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

gopu_36 gopu_36 at yahoo.com
Sun Mar 15 06:08:42 EDT 2009


Hi Jason,

I have a doubt now. I started blat with psl output as well as with blast
output format. But when I try to compare the results, the total number of
results vary. For blast output when I grep for Identities, it is more than
the psl results. But why is it happening? I thought only the ouput format is
going to be in BLAST like but why there is change the number of results? Am
I missing something. Basically, I want to get some fields from psl output
and trying to get the identity score from blast output result file. Is it
not possible?

or can I use as below:

percent_id = 100x($matches + $rep_matches)/( $matches + $mismatches +
$rep_matches ) or 
percentage identity =  ( matches not in repeats + matches in repeats ) /
query length    

Please let me know as I am keen in parsing psl as I don't have bioperl to
start parsing blast output. Thanks.


gopu_36 wrote:
> 
> Yes Jason, Thanks and I did it using -out=type. Thanks.
> 
> Jason Stajich-3 wrote:
>> 
>> 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.
>>>>>>
>>>>>
>>>>> -- 
>>>>> View this message in context:
>>>>> http://www.nabble.com/script-to-calculate-percentage-identity-for-BLAT-psl-tp22476983p22519073.html
>>>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Jason Stajich
>>>> jason at bioperl.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>> Quoted from:
>>> http://www.nabble.com/script-to-calculate-percentage-identity-for-BLAT-psl-tp22476983p22519116.html
>>>
>> 
>> Jason Stajich
>> jason at bioperl.org
>> 
>> 
>> 
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> 
> 
> 

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