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alan | 1 Oct 03:53
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exonerate

Hi,

>> I am calling exonerate.pm within my script while attempting to  
>> align cDNA  to multiple genomic fragments. After processing about  
>> 120+ genomic fragments my code crashes with the following error:
>>
>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>> aborting...
>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF / 
>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>
>> The code in Exonerate.pm closes the tmpfile at the end of the  
>> routine yet I get the error message about "too many open files".
>> Any suggestions on how I should be closing these files?
>>
>>
>> Extract from my code that runs exonerate is listed below.
>>
>> foreach my $f(@files) {
>>   next unless (-f  "$dir/$f");
>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>   my $query_obj = $q_in->next_seq();
>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", - 
>> format=>"Fasta");
>>   my $target_obj = $target_in->next_seq();
>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
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issam outaleb | 1 Oct 13:46
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help about Fasta file???


hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;

all 

#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and
Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and
Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht möglich zum öffnen!!" ;open
(OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen
Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;       
if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {       
#print OUT $1."\n"; #print this IPIs in this file.

 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new
file with the description

#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    

		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){

$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien
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Shameer Khadar | 1 Oct 18:57
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How to draw Phylogeny Tree using Bioperl ?

Dear All,

Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
 My input file are in phylip  treefile format. Any Modules / codes in
Bio::Graphics / Phylogeny sections ?

Input file :
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000)
 :1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74
 719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);

--

-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in
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Lucia Peixoto | 1 Oct 20:03
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Re: How to draw Phylogeny Tree using Bioperl ?

I think you'll have better luck using some of already available programs to do
that, you'll get better looking trees. If you just have one tree to draw I
recommend you use:
http://itol.embl.de/

Lucia

Quoting Shameer Khadar <shameer <at> ncbs.res.in>:

> Dear All,
>
> Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
>  My input file are in phylip  treefile format. Any Modules / codes in
> Bio::Graphics / Phylogeny sections ?
>
> Input file :
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000)
 :1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
> 
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.747
 19,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
> 
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
(Continue reading)

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Shameer Khadar | 1 Oct 20:39
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Re: How to draw Phylogeny Tree using Bioperl ?

Dear Lucia,

Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
methods. Some how missed this excellent HOWTO :
http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
tried that and it worked very nicely. I have to work around to beautify
the tree and I am just going to do that.

Thanks & Cheers,
Shameer

> OK
>
> you can use the implementations in Bio::TreeIO
>
> you can basically read the tree in newick format and out as an svg graph
> something like this:
>
> my $in = new Bio::TreeIO(-file => 'input',
>                          -format => 'newick');
> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>                           -format => 'svggraph');
> while( my $tree = $in->next_tree ) {
>     $out->write_tree($tree);
> }
>
> you can also use Bio::Tree::Draw
>
> hope that helps
>
(Continue reading)

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Lucia Peixoto | 1 Oct 20:48
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Re: How to draw Phylogeny Tree using Bioperl ?

Yes,
that's the issue about those commands, trees are not pretty at all
that's why for a one tree only kind of thing I rather use ITOL
other thing to try is the tree drawer of the Mesquite package
glad I could help

Lucia

Quoting Shameer Khadar <shameer <at> ncbs.res.in>:

> Dear Lucia,
>
> Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
> methods. Some how missed this excellent HOWTO :
> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
> tried that and it worked very nicely. I have to work around to beautify
> the tree and I am just going to do that.
>
> Thanks & Cheers,
> Shameer
>
> > OK
> >
> > you can use the implementations in Bio::TreeIO
> >
> > you can basically read the tree in newick format and out as an svg graph
> > something like this:
> >
> > my $in = new Bio::TreeIO(-file => 'input',
> >                          -format => 'newick');
(Continue reading)

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Jason Stajich | 1 Oct 21:32
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Re: How to draw Phylogeny Tree using Bioperl ?

I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
for prettier trees - you get postscript out but you can render this  
to png or jpg with unix tools.  If there is a better stand alone tree  
drawing engine we're happy to try and integrate it into bioperl - the  
modules here are native Perl only and you can use the bioperl-run  
modules that wrap DrawTree and DrawGram from EMBOSS to get other PS  
rendering output.

Mesquite, TreeView or other tools are usually much better but not  
always an option if you want to auto-render these images for a  
website, etc.

-jason

On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:

> Yes,
> that's the issue about those commands, trees are not pretty at all
> that's why for a one tree only kind of thing I rather use ITOL
> other thing to try is the tree drawer of the Mesquite package
> glad I could help
>
> Lucia
>
> Quoting Shameer Khadar <shameer <at> ncbs.res.in>:
>
>> Dear Lucia,
>>
>> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
>> Tree::Draw
(Continue reading)

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outaleb Issame | 2 Oct 04:37
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need help ??parse AcNum from fasta?

Hi every body,
i have some AccNum in a file-> IPI67675
                                                 IPI98976.
                                                 ...

what i want is how can i look in the fasta file (db fasta) if there is 
some match
if yes then copy the entire entry into a new fasta file.
i tried with bioperl but cause i m noob:-(( i don t get it.
thx all
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Kevin Lam | 2 Oct 08:21

divide and blast blastunsplit blast subsequence

Hi!
I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
sequence)
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in
bioperl.

I found similar solutions like
http://www.bio.davidson.edu/projects/DAB/DAB.html
divide and blast (but I need to specify coords)

there also this from the bioperl archives
http://bioinformatics.org/pipermail/bioclusters/2002-August/000375.html

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?
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Nathan S. Haigh | 2 Oct 09:56
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Re: need help ??parse AcNum from fasta?

outaleb Issame wrote:
> Hi every body,
> i have some AccNum in a file-> IPI67675
>                                                  IPI98976.
>                                                  ...
>
> what i want is how can i look in the fasta file (db fasta) if there is 
> some match
> if yes then copy the entire entry into a new fasta file.
> i tried with bioperl but cause i m noob:-(( i don t get it.
> thx all
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   

Can you state clearly, what is in the "AccNum" file exactly, some sample
text from the actual file would be good. Is the FASTA file containing
the sequences in raw FASTA format or has it been processed using
somthing like formatdb from the BLAST software?

A few more details will help people understand and in turn help you with
a swift solution.

Cheers
Nath
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Gmane