in reply to parsing mismatch from blast output

I couldn't find any files of the correct format. I tried blastn at NCBI on NC_000009.11, but after waiting 45 minutes it said: "Informational Message: blastsrv4.REAL: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24)." which probably just goes to show I don't know what the .... I'm doing.

So I based this upon your sample: 

#! perl -slw
use strict;

my( $ID, $query, $off );
while( <DATA> ) {
    if( m[^>]  ) {
        ( $ID ) = (split '\|', $_)[ 1 ];
        next;
    }
    if( m[^Query] ) {
        ( $query ) = m[^Query\s+(\d+)];
        my $top = substr $_, 15;
        my $pipes = substr <DATA>, 15;
        my $bot = substr <DATA>, 15;
        my $p = 0;
        while( $p = 1+index $pipes, ' ', $p ) {
            printf "%20s :(%d) %1s/%1s\n",
             $ID, $query+$p,
             substr( $top, $p-1, 1 ),
             substr( $bot, $p-1, 1 );
        }
    }
}

__DATA__

[download]
>lcl|14079 ref|NC_000009.11|:4900000-5300000 Homo sapiens chromosome 9
+,
GRCh37 primary reference assembly
Length=400001
 Score =  270 bits (146),  Expect = 2e-74
 Identities = 148/149 (99%), Gaps = 0/149 (0%)
 Strand=Plus/Minus

Query  1      TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  60
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48784  TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  48725

Query  61     AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  120
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48724  AATGGGATCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  48665

Query  121    ACAGGCAACCTACAGAATGGGAGAACATT  149
              |||||||||||||||||||||||||||||
Sbjct  48664  ACAGGCAACCTACAGAATGGGAGAACATT  48636

>lcl|14080 ref|NC_000009.11|:4900000-5300000 Homo sapiens chromosome 9
+,
GRCh37 primary reference assembly
Length=400001
 Score =  270 bits (146),  Expect = 2e-74
 Identities = 148/149 (99%), Gaps = 0/149 (0%)
 Strand=Plus/Minus

Query  1      TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  60
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48784  TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  48725

Query  61     AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  120
              ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||
+||||
Sbjct  48724  AATGGGATCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  48665

Query  121    ACAGGCAACCTACAGAATGGGAGAACATT  149
              ||| |||| |||||| |||||||||||
Sbjct  48664  ACAGGCAACCTACAGAATGGGAGAACATT  48636

>lcl|14081 ref|NC_000009.11|:4900000-5300000 Homo sapiens chromosome 9
+,
GRCh37 primary reference assembly
Length=400001
 Score =  270 bits (146),  Expect = 2e-74
 Identities = 148/149 (99%), Gaps = 0/149 (0%)
 Strand=Plus/Minus

Query  1      TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  60
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48784  TGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATT
+GACA  48725

Query  61     AATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  120
              |||||||||||||| |||||||||||||||||||||||||||||||||||||||||
+||||
Sbjct  48724  AATGGGATCTAATTCAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGA
+GTGA  48665

Query  121    ACAGGCAACCTACAGAATGGGAGAACATT  149
              |||||||||||||||||||||||||||||
Sbjct  48664  ACAGGCAACCTACAGAATGGGAGAACATT  48636

[download]

Outputs:

c:\test\blast>..\853819.pl
           14079 ref :(75) A/C
           14080 ref :(15) A/A
           14080 ref :(90) T/T
           14080 ref :(124) G/G
           14080 ref :(129) C/C
           14080 ref :(136) A/A
           14081 ref :(75) A/C

[download]
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
RIP an inspiration; A true Folk's Guy

Replies are listed 'Best First'.
Re^2: parsing mismatch from blast output
by Anonymous Monk on Aug 11, 2010 at 09:34 UTC
    HI Thanks for that! Insted of getting the position in reference to Query, I qould like to have them in reference to Subject. So, the output should be something like this. 14079 ref 487239 A/C. my tweaks other than your suggestions are here 
    #!/usr/local/bin/perl -sl
#

use strict;
use Getopt::Long;

my $home = $ENV{'HOME'};


my($ID, $query, $off, $idi, $subject);
print "ID\tposition\tvariation\n";
while(<DATA>) {
  next if $. <20;

  if(m[^>]) {
  
   ($ID) = (split '\|',$_)[1];
   
   #!/usr/local/bin/perl -sl
#

use strict;
use Getopt::Long;

my $home = $ENV{'HOME'};


my($ID, $query, $off, $idi, $subject);
print "ID\tposition\tvariation\n";
while(<DATA>) {
  next if $. <20;

  if(m[^>]) {
  
   ($ID) = (split '\|',$_)[1];
   
   
  }
 if(/^\s+Identities/){
   
   my($identity, undef) = split/,/ ;
   ($idi) = $identity =~ /\sIdentities\s\=\s\d{3}\/\d{3}\s\((\d{2,3}\%
+)\)$/;
 } 
  
 if($idi eq "95%") {
 
  if(m/^Query/) {
  ($query) = m[^Query\s+(\d+)];
   my $top = substr $_, 15;
   my $pipes = substr <DATA>,15;
   my $bot = substr <DATA>, 15;
   my $p = 0 ;
   while ($p = 1+index $pipes,' ', $p) {
     
    printf "%20s\t%d\t%1s/%1s\n",$ID,$query+$p, substr( $top, $p-1, 1 
+),substr( $bot, $p-1, 1 );
    
   }
 }
}
   
}
  }
 if(/^\s+Identities/){
   
   my($identity, undef) = split/,/ ;
   ($idi) = $identity =~ /\sIdentities\s\=\s\d{3}\/\d{3}\s\((\d{2,3}\%
+)\)$/;
 } 
  
 if($idi eq "95%") {
 
  if(m/^Query/) {
  ($query) = m[^Query\s+(\d+)];
   my $top = substr $_, 15;
   my $pipes = substr <DATA>,15;
   my $bot = substr <DATA>, 15;
   my $p = 0 ;
   while ($p = 1+index $pipes,' ', $p) {
     
    printf "%20s\t%d\t%1s/%1s\n",$ID,$query+$p, substr( $top, $p-1, 1 
+),substr( $bot, $p-1, 1 );
    
   }
 }
}
   
}

    [download]
    Thanks.
[reply]
[d/l]
      OH Yes, I managed find a way through it thanks for al wonderful suggestions.
[reply]

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