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Hilmar Lapp | 2 Aug 2011 00:36
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[Biopython] Job opportunity: User Interface Design and Web Application Developer

(Apologies if you have received this already or if this is considered  
spam - we're trying to reach out as broad as possible and I know that  
quite a few in the Bio* communities would be well qualified. Please  
feel free to pass on to anyone who might be interested, or might know  
someone who is.)

User Interface Design and Web Application Developer

The National Evolutionary Synthesis Center (NESCent) seeks a creative  
and enthusiastic individual to design user interfaces and web  
applications for scientific applications that manage, analyze,  
visualize and share data in support of evolutionary research. The  
incumbent will work as part of a small informatics team in close  
collaboration with domain scientists.

NESCent (http://nescent.org) is an NSF-funded center dedicated to  
cross-disciplinary research in evolutionary science. Our informatics  
team works closely with visiting and resident scientists to support  
their custom software and database development needs (http://informatics.nescent.org 
), and collaborates broadly with other biodiversity informatics  
projects.  All NESCent software products are open-source, and the  
Center has a number of initiatives to actively promote collaborative  
development of community software resources. Above all, we are  
enthusiastic about our work, about the mission of the Center, and  
about the contribution of informatics to that mission.

Job description: The incumbent will design and develop user interfaces  
and web applications for databases and other software tools for  
sponsored scientists and staff. The job responsibilities include all  
stages of the software development process, including requirements
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Stefanie Lück | 2 Aug 2011 15:15
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[Biopython] clustalW output format

Hello!

I’m using ClustalW2 for my alignments and would like to have the aln1 output
format (http://www.ebi.ac.uk/Tools/msa/clustalw2/help/). This should show
the line numbers. Actually this should be the default but it’s not. 

I tried to add aln1 in \Bio\Align\Applications\_Clustalw.py in line 100+

Option(["-output", "-OUTPUT", "OUTPUT", "output"],

["input"],

lambda x: x in ["GCG", "GDE", "PHYLIP", "PIR", "NEXUS",”ALN1”

                         "gcg", "gde", "phylip", "pir", "nexus", “aln1”]

but it doesn’t work.

Any ideas?

Thanks in advance!

Stefanie

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Peter Cock | 2 Aug 2011 16:54
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Re: [Biopython] clustalW output format

On Tue, Aug 2, 2011 at 2:15 PM, Stefanie Lück <lueck <at> ipk-gatersleben.de> wrote:
> Hello!
>
> I’m using ClustalW2 for my alignments and would like to have the aln1 output
> format (http://www.ebi.ac.uk/Tools/msa/clustalw2/help/). This should show
> the line numbers. Actually this should be the default but it’s not.

I have version 2.1 installed and the default output format is traditional
Clustal output with no residue/base numbers (according to -help).

Which version of ClustalW2 are you using?

I'm expecting we'll need a new wrapper for Clustal Omega (I don't know
why they didn't call it Clustalw v3).

We'll probably also need to update Clustalw parser to cope with base/residue
numbering in the output as well.

Peter

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IRVIN, STEVEN (AG-Contractor/1000 | 2 Aug 2011 17:47
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[Biopython] Bio.Blast.Applications issue with outfmt="quoted string"

Hello,

I am having an issue with the Biopython module making BLAST+ queries.

I am wondering if there is any support in Bio.Blast.Applications  for using the multiple arguments to
-outfmt allowed by NCBI BLAST+ programs such as blastn.

I need to use this for example:

    blastn_cline = NcbiblastnCommandline(query='somefastafile.fas', db='tomato_cdna.db',
evalue=1000, word_size=7, outfmt='10 qseqid sseqid length pident', out='outfile.txt')

The multiple arguments allowed to blastn -outfmt  allow the choice of specific columns output to the csv or
tab separated file such subject_id, etc.

Biopython is returning non-zero exit status 1: USAGE when I run my program with above statement.

Here is a an example coomand line for BLAST+:

prompt_: blastn -query seq_fasta.fas -db local_db.db -out csv_out.csv -dust no -num_alignments 20
-num_descriptions 20 -evalue 1000 -word_size 7 -task blastn -outfmt "10 qseqid sseqid length pident"

I do not yet know if something in Bio.Blast.Applications needs to be modified to support this.

Steve

Steven D Irvin, MS
Bioinformatics Analyst
[cid:image003.png <at> 01CC1925.F25B8430] CC214-A
Monsanto Research Center
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Peter Cock | 2 Aug 2011 18:14
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Re: [Biopython] Bio.Blast.Applications issue with outfmt="quoted string"

On Tue, Aug 2, 2011 at 4:47 PM, IRVIN, STEVEN (AG-Contractor/1000)
<steven.irvin <at> monsanto.com> wrote:
> Hello,
>
> I am having an issue with the Biopython module making BLAST+ queries.
>
> I am wondering if there is any support in Bio.Blast.Applications  for using the multiple arguments to
-outfmt allowed by NCBI BLAST+ programs such as blastn.
>
> I need to use this for example:
>
>    blastn_cline = NcbiblastnCommandline(query='somefastafile.fas', db='tomato_cdna.db',
evalue=1000, word_size=7, outfmt='10 qseqid sseqid length pident', out='outfile.txt')
>
> The multiple arguments allowed to blastn -outfmt  allow the choice of specific columns output to the csv
or tab separated file such subject_id, etc.

