative to the current dir</font>
<br><font size=2 face="Courier New"> (note these
are needed by the client as well as the server)</font>
<br><font size=2 face="Courier New"> in.fa is a fasta format
file. May contain multiple records</font>
<br><font size=2 face="Courier New"> out.psl where to put the
output</font>
<br><font size=2 face="Courier New">options:</font>
<br><font size=2 face="Courier New"> -t=type
Database type. Type is one of:</font>
<br><font size=2 face="Courier New">
dna - DNA sequence</font>
<br><font size=2 face="Courier New">
prot - protein sequence</font>
<br><font size=2 face="Courier New">
dnax - DNA sequence translated in six frames
to protein</font>
<br><font size=2 face="Courier New">
The default is dna</font>
<br><font size=2 face="Courier New"> -q=type
Query type. Type is one of:</font>
<br><font size=2 face="Courier New">
dna - DNA sequence</font>
<br><font size=2 face="Courier New">
rna - RNA sequence</font>
<br><font size=2 face="Courier New">
prot - protein sequence</font>
<br><font size=2 face="Courier New">
dnax - DNA sequence translated in six frames
to protein</font>
<br><font size=2 face="Courier New">
rnax - DNA sequence translated in three frames
to protein</font>
<br><font size=2 face="Courier New"> -prot
Synonymous with -d=prot -q=prot</font>
<br><font size=2 face="Courier New"> -dots=N Output
a dot every N query sequences</font>
<br><font size=2 face="Courier New"> -nohead Suppresses
psl five line header</font>
<br><font size=2 face="Courier New"> -minScore=N sets minimum
score. This is twice the matches minus the </font>
<br><font size=2 face="Courier New">
mismatches minus some sort of gap penalty. Default
is 30</font>
<br><font size=2 face="Courier New"> -minIdentity=N Sets minimum
sequence identity (in percent). Default is</font>
<br><font size=2 face="Courier New">
90 for nucleotide searches, 25 for protein or translated</font>
<br><font size=2 face="Courier New">
protein searches.</font>
<br><font size=2 face="Courier New"> -out=type Controls
output file format. Type is one of:</font>
<br><font size=2 face="Courier New">
psl - Default. Tab separated format
without actual sequence</font>
<br><font size=2 face="Courier New">
pslx - Tab separated format with sequence</font>
<br><font size=2 face="Courier New">
axt - blastz-associated axt format</font>
<br><font size=2 face="Courier New">
maf - multiz-associated maf format</font>
<br><font size=2 face="Courier New">
sim4 - similar to sim4 format</font>
<br><font size=2 face="Courier New">
wublast - similar to wublast format</font>
<br><font size=2 face="Courier New">
blast - similar to NCBI blast format</font>
<br><font size=2 face="Courier New">
blast8- NCBI blast tabular format</font>
<br><font size=2 face="Courier New">
blast9 - NCBI blast tabular format with
comments</font>
<br><font size=2 face="Courier New"> -maxIntron=N Sets
maximum intron size. Default is 750000</font>
<br>
<br>
<br><font size=2 face="sans-serif">Best regards,</font>
<br>
<br><font size=2 face="sans-serif">Volker</font>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td width=40%><font size=1 face="sans-serif"><b>Hiram Clawson <hiram@soe.ucsc.edu></b>
</font>
<p><font size=1 face="sans-serif">23.09.2010 18:01</font>
<td width=59%>
<table width=100%>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">To</font></div>
<td><font size=1 face="sans-serif">volker.weinberger@novartis.com</font>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">cc</font></div>
<td><font size=1 face="sans-serif">dev@ensembl.org</font>
<tr valign=top>
<td>
<div align=right><font size=1 face="sans-serif">Subject</font></div>
<td><font size=1 face="sans-serif">Re: [ensembl-dev] R59: -stepSize=5
in blat_gfclient.pm</font></table>
<br>
<table>
<tr valign=top>
<td>
<td></table>
<br></table>
<br>
<br>
<br><tt><font size=2>The case on the arguments is important. It is
-stepSize<br>
<br>
See also: http://www.kentinformatics.com/contact-us.html<br>
<br>
--Hiram<br>
<br>
volker.weinberger@novartis.com wrote:<br>
> Hi,<br>
> <br>
> I'm confused about the option settings for gfClient in <br>
> modules/Bio/Tools/Run/Search/blat_gfclient.pm :<br>
> <br>
> "-out=wublast -stepSize=5 -minScore=20"<br>
> <br>
> as our internal version of gfClient (from BLAT34) doesn't support
the <br>
> "-stepsize" option.<br>
> <br>
> Do you use a customized version of BLAT or any version other than
34 ?<br>
> <br>
> BTW it would be great if the path to the gfClient executable was <br>
> configurable in one of the configuration files rather than hard-coded.<br>
> <br>
> Best regards,<br>
> <br>
> Volker<br>
</font></tt>
<br><font size=2 face="sans-serif"><br>
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