Raw content of Bio::Variