-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+use warnings;
use strict;
use Maasha::Biopieces;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @vals, $i );
+my ( $options, $in, $out, $record, $beg, $end, $len );
$options = Maasha::Biopieces::parse_options(
[
- { long => 'key', short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'keys', short => 'K', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'delimit', short => 'd', type => 'string', mandatory => 'no', default => '_', allowed => undef, disallowed => undef },
+ { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
]
);
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-while ( $record = Maasha::Biopieces::get_record( $in ) )
+if ( not defined $options->{ "beg" } or $options->{ "beg" } < 0 ) {
+ $beg = 0;
+} else {
+ $beg = $options->{ "beg" } - 1; # correcting for start offset
+}
+
+if ( defined $options->{ "end" } and $options->{ "end" } - 1 < $beg ) {
+ $end = $beg - 1;
+} elsif ( defined $options->{ "end" } ) {
+ $end = $options->{ "end" } - 1; # correcting for start offset
+}
+
+$len = $options->{ "len" };
+
+# print "beg->$beg, end->$end, len->$len\n";
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( exists $options->{ 'key' } and exists $record->{ $options->{ 'key' } } )
+ if ( $record->{ "SEQ" } )
{
- @vals = split /$options->{ 'delimit' }/, $record->{ $options->{ 'key' } };
-
- if ( scalar @vals > 1 )
+ if ( defined $beg and defined $end )
{
- for ( $i = 0; $i < @vals; $i++ )
+ if ( $end - $beg + 1 > length $record->{ "SEQ" } )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ $record->{ "SCORES" } = substr $record->{ "SEQ" }, $beg if $record->{ "SCORES" };
+ }
+ else
{
- if ( defined $options->{ "keys" } and defined $options->{ "keys" }->[ $i ] ) {
- $record->{ $options->{ "keys" }->[ $i ] } = $vals[ $i ];
- } else {
- $record->{ $options->{ 'key' } . "_$i" } = $vals[ $i ];
- }
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $end - $beg + 1 if $record->{ "SCORES" };
}
}
+ elsif ( defined $beg and defined $len )
+ {
+ if ( $len > length $record->{ "SEQ" } )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
+ }
+ else
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg, $len if $record->{ "SCORES" };
+ }
+ }
+ elsif ( defined $beg )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ $record->{ "SCORES" } = substr $record->{ "SCORES" }, $beg if $record->{ "SCORES" };
+ }
+
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
}
Maasha::Biopieces::put_record( $record, $out );
}
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
BEGIN
{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
+ Maasha::Biopieces::status_set();
}
END
{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
-
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+ Maasha::Biopieces::status_log();
}
__END__
-