# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, @vals, $i );
+my ( $run_time_beg, $run_time_end, $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 ( defined $options->{ "keys" } and defined $options->{ "keys" }->[ $i ] ) {
- $record->{ $options->{ "keys" }->[ $i ] } = $vals[ $i ];
- } else {
- $record->{ $options->{ 'key' } . "_$i" } = $vals[ $i ];
- }
+ if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ } else {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
}
}
+ elsif ( defined $beg and defined $len )
+ {
+ if ( $len > length $record->{ "SEQ" } ) {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ } else {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
+ }
+ }
+ elsif ( defined $beg )
+ {
+ $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
+ }
+
+ $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
}
Maasha::Biopieces::put_record( $record, $out );
--- /dev/null
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Prints a wiki page in ASCII format.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use strict;
+use Maasha::Biopieces;
+use Maasha::Gwiki;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $default, $wiki, $lines );
+
+$default = $ENV{ 'BP_DIR' } . "/bp_usage/" . ( split "/", $0 )[ -1 ]. ".wiki";
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'data_in', short => 'i', type => 'file!', mandatory => 'no', default => $default, allowed => undef, disallowed => undef },
+ ]
+);
+
+$wiki = Maasha::Gwiki::gwiki_read( $options->{ 'data_in' } );
+
+( $wiki->[ 2 ], $wiki->[ 3 ], $wiki->[ 0 ], $wiki->[ 1 ] ) = ( $wiki->[ 0 ], $wiki->[ 1 ], $wiki->[ 2 ], $wiki->[ 3 ] );
+
+if ( not $options->{ "help" } ) {
+ @{ $wiki } = grep { $_->[ 0 ]->{ 'SECTION' } =~ /Biopiece|summary|Usage|Options|Help/ } @{ $wiki };
+}
+
+$lines = Maasha::Gwiki::gwiki2ascii( $wiki );
+
+print STDERR "$_\n" foreach @{ $lines };
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ $run_time_beg = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+ $run_time_end = Maasha::Biopieces::run_time();
+
+ Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
+
elsif ( $script eq "transliterate_seq" ) { script_transliterate_seq( $in, $out, $options ) }
elsif ( $script eq "transliterate_vals" ) { script_transliterate_vals( $in, $out, $options ) }
elsif ( $script eq "translate_seq" ) { script_translate_seq( $in, $out, $options ) }
- elsif ( $script eq "extract_seq" ) { script_extract_seq( $in, $out, $options ) }
elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) }
elsif ( $script eq "get_genome_phastcons" ) { script_get_genome_phastcons( $in, $out, $options ) }
elsif ( $script eq "fold_seq" ) { script_fold_seq( $in, $out, $options ) }
frames|f=s
);
}
- elsif ( $script eq "extract_seq" )
- {
- @options = qw(
- beg|b=s
- end|e=s
- len|l=s
- );
- }
elsif ( $script eq "get_genome_align" )
{
@options = qw(
}
-sub script_extract_seq
-{
- # Martin A. Hansen, August 2007.
-
- # Extract subsequences from sequences in record.
-
- my ( $in, # handle to in stream
- $out, # handle to out stream
- $options, # options hash
- ) = @_;
-
- # Returns nothing.
-
- my ( $beg, $end, $len, $record );
-
- 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 ( $record->{ "SEQ" } )
- {
- if ( defined $beg and defined $end )
- {
- if ( $end - $beg + 1 > length $record->{ "SEQ" } ) {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- } else {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $end - $beg + 1;
- }
- }
- elsif ( defined $beg and defined $len )
- {
- if ( $len > length $record->{ "SEQ" } ) {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- } else {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg, $len;
- }
- }
- elsif ( defined $beg )
- {
- $record->{ "SEQ" } = substr $record->{ "SEQ" }, $beg;
- }
- }
-
- $record->{ "SEQ_LEN" } = length $record->{ "SEQ" };
-
- Maasha::Biopieces::put_record( $record, $out );
- }
-}
-
-
sub script_get_genome_align
{
# Martin A. Hansen, April 2008.
if ( $script ne 'print_wiki' )
{
- # if ( exists $options{ 'help' } or not ( exists $options{ 'stream_in' } or exists $options{ 'data_in' } or not -t STDIN ) )
- if ( exists $options->{ 'help' } or ( scalar keys %{ $options } == 0 or exists $options->{ 'data_in' } or not -t STDIN ) )
+ if ( exists $options->{ 'help' } or -t STDIN )
{
- $wiki = $ENV{ 'BP_DIR' } . "/bp_usage/$script.wiki";
-
- if ( exists $options->{ 'help' } ) {
- `print_wiki --data_in=$wiki --help`;
- } elsif ( $script =~ /^(list_biopieces|list_genomes)$/ ) {
- return;
- } else {
- `print_wiki --data_in=$wiki`;
+ if ( not ( exists $options->{ 'stream_in' } or $options->{ 'data_in' } ) )
+ {
+ if ( scalar keys %{ $options } <= 1 )
+ {
+ $wiki = $ENV{ 'BP_DIR' } . "/bp_usage/$script.wiki";
+
+ if ( exists $options->{ 'help' } ) {
+ `print_wiki --data_in=$wiki --help`;
+ } elsif ( $script =~ /^(list_biopieces|list_genomes)$/ ) {
+ return;
+ } else {
+ `print_wiki --data_in=$wiki`;
+ }
+
+ exit;
+ }
}
-
- exit;
}
}
}
projects / biopieces.git / commitdiff