From: martinahansen Date: Tue, 8 Dec 2009 14:21:21 +0000 (+0000) Subject: added read_ace X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=81ed3d3131ca75925239b255fdbcbbeaf117c6c6;p=biopieces.git added read_ace git-svn-id: http://biopieces.googlecode.com/svn/trunk@798 74ccb610-7750-0410-82ae-013aeee3265d --- diff --git a/bp_bin/read_ace b/bp_bin/read_ace new file mode 100755 index 0000000..83b1244 --- /dev/null +++ b/bp_bin/read_ace @@ -0,0 +1,100 @@ +#!/usr/bin/env perl + +# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Read ACE entries from one or more files. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +use warnings; +use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::ACE; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $options, $in, $out, $record, $data_in, $num, $entries, $entry ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'num', short => 'n', 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 ) ) { + Maasha::Biopieces::put_record( $record, $out ); +} + +if ( $options->{ 'data_in' } ) +{ + $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } ); + + $num = 1; + + while ( $entries = Maasha::ACE::ace_entries_get( $data_in ) ) + { + foreach $entry ( @{ $entries } ) + { + Maasha::Biopieces::put_record( $entry, $out ); + + last if $options->{ "num" } and $num == $options->{ "num" }; + + $num++; + } + + last if $options->{ "num" } and $num == $options->{ "num" }; + } + + close $data_in; +} + +Maasha::Biopieces::close_stream( $in ); +Maasha::Biopieces::close_stream( $out ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + Maasha::Biopieces::status_set(); +} + + +END +{ + Maasha::Biopieces::status_log(); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ diff --git a/code_perl/Maasha/ACE.pm b/code_perl/Maasha/ACE.pm new file mode 100644 index 0000000..b50f240 --- /dev/null +++ b/code_perl/Maasha/ACE.pm @@ -0,0 +1,213 @@ +package Maasha::ACE; + +# Copyright (C) 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +# Routines to parse ACE format. + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +use warnings; +use strict; +use Data::Dumper; +use Storable; +use Maasha::Common; +use Maasha::Filesys; +use Maasha::KISS; +use Maasha::Seq; +use vars qw ( @ISA @EXPORT ); + + +@ISA = qw( Exporter ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +sub ace_entries_get +{ + # Martin A. Hansen, December 2009. + # + # Fetches the next contig from an ACE file. + + my ( $fh, + ) = @_; + + my ( $block, $line, @lines, $records ); + + local $/ = "\nCO "; + + while ( $block = <$fh> ) + { + chomp $block; + + next if $block =~ /^AS/; + + if ( defined $block ) + { + @lines = split "\n", "CO $block"; + + $records = ace_entry_parse( \@lines ); + + return wantarray ? @{ $records } : $records; + } + } +} + + +sub ace_entry_parse +{ + # Martin A. Hansen, December 2009. + + # Parses an ACE entry given as a list of lines and + # returns a list of hashref. + + my ( $entry, # list of lines + ) = @_; + + # Returns a list. + + my ( $i, $contig, $reads, $read_name, $read_seq, $record, @records ); + + $i = 0; + + while ( $i < scalar @{ $entry } ) + { + if ( $entry->[ $i ] =~ /^CO ([^ ]+) (\d+) (\d+) (\d+) (U|C)/ ) + { + $contig->{ 'CONTIG_NAME' } = $1; + $contig->{ 'CONTIG_BASES' } = $2; + $contig->{ 'CONTIG_READS' } = $3; + $contig->{ 'CONTIG_SEGMENT' } = $4; + $contig->{ 'CONTIG_COMPLEMENT' } = $5; + $contig->{ 'CONTIG_SEQ' } = ""; + + $i++; + + while ( $entry->[ $i ] ne "" ) + { + $contig->{ 'CONTIG_SEQ' } .= $entry->[ $i ]; + + $i++; + } + } + elsif ( $entry->[ $i ] =~ /^AF ([^ ]+) (U|C) (-?\d+)/ ) + { + $reads->{ $1 }->{ 'AF_READ_COMPLEMENT' } = $2; + $reads->{ $1 }->{ 'AF_READ_BEG' } = ( $3 - 1 ); + } + elsif ( $entry->[ $i ] =~ /^BS (\d+) (\d+) (.+)/ ) + { + # skip + } + elsif ( $entry->[ $i ] =~ /^RD ([^ ]+) (\d+) (\d+) (\d+)/ ) + { + $read_name = $1; + + $reads->{ $read_name }->{ 'RD_READ_LEN' } = $2; + $reads->{ $read_name }->{ 'RD_READ_ITEMS' } = $3; + $reads->{ $read_name }->{ 'RD_READ_TAGS' } = $4; + + $read_seq = ""; + + $i++; + + while ( $entry->[ $i ] ne "" ) + { + $read_seq .= $entry->[ $i ]; + + $i++; + } + + $reads->{ $read_name }->{ 'RD_READ_SEQ' } = $read_seq; + } + elsif ( $entry->[ $i ] =~ /^QA (\d+) (\d+) (\d+) (\d+)/ ) + { + $reads->{ $read_name }->{ 'QA_CLIP_BEG' } = ( $1 - 1 ); + $reads->{ $read_name }->{ 'QA_CLIP_END' } = ( $2 - 1 ); + $reads->{ $read_name }->{ 'QA_ALIGN_BEG' } = ( $3 - 1 ); + $reads->{ $read_name }->{ 'QA_ALIGN_END' } = ( $4 - 1 ); + } + + $i++; + } + + my ( $read, $s_seq, $q_seq, $len, $align ); + + foreach $read ( keys %{ $reads } ) + { + $len = $reads->{ $read }->{ 'QA_ALIGN_END' } - $reads->{ $read }->{ 'QA_ALIGN_BEG' } + 1; + $s_seq = substr $contig->{ 'CONTIG_SEQ' }, $reads->{ $read }->{ 'AF_READ_BEG' } + $reads->{ $read }->{ 'QA_ALIGN_BEG' }, $len; + $q_seq = substr $reads->{ $read }->{ 'RD_READ_SEQ' }, $reads->{ $read }->{ 'QA_ALIGN_BEG' }, $len; + + $s_seq =~ tr/*/-/; + $q_seq =~ tr/*/-/; + + if ( $reads->{ $read }->{ 'AF_READ_COMPLEMENT' } eq 'C' ) + { + $record->{ 'STRAND' } = '-'; + + Maasha::Seq::dna_comp( \$s_seq ); + Maasha::Seq::dna_comp( \$q_seq ); + } + else + { + $record->{ 'STRAND' } = '+'; + } + + # print Dumper( $read, $reads->{ $read } ); + + $align = Maasha::KISS::kiss_align_enc( \$s_seq, \$q_seq, $reads->{ $read }->{ 'QA_ALIGN_BEG' } ); + + $record->{ 'S_ID' } = $contig->{ 'CONTIG_NAME' }; + $record->{ 'S_BEG' } = $reads->{ $read }->{ 'AF_READ_BEG' }; + $record->{ 'S_END' } = $record->{ 'S_BEG' } + $len - 1; # FIXME + $record->{ 'Q_ID' } = $read; + $record->{ 'Q_ID' } =~ s/\..+//; + $record->{ 'ALIGN' } = join ",", @{ $align }; + + if ( 0 ) # DEBUG + { + print "LEN: $len\n"; + print "S_SEQ: $s_seq\n"; + print "Q_SEQ: $q_seq\n\n"; + print "READ: $read\n"; + print Dumper( $reads->{ $read } ); + print Dumper( $record ); + } + + if ( $record->{ 'S_BEG' } >= 0 ) # FIXME + { + push @records, Storable::dclone $record; + } + } + + return wantarray ? @records : \@records; +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +1;