Re: 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]

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]

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Comment on Re: parsing mismatch from blast output Select or Download Code

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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]
Re^3: parsing mismatch from blast output by Anonymous Monk on Aug 11, 2010 at 14:19 UTC
OH Yes, I managed find a way through it thanks for al wonderful suggestions.	[reply]


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