From 4ca5508a67a6b1b0e594d05f314d8ca1a28178ae Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 28 May 2009 10:14:12 +0000 Subject: [PATCH] migrated tile_seq git-svn-id: http://biopieces.googlecode.com/svn/trunk@441 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/tile_seq | 108 +++++++++++++++++++++++++++++++++++-- code_perl/Maasha/BioRun.pm | 55 +------------------ 2 files changed, 106 insertions(+), 57 deletions(-) diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq index fdf5bd2..500f705 100755 --- a/bp_bin/tile_seq +++ b/bp_bin/tile_seq @@ -1,6 +1,108 @@ -#!/usr/bin/env perl +#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Using the first sequence in the stream as reference, tile all subsequent sequences based on pairwise alignments. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Align; + +use constant { + SEQ_NAME => 0, + SEQ => 1, +}; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $first, $ref_entry, @entries ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'identity', short => 'i', type => 'uint', mandatory => 'no', default => 70, allowed => undef, disallowed => 0 }, + { long => 'supress_indels', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$first = 1; + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) + { + if ( $first ) + { + $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; + + $first = 0; + } + else + { + push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; + } + } + else + { + Maasha::Biopieces::put_record( $record, $out ); + } +} + +@entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options ); + +map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + $run_time_beg = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::log_biopiece(); +} + + +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 ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index aa82088..e8a5d5a 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -135,7 +135,6 @@ sub run_script elsif ( $script eq "remove_indels" ) { script_remove_indels( $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 "tile_seq" ) { script_tile_seq( $in, $out, $options ) } elsif ( $script eq "soap_seq" ) { script_soap_seq( $in, $out, $options ) } elsif ( $script eq "write_bed" ) { script_write_bed( $in, $out, $options ) } elsif ( $script eq "write_psl" ) { script_write_psl( $in, $out, $options ) } @@ -322,13 +321,6 @@ sub get_options flank|f=s ); } - elsif ( $script eq "tile_seq" ) - { - @options = qw( - identity|i=s - supress_indels|s - ); - } elsif ( $script eq "soap_seq" ) { @options = qw( @@ -582,7 +574,7 @@ sub get_options # print STDERR Dumper( \%options ); - $real = "beg|end|word_size|wrap|tile_size|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size"; + $real = "beg|end|word_size|wrap|len|prefix_length|mismatches|offset|num|skip|cpus|window_size|step_size"; foreach $opt ( keys %options ) { @@ -1672,51 +1664,6 @@ sub script_get_genome_phastcons } -sub script_tile_seq -{ - # Martin A. Hansen, February 2008. - - # Using the first sequence in stream as reference, tile - # all subsequent sequences based on pairwise alignments. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $first, $ref_entry, @entries ); - - $first = 1; - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "SEQ_NAME" } and $record->{ "SEQ" } ) - { - if ( $first ) - { - $ref_entry = [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; - - $first = 0; - } - else - { - push @entries, [ $record->{ "SEQ_NAME" }, $record->{ "SEQ" } ]; - } - } - else - { - Maasha::Biopieces::put_record( $record, $out ); - } - } - - @entries = Maasha::Align::align_tile( $ref_entry, \@entries, $options ); - - map { Maasha::Biopieces::put_record( { SEQ_NAME => $_->[ SEQ_NAME ], SEQ => $_->[ SEQ ] }, $out ) } @entries; -} - - sub script_soap_seq { # Martin A. Hansen, July 2008. -- 2.39.5