Yes, and they are very useful. Try:

blastn_cline = NcbiblastnCommandline(query='somefastafile.fas',
db='tomato_cdna.db', evalue=1000, word_size=7, outfmt='"10 qseqid
sseqid length pident"', out='outfile.txt')

i.e. Include the extra quotes explicitly. That's single quote, double
quote, text, double quote, single quote.
(There are other ways to embed double quote characters in a Python
string but that works for me.)

Peter
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Stefanie Lück | 3 Aug 2011 13:19
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Re: [Biopython] clustalW output format

Thanks Peter!

I'm also using version 2.1. I didn't check the -help, only the homepage
where they say "Default value is: Aln w/numbers [aln1]", which confused
me...
Thanks for mentioning Clustal Omega, I didn't know that say changed the
names.
Stefanie

-----Ursprüngliche Nachricht-----
Von: Peter Cock [mailto:p.j.a.cock <at> googlemail.com] 
Gesendet: Dienstag, 2. August 2011 16:55
An: Stefanie Lück
Cc: biopython <at> lists.open-bio.org
Betreff: Re: [Biopython] clustalW output format

On Tue, Aug 2, 2011 at 2:15 PM, Stefanie Lück <lueck <at> ipk-gatersleben.de>
wrote:
> Hello!
>
> I’m using ClustalW2 for my alignments and would like to have the aln1
output
> format (http://www.ebi.ac.uk/Tools/msa/clustalw2/help/). This should show
> the line numbers. Actually this should be the default but it’s not.

I have version 2.1 installed and the default output format is traditional
Clustal output with no residue/base numbers (according to -help).

Which version of ClustalW2 are you using?
(Continue reading)

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Jessica Grant | 8 Aug 2011 20:08

[Biopython] deleting in-group paralogs from newick trees

Hello,

I am looking at large phylogenetic trees that have many paralogs.  I  
would like to simplify my trees so that all monophyletic paralog  
groups are collapsed--or all sequences except the shortest branch are  
deleted.  Is there a Biopython module that can help?  I started  
looking at Phylo, but couldn't see an obvious way.

Thanks,

Jessica

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Eric Talevich | 8 Aug 2011 21:33
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Re: [Biopython] deleting in-group paralogs from newick trees

On Mon, Aug 8, 2011 at 2:08 PM, Jessica Grant <jgrant <at> smith.edu> wrote:

> Hello,
>
> I am looking at large phylogenetic trees that have many paralogs.  I would
> like to simplify my trees so that all monophyletic paralog groups are
> collapsed--or all sequences except the shortest branch are deleted.  Is
> there a Biopython module that can help?  I started looking at Phylo, but
> couldn't see an obvious way.
>

Hi Jessica,

Yes, Phylo is the right module to use. If I understand your problem
correctly, the tree methods you want are is_monophyletic() and
collapse_all(). Both operate on a clade within the tree. You'd traverse the
tree with get_nonterminals(), check if a paralog group under a clade is
monophyletic, and if so, collapse it.

Do you have a list of paralogs already? And, do you know which groups might
be monophyletic?

If you have groups/clades already, it's simple:

>>> tree = Phylo.read('mytree.nwk', 'newick')
>>> for clade in tree.get_nonterminals(order='postorder'):
...     mono_parent = clade.is_monophyletic([SOME_PARALOG_GROUP])
...     if mono_parent:
...         mono_parent.collapse_all()
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Chris Fields | 9 Aug 2011 22:09
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Re: [Biopython] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour

I'm reviving this thread to see what the current status is (if anything has changed).  The bioperl parser has
the same problem; at the moment we're bascially stuck until NCBI gives some indication as to whether this
is a bug or not.  Any word back from them yet?

(and agreed, it would be nice to have an external bug tracker from NCBI).

chris

On May 4, 2011, at 5:36 AM, Peter Cock wrote:

> On Wed, May 4, 2011 at 10:59 AM, Michal <mictadlo <at> gmail.com> wrote:
>> Hi Peter,
>> Do you have the script which read
>> 
>> https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml
>> 
>> 
>> and what would be the correct output?
>> 
>> Thank you in advance.
>> 
>> Cheers,
>> Michal
> 
> Hi Michal,
> 
> I'm not quite sure what you're asking, but I'll try. First, the three
> data files:
> 
> $ wget https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml
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Peter Cock | 10 Aug 2011 11:15
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Re: [Biopython] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour

On Tue, Aug 9, 2011 at 9:09 PM, Chris Fields <cjfields <at> illinois.edu> wrote:
> I'm reviving this thread to see what the current status is (if anything has
> changed).  The bioperl parser has the same problem; at the moment we're
> bascially stuck until NCBI gives some indication as to whether this is a
> bug or not.  Any word back from them yet?
>
> (and agreed, it would be nice to have an external bug tracker from NCBI).
>
> chris

Hi Chris,

My email to the NCBI on 17 May had a reply from Tao Tao (NCBI User
services) saying it would be brought to their developers' attention.

For reference, the email subject line was:
"Multiple iteration blocks per query in FASTA vs FASTA BLAST XML"

I have just emailed back to enquire if there is any news to report.

Peter

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