[Bioperl-l] script to calculate percentage identity for BLAT psl
gopu_36
gopu_36 at yahoo.com
Sun Mar 15 10:08:42 UTC 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
>>
>>
>
>
--
View this message in context: http://www.nabble.com/script-to-calculate-percentage-identity-for-BLAT-psl-tp22476983p22521531.html
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
More information about the Bioperl-l
mailing list