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Torsten Seemann | 1 Nov 2007 02:27
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Re: BLAST output parsing

Swapna,

> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
> it.  I did use -m 9 option to get a tabular information of the blast data.
> But it does not include the gene names or the names of the organisms of each
> hit.  Are there any parsers that can do this job ??

The -m 9 tabular output does not include gene descriptions and
organisms. It only includes the "gene id" that was present immediately
after the ">" sign in the FASTA file that was used to create the BLAST
database you specified with the -d option when you ran BLAST.

Hence, no parser will help you. You either have to re-do the BLAST
with a different -m value that includes the information you desire, or
write code to convert your gene IDs into what you want.

--

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
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swapna26 | 1 Nov 2007 04:49
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Re: BLAST output parsing


which -m option do you think will be helpful.  

swapna

Torsten Seemann wrote:
> 
> Swapna,
> 
>> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to
>> parse
>> it.  I did use -m 9 option to get a tabular information of the blast
>> data.
>> But it does not include the gene names or the names of the organisms of
>> each
>> hit.  Are there any parsers that can do this job ??
> 
> The -m 9 tabular output does not include gene descriptions and
> organisms. It only includes the "gene id" that was present immediately
> after the ">" sign in the FASTA file that was used to create the BLAST
> database you specified with the -d option when you ran BLAST.
> 
> Hence, no parser will help you. You either have to re-do the BLAST
> with a different -m value that includes the information you desire, or
> write code to convert your gene IDs into what you want.
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Monash University
> _______________________________________________
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Barry Moore | 1 Nov 2007 05:03
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Re: BLAST output parsing

Swapna-

If you are using NCBI fasta files you can use files from NCBIs gene  
database to map your gene IDs to names and organisms.  Look in  
particular at the files gene2accession, gene2refseq, and gene_info.   
For example, if you had RefSeq protein IDs like NP_123456, you could  
use gene2refseq to map those RefSeq accessions to gene IDs and then  
gene_info to map the gene IDs to organisms and gene name.

B

On Oct 31, 2007, at 7:27 PM, Torsten Seemann wrote:

> Swapna,
>
>> I am new to bioperl.  I did BLAST search of ~4000 genes and I need  
>> to parse
>> it.  I did use -m 9 option to get a tabular information of the  
>> blast data.
>> But it does not include the gene names or the names of the  
>> organisms of each
>> hit.  Are there any parsers that can do this job ??
>
> The -m 9 tabular output does not include gene descriptions and
> organisms. It only includes the "gene id" that was present immediately
> after the ">" sign in the FASTA file that was used to create the BLAST
> database you specified with the -d option when you ran BLAST.
>
> Hence, no parser will help you. You either have to re-do the BLAST
> with a different -m value that includes the information you desire, or
(Continue reading)

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Rohit Ghai | 1 Nov 2007 10:45
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bioperl: cannot run emboss programs using bioperl on windows

Dear all,

I have emboss installed on a windows machine. (Embosswin). I can run
this from the dos command line and the path is present. However, when I 
try to call
an emboss application from bioperl I get a "Application not found error"

  my $f = Bio::Factory::EMBOSS->new();
  # get an EMBOSS application  object from the factory
  my $fuzznuc = $f->program('fuzznuc');
    $fuzznuc->run(
                  { -sequence  => $infile,
                        -pattern   => $motif,
                       -outfile   => $outfile                       
              });
 gives the following error

-------------------- WARNING ---------------------
MSG: Application [fuzznuc] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at searchPatterns.pl line 
102.

Can somebody help me fix this ?

best regards
Rohit

--

--
(Continue reading)

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Jason Stajich | 1 Nov 2007 15:22
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PAML/Codeml parsing

PAML4 breaks our PAML parser right now because the order of things in  
the result file has changed.  Now sequences precede the information  
about the version or the program run.  This means that $result- 
 >get_seqs() fails because we don't parse the sequences.

We'll see what we can do, but as usual with supporting 3rd party  
programs it is brittle when file formats change.  Th

-jason

--
Jason Stajich
jason <at> bioperl.org
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Jason Stajich | 1 Nov 2007 15:32
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Re: bioperl: cannot run emboss programs using bioperl on windows

Presumably the PATH is not getting set properly - you should play  
around printing the $ENV{PATH} variable in a perl script to see if  
actually contains the directory where the emboss programs are  
installed.  Bioperl can only guess so much as to where to find an  
application.  It is also possible that we aren't creating the proper  
path to the executable - you can print the executable path with
print $fuzznuc->executable
I believe unless it is throwing an error at the program() line.

It looks like the code in the Factory object is a little fragile  
assuming that the programs HAVE to be in your $PATH.  I don't know if  
windows+perl is special in any way that it run things so I can't  
really tell if there is specific things you have to do here. You may  
have to run this through cygwin in case PATH and such are just not  
available properly to windowsPerl.

-jason
On Nov 1, 2007, at 5:45 AM, Rohit Ghai wrote:

> Dear all,
>
> I have emboss installed on a windows machine. (Embosswin). I can run
> this from the dos command line and the path is present. However,  
> when I
> try to call
> an emboss application from bioperl I get a "Application not found  
> error"
>
>
>   my $f = Bio::Factory::EMBOSS->new();
(Continue reading)

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Chris Fields | 1 Nov 2007 15:54
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Re: bioperl: cannot run emboss programs using bioperl on windows

This worked for me previously when I tested with WinXP on my old  
machine using EMBOSS v5:

ftp://emboss.open-bio.org/pub/EMBOSS/windows

I haven't tried it with EMBOSSWin (latest is v 2.7); it's probably  
better to use the latest EMBOSS version anyway so I suggest trying  
the version in the above link.  I'll test it again today and let you  
know what I find.

chris

On Nov 1, 2007, at 9:32 AM, Jason Stajich wrote:

> Presumably the PATH is not getting set properly - you should play
> around printing the $ENV{PATH} variable in a perl script to see if
> actually contains the directory where the emboss programs are
> installed.  Bioperl can only guess so much as to where to find an
> application.  It is also possible that we aren't creating the proper
> path to the executable - you can print the executable path with
> print $fuzznuc->executable
> I believe unless it is throwing an error at the program() line.
>
> It looks like the code in the Factory object is a little fragile
> assuming that the programs HAVE to be in your $PATH.  I don't know if
> windows+perl is special in any way that it run things so I can't
> really tell if there is specific things you have to do here. You may
> have to run this through cygwin in case PATH and such are just not
> available properly to windowsPerl.
>
(Continue reading)

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Jason Stajich | 1 Nov 2007 16:31
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PAML3 vs 4

Small tweaks were needed to parse PAML4 results.

Pairwise Ka, Ks parsing (runmode -2) should be working more smoothly  
now on both PAML 3 and 4.
You'll need to get the latest code from CVS in order to see the  
changes to Bio/Tools/Phylo/PAML.pm

I've added tests for PAML4 in the parser and the run code.

If you have scripts that use codeml please give it a try.  I have not  
attempted to play with BASEML or AAML results at this point so if you  
also have codes that use those programs, please try it out and  
provide bugreports if we need to fix things.

-jason

--
Jason Stajich
jason <at> bioperl.org
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Kevin Brown | 1 Nov 2007 18:25
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Re: bioperl: cannot run emboss programs using bioperl onwindows

Sounds like a path issue.  Try to tell bioperl the full path to the
executable rather than just the executable name. 

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org 
> [mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of Rohit Ghai
> Sent: Thursday, November 01, 2007 2:46 AM
> To: bioperl-l <at> lists.open-bio.org
> Subject: [Bioperl-l] bioperl: cannot run emboss programs 
> using bioperl onwindows
> 
> Dear all,
> 
> I have emboss installed on a windows machine. (Embosswin). I can run
> this from the dos command line and the path is present. 
> However, when I 
> try to call
> an emboss application from bioperl I get a "Application not 
> found error"
> 
> 
>   my $f = Bio::Factory::EMBOSS->new();
>   # get an EMBOSS application  object from the factory
>   my $fuzznuc = $f->program('fuzznuc');
>     $fuzznuc->run(
>                   { -sequence  => $infile,
>                         -pattern   => $motif,
>                        -outfile   => $outfile                       
>               });
>  gives the following error
(Continue reading)

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Rohit Ghai | 1 Nov 2007 19:06
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Re: bioperl: cannot run emboss programs using bioperlon windows


Thanks for all the suggestions... but I unfortunately still cannot run 
emboss. I am running the latest version of embosswin  (2.10.0-Win-0.8), 
and the
path is set correctly. I printed $ENV{$PATH} and this contains 
C:\EMBOSSwin which is the correct location.
I also tried setting the path directly but I'm not sure how to do this, 
so I tried this...

my $fuzznuc = $f->program('C:\\EMBOSSwin\\fuzznuc');

this also did not work.

Also tried printing...
$fuzznuc->executable()

gave the following error again
-------------------- WARNING ---------------------
MSG: Application [C:\EMBOSSwin\fuzznuc] is not available!
---------------------------------------------------

Any more ideas ?

thanks !
Rohit

here's the code...

use strict;
use Bio::Factory::EMBOSS;
(Continue reading)

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