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Florent Angly | 1 May 2011 01:19
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Re: Bioperl-l Digest, Vol 96, Issue 28

Kamal,
It looks like you have a typo somewhere: what is 'clustaw'? You probably 
mean 'clustalw'.
Florent

On 29/04/11 16:34, khush ........ wrote:
> Dear,
>
> I am trying to calculate the Ka/ks ratio of my aligned sequences by clustalx
> and for the same I am using
>
> So I am using the the scrip given at
> https://github.com/bioperl/bioperl-live/blob/master/scripts/utilities/pairwise_kaks.PLS
>
> when I am trying to run the It alert me to chage the line
>
>   "warn("Could not find the executable for $aln_prog, make sure you have
> installed it and have either set ".uc($aln_prog)."DIR or it is in your
> PATH");"
>
> "Could not find the executable for clustaw, make sure you have installed it
> and have either set CLUSTAWDIR or it is in your PATH at kaks.pl line 52."
>
> I have clustalw2 and clustalx installed on my system. How to and where to
> set the path for the same and how to calculate the Ka/Ks raio for my
> sequences.
>
> Thank you
> Kamal
>
(Continue reading)

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duxroq | 2 May 2011 00:26
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Re: Clustalw problems!!!


Thank you so much for your help, it now runs perfectly :-)  I guess
misunderstood how CLUSTALWDIR works.

Chris Fields-5 wrote:
> 
> I don't have access to a Windows machine to test this, unfortunately.  I
> did notice you set CLUSTALWDIR to the actual executable, NOT the directory
> it is in.  Also, the executable name is 'clustalw.exe', not 'clustalw', so
> possibly change that prior to instantiation:
> 
> $Bio::Tools::Run::Alignment::ClustalW::PROGRAM_NAME = 'clustalw.exe';
> 
> Maybe that's a start?
> 
> chris
> 
> On Apr 29, 2011, at 5:45 PM, duxroq wrote:
> 
>> 
>> Hi, I'm not sure whether my program is not finding the clustal w
>> exceutable
>> or if it is having trouble with the module itself.  Here is my error, in
>> the
>> image below:
>> 
>> http://old.nabble.com/file/p31509401/Untitled.png Untitled.png 
>> 
>> here is my code:
>>
(Continue reading)

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Florent Angly | 2 May 2011 04:17
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Re: Convert fastq to fasta

You need to use this module: Bio::SeqIO::fastq
Read this for explanations: 
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqIO/fastq.html
Regards,
Florent

On 28/04/11 10:26, perlbio007 wrote:
> Iam new to Bioperl. Pls help.
> I have a zip folder of sequences which is in fastq format. I need to convert
> it in fasta format?
> How I do that using bioperl?What module do I need?
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khush ........ | 2 May 2011 08:02
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Re: Bioperl-l Digest, Vol 96, Issue 28

Dear Florent,

Thanks for your reply. Yes its clustalw, but I have clustalw2 and clustalx
installed on my fc13 machine. I am not sure where to set the path for the
same. I have some 400 nucleotide sequences for which I have to do the
analysis i.e is y I found this script useful to me.

help me...

Thank you
Kamak

On Sun, May 1, 2011 at 4:49 AM, Florent Angly <florent.angly <at> gmail.com>wrote:

> Kamal,
> It looks like you have a typo somewhere: what is 'clustaw'? You probably
> mean 'clustalw'.
> Florent
>
>
>
> On 29/04/11 16:34, khush ........ wrote:
>
>> Dear,
>>
>> I am trying to calculate the Ka/ks ratio of my aligned sequences by
>> clustalx
>> and for the same I am using
>>
>> So I am using the the scrip given at
(Continue reading)

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sukeerthi teja Rallapalli | 2 May 2011 20:12
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Doubt - Regarding Stand Alone Blast

Dear Sir,

I am trying to create a stand alone database in Mac using Blast.

I have installed Blast. I have pasted my 2 files (input file and the large
database file) also in the same folder as in Blast.

