[Bioperl-l] script to calculate percentage identity for BLAT psl

[Jason Stajich]

you should read the blat documentation - if you type blat alone on the  
command-line or read any of the documentation UCSC provides for the  
tool  it gives you lots of detailed information on how to run it. I  
bet you can figure out how to specify a different output format based  
on reading that documentation.

-jason
On Mar 14, 2009, at 7:39 PM, gopu_36 at yahoo.com wrote:

> Hi Jason,
> Thanks for your help.
>
> I did try as below for testing purpose:
>
> blat  database.fa query.fa output.psl
> blat  database.fa query.fa output.blast
>
> Both the results looks the same and the output.blast also lokks  
> lo=ike normal psl format. As I have always used .psl format, I am  
> not sure what the problem while getting the blast like output? Could  
> you please let me know?
> Jason Stajich-3 wrote:
>>
>> well you could just output it in blast9 output and then the 3rd  
>> column
>> is percent identity.
>>
>> On Mar 14, 2009, at 6:04 PM, gopu_36 wrote:
>>
>>>
>>> Please let me know whether any other way of calculating the  
>>> precentage
>>> identity for commandline BLAT results? . Thanks.
>>>
>>> gopu_36 wrote:
>>>>
>>>> Hi,
>>>>
>>>> I did go through FAQ from BLAT on how to calculate the precentage
>>>> identity
>>>> from http://genome.ucsc.edu/FAQ/FAQblat#blat4
>>>> As a new comer, I don;t usederstand on how to implement this.
>>>> Please let
>>>> me know how to plugin the script for my output.psl file. Please let
>>>> me
>>>> know. It would be of great help.
>>>>
>>>> Thanks and Regards.
>>>>
>>>
>>> -- 
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>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>>
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>>
>> Jason Stajich
>> jason at bioperl.org
>>
>>
>>
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>>
> Quoted from:
> http://www.nabble.com/script-to-calculate-percentage-identity-for-BLAT-psl-tp22476983p22519116.html
>

Jason Stajich
jason at bioperl.org