Andreo Beck | 1 Aug 04:59 2006
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$hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

  Hi,

  Can $hit_object->frac_aligned_hit or $hit_object->frac_aligned_query give outputs > 1 ?
  I get some > 1 values. Does using  the parentheses (e.g. $hit_object->frac_aligned_hit()) make any difference?

  Thanks,
  Andy

 		
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Andreo Beck | 1 Aug 04:56 2006
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$hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Hi,

  Can $hit_object->frac_aligned_hit or $hit_object->frac_aligned_query give outputs > 1 ?
  I get them. Does using  the parentheses (e.g. $hit_object->frac_aligned_hit()) make any difference?

  Thanks,
  Andy

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Sendu Bala | 1 Aug 08:49 2006
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Re: $hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Andreo Beck wrote:
>   Hi,
>    
>   Can $hit_object->frac_aligned_hit or $hit_object->frac_aligned_query give outputs > 1 ?
>   I get some > 1 values. 

That might depend on what $hit_object is (Bio::Search::Hit::GenericHit 
?), but I'd say it's probably a bug if you get over 1. Can you give an 
example where you got over 1? Provide the code and the input data.

> Does using  the parentheses (e.g. $hit_object->frac_aligned_hit()) make any difference?

No, empty parentheses are only needed to make it clear to the perl 
interpreter you are calling a subroutine in ambiguous cases; 
$obj->method isn't ambiguous.
Yuval Itan | 1 Aug 15:36 2006
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Re: Getting sequences by base pair locations

Thank you all for all the helpful answers!
Malcolm- I've used the UCSC server to do the BLAT search (because I 
couldn't run it locally due to memory problems)- so I could not get the 
chimp sequences in a convenient way. I have the results also in a 
normal Blat output including all usual fields: chromosome number etc.
Wade- thanks a lot for your offer, that would be great. The chimp 
genome is just one large fasta format file.
Cheers,
Yuval
On 28 Jul 2006, at 14:30, Sean Davis wrote:

> Yuval Itan wrote:
>> Hello all,
>> I was BLATing a few hundred human genes against the chimp genome, and 
>> kept the best chimp hits for every human gene.
>> I have the base pair start and end location for every chimp hit, and 
>> I need to get the sequence for each of these chimp hits. Here is an 
>> example for a few chimp hits bp locations:
>> Start End*
>> *142854 144504
>> 154479 155198
>> 153066 167370
>> 163146 163559
>> I have one chimp genome file (about 3GB) including all chromosomes, 
>> but I could also get one file per chromosome if that would make 
>> things easier. Does anyone have a script or a link for an interface 
>> that can do the job?
Cook, Malcolm | 1 Aug 17:12 2006

Re: Getting sequences by base pair locations

Yuval,

Glad to help.  Given that you are not running blat suite locally, but at
ucsc, you should try this approach:

upload/paste your blat results (in blat's native output format, psl) as
a custom track in the genome browser, named, say, myhumanhits
(i.e. just give the blat results a new first line like: `track
name="myhumanhits" description="myhumanhits from my favorite human
genes" visibility=2`)
then goto the table browser and configure it 
	group = 'custom tracks'
	track = 'myhumanhits'
	retion = genome
	output format = sequence
	output file = myhumanhits.fasta

submit it

When prompted, Save the myhumanhits.fasta to your computer and take it
from there.

I'm not sure how many hits this will work for, but i just did this on a
small track and it works just fine.  Only problem, the first word in the
fasta defline is always the same for all sequences.  You'll have to
'uniqify' these names somehow probably (depedning of course on your
application).

Let us know & Good luck & ask for good email support on ucsc genome
browser subscribe to
(Continue reading)

Andreo Beck | 1 Aug 19:51 2006
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Re: (no subject)

I attach 1 "erroneous" part (record 9) and 1 correct part (record 8)...the entire file is ~500mb...

Sendu Bala <bix <at> sendu.me.uk> wrote: 
  Andreo Beck wrote:
> Thanks Sendu.I get this when I try parsing a WUBLASTP report (thats too 
> huge to upload).

Unfortunately that's the most important thing for figuring out what's 
going on. Could you compress it (zip or tar.gz) along with the fasta 
file you used to do the blast? If its only a few MB you can email it to 
me directly, or create a bug report at 
http://bugzilla.bioperl.org/index.cgi and upload the files that way.