So far these are the commands that i have used are these

*"**formatdb -i sequences.fasta -p T -o T *
*
*
*
*

*blastall -p blastp -d homologene_result.fasta -i sequences.fasta -o stdout
-a 1 -e 10*

*
*

*
*

*OR*

*
*

 *makeblastdb -in** **sequences.fasta** **-dbtype **prot*
(Continue reading)

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Jonathan "Duke" Leto | 2 May 2011 20:24
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Re: GSoC/BioPerl Reorganization Project

Howdy,

>> One additional question: how are we dealing with commit history?  I don't
>> think there is an easy way of carrying that over to a brand-new repo...
>>
>> Not that it's a problem, but something to think about.
>
>
> I believe git filter-branch can be used:
>
> "filter-branch is commonly used on a clone of the repo to split a too-large
> repo into smaller ones."
>
> https://github.com/matthewmccullough/git-workshop/raw/master/workbook/htmls/27-Filter-Branch.html

No commit history needs to get dropped on the floor. I can help with the git
filter-branch stuff, just let me know.

Duke

--

-- 
Jonathan "Duke" Leto <jonathan <at> leto.net>
209.691.DUKE // http://leto.net
NOTE: Personal email is only checked twice a day at 10am/2pm PST,
please call/text for time-sensitive matters.
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Chris Fields | 2 May 2011 20:30
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Re: GSoC/BioPerl Reorganization Project

On May 2, 2011, at 1:24 PM, Jonathan Duke Leto wrote:

> Howdy,
> 
>>> One additional question: how are we dealing with commit history?  I don't
>>> think there is an easy way of carrying that over to a brand-new repo...
>>> 
>>> Not that it's a problem, but something to think about.
>> 
>> 
>> I believe git filter-branch can be used:
>> 
>> "filter-branch is commonly used on a clone of the repo to split a too-large
>> repo into smaller ones."
>> 
>> https://github.com/matthewmccullough/git-workshop/raw/master/workbook/htmls/27-Filter-Branch.html
> 
> No commit history needs to get dropped on the floor. I can help with the git
> filter-branch stuff, just let me know.
> 
> Duke

I *hate* it when I drop my commit history on the floor. :)

On a more serious note, it's very possible as we edge towards coding we will need help, so that would be great!

chris
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Peter Cock | 3 May 2011 11:24
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Interesting BLAST 2.2.25+ XML behaviour

Hello all,

I've CC'd the BioPerl, BioRuby, BioJava and Biopython development mailing
lists to make sure you're aware of this, but can we continue any discussion
on the cross-project open-bio-l mailing list please?

I noticed that recent versions of BLAST are not using a single <iteration>
block for each query, which was the historical behaviour and assumed
by the Biopython BLAST XML parser. This may be a bug in BLAST.
See link below for an example.

Has anyone else noticed this, and has it been reported to the NCBI yet?

Thanks,

Peter

(Not for the first time, I wish there was a public bug tracker for BLAST,
or at least a private bug tracker so we could talk about issues with an
NCBI assigned reference number.)

---------- Forwarded message ----------
From: Peter Cock <p.j.a.cock <at> googlemail.com>
Date: Wed, Apr 20, 2011 at 6:08 PM
Subject: Interesting BLAST 2.2.25+ XML behaviour
To: Biopython-Dev Mailing List <biopython-dev <at> biopython.org>

Hi all,

Have a look at this XML file from a FASTA vs FASTA search
(Continue reading)

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Dave Messina | 3 May 2011 11:16
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Re: Doubt - Regarding Stand Alone Blast

>
> formatdb -i sequences.fasta -p T -o T
>

The above command makes a database of the sequences.fasta file.

> blastall -p blastp -d homologene_result.fasta -i sequences.fasta -o stdout
> -a 1 -e 10
>

But then you ask for a database made from the homologene_result.fasta file.

For the above blastall command to work, you will have to use the following
formatdb command:

 formatdb -i homologene_result.fasta -p T -o T

Dave
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Dave Messina | 3 May 2011 14:06
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Re: Doubt - Regarding Stand Alone Blast

Hi Teja,

Please 'reply all' to keep the mailing list Cc'd so that it can be archived
and everyone can follow along.

On Tue, May 3, 2011 at 13:45, sukeerthi teja Rallapalli <tejaminnu <at> gmail.com
> wrote:

> Hi David,
>
> I basically have these 2 files, the
>
> Input file        = sequences.txt
> Database file  = homologene_result.txt
>
> Isn't "blastall" an older version command ? That is why i was using
> makeblastdb
>

In your previous email, you made the same mistake with both formatdb and
makeblastdb. (making a database for one file but specifying the other file's
name as the database when you tried to run blast)

> This is what i typed
>
> 172-30-8-231:bin sukeerthiteja$ makeblastdb -in homologene_result.txt
> -dbtype prot -parse_seqids -out teja1 blastp -query sequences.txt -db teja2
>

You've combined two separate commands on the same line here.
(Continue reading)

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