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__
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
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.
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