(You could also try cutting both files down to just the sequence and 
hits that give results > 1, with a few < 1 for comparison - just make 
sure it still works after you edit the files)

FYI, at a glance your code looked fine.

Cheers,
Sendu.

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Reference:  Gish, W. (1996-2004) http://blast.wustl.edu

Query=  AT1G70120.1 | Symbol: None | hypothetical protein |
(Continue reading)

Chris Fields | 2 Aug 00:52 2006
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Re: (no subject)

Andreo,

Okay, not cool to email an entire BLAST file to the entire Bioperl-l  
list!  Sendu wanted it emailed to him, not everybody!

Chris

On Aug 1, 2006, at 12:51 PM, Andreo Beck wrote:

> I attach 1 "erroneous" part (record 9) and 1 correct part (record  
> 8)...the entire file is ~500mb...
>
>
> Sendu Bala <bix <at> sendu.me.uk> wrote:
>   Andreo Beck wrote:
>> Thanks Sendu.I get this when I try parsing a WUBLASTP report  
>> (thats too
>> huge to upload).
>
> Unfortunately that's the most important thing for figuring out what's
> going on. Could you compress it (zip or tar.gz) along with the fasta
> file you used to do the blast? If its only a few MB you can email  
> it to
> me directly, or create a bug report at
> http://bugzilla.bioperl.org/index.cgi and upload the files that way.
>
> ....

Christopher Fields
Postdoctoral Researcher
(Continue reading)

Kevin Brown | 2 Aug 00:43 2006
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Re: Getting sequences by base pair locations

Perl Mechanize is a great way to submit web forms repeatedly.  I do it
for things like MHC epitope prediction sites as well as a way to grab
things like journal articles matching certain keywords.

http://www.perl.com/pub/a/2003/01/22/mechanize.html
http://search.cpan.org/dist/WWW-Mechanize/lib/WWW/Mechanize.pm 

> -----Original Message-----
> From: bioperl-l-bounces <at> lists.open-bio.org 
> [mailto:bioperl-l-bounces <at> lists.open-bio.org] On Behalf Of 
> Cook, Malcolm
> Sent: Tuesday, August 01, 2006 8:12 AM
> To: Yuval Itan; bioperl-l <at> lists.open-bio.org
> Subject: Re: [Bioperl-l] Getting sequences by base pair locations
> 
> Yuval,
> 
> Glad to help.  Given that you are not running blat suite 
> locally, but at
> ucsc, you should try this approach:
> 
> upload/paste your blat results (in blat's native output 
> format, psl) as
> a custom track in the genome browser, named, say, myhumanhits
> (i.e. just give the blat results a new first line like: `track
> name="myhumanhits" description="myhumanhits from my favorite human
> genes" visibility=2`)
> then goto the table browser and configure it 
> 	group = 'custom tracks'
> 	track = 'myhumanhits'
(Continue reading)

杨 鹏程 | 2 Aug 07:51 2006
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Develop with perl on oracle?

hi, i am a novice on the database. i want to construct a database about esophegeal carcinoma or else use
oracle and develop with perl. on end i want to publish my database use cgi which programmed by perl script.
anyone has the same thought or has the same experience can give me some advice!! thanks a lot!

  Yang PCh from China

 		
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Sendu Bala | 2 Aug 13:23 2006
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Re: $hit_object->frac_aligned_hit/$hit_object->frac_aligned_query

Andreo Beck wrote:
> Can $hit_object->frac_aligned_hit or $hit_object->frac_aligned_query
> give outputs > 1 ? I get some > 1 values.

This should now be fixed in CVS. You should be able to grab just 
Bio/Search/SearchUtils.pm if you don't want to install all of bioperl-live.

( http://code.open-bio.org/cgi/viewcvs.cgi/bioperl-live/ )

It should be noted that all frac_* statistics and probably others from 
hit objects have had a high chance of being wrong in the past, and 
frac_identical and frac_conserved can still be very wrong*. It would be 
a good idea if someone were to make these methods return slightly more 
sane numbers.

[*] which is to say, more wrong than you might reasonably expect, given 
the limitations with gapped or alignment-free blasts

Gmane