[Bioperl-l] need BLAT parse code

[Sean Davis]

Neeti,

You could simply put the file in a text editor and take out the header.
Alternatively, type:

 blat 

without any arguments.  You will notice that there are many options to blat,
one of which is -noHead, which suppresses the header.  Or, look at only
lines that begin with a number using a regular expression.

Ultimately, I think that it will serve you well to read a perl book, though,
as parsing a text file is an important and basic topic to grasp if you want
to use perl for data analysis.

Sean

On 11/29/05 9:43 AM, "Jason Stajich" <jason.stajich at duke.edu> wrote:

> 
> 
> Begin forwarded message:
> 
>> From: neeti somaiya <neetisomaiya at gmail.com>
>> Date: November 29, 2005 1:27:27 AM EST
>> To: Jason Stajich <jason.stajich at duke.edu>
>> Subject: Re: [Bioperl-l] need BLAT parse code
>> 
>> I use the following code :
>> 
>> open(FH,"output.psl");
>> while(<FH>)
>> {
>>     if( /^psLayout/ )
>>     {
>>           for( 1..4 ) { <> }
>>       }
>>      my @line = split;
>>      my ( $matches,$mismatches,$rep_matches,$n_count,
>>             $q_num_insert,$q_base_insert,
>>             $t_num_insert, $t_base_insert,
>>             $strand, $q_name, $q_length, $q_start,
>>             $q_end, $t_name, $t_length,$t_start, $t_end, $block_count,
>>             $block_sizes,  $q_starts,      $t_starts
>>             ) = split;
>> 
>> 
>>       print $t_start;
>>       print "\n";
>>       print $t_end;
>> 
>> }
>> 
>> for output.psl file :
>> 
>> match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap
>> strand  Q               Q       Q       Q       T
>> T       T       T       block   blockSizes      qStarts  tStarts
>>         match   match           count   bases   count
>> bases           name            size    start   end
>> name            size    start   end     count
>> ----------------------------------------------------------------------
>> ----------------------------------------------------------------------
>> -------------------
>> 27025   0       0       0       0       0       0       0
>> +       query_sequence3 27025   0       27025
>> database_sequence3      57701691        132995  160020  1
>> 27025,  0,      132995,
>> ~
>> 
>> 
>> It gave me output :
>> 
>> Q
>> Q
>> 
>> 132995
>> 160020
>> 
>> What is the Q? Cant I obtain the coordinates (132995, 160020) alone?
>> 
>> Please let me know.
>> Thanks.
>> 
>> On 11/28/05, Jason Stajich <jason.stajich at duke.edu> wrote:
>> Bio::SearchIO::psl can parse psl output.
>> 
>> or more simply:
>> 
>> while(<>) {
>>    if( /^psLayout/ ) { # if there is a header
>>    for( 1..4 ) { <> }  # take next 4 lines to skip the header
>>    }
>>   my @line = split;
>>   my ( $matches,$mismatches,$rep_matches,$n_count,
>>              $q_num_insert,$q_base_insert,
>>              $t_num_insert, $t_base_insert,
>>              $strand, $q_name, $q_length, $q_start,
>>              $q_end, $t_name, $t_length,$t_start, $t_end,
>> $block_count,
>>              $block_sizes,  $q_starts,      $t_starts
>>              ) = split;
>> 
>>   #  query aln vals are  $q_start, and $q_end values
>>   # hit aln vals are $t_start, $t_end
>> }
>> 
>> On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote:
>> 
>>> Hi,
>>> 
>>> I am using BLAT in a project.I am having simple .psl output files
>>> after
>>> running BLAT of a gene sequences against full chromosomal
>>> sequences.Doesanyone have a simple BLAT parse code. I am only
>>> interested in obtaining the
>>> alignment start and end positions on the target.
>>> --
>>> -Neeti
>>> Even my blood says, B positive
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>> 
>> --
>> Jason Stajich
>> Duke University
>> http://www.duke.edu/~jes12
>> 
>> 
>> 
>> 
>> 
>> -- 
>> -Neeti
>> Even my blood says, B positive
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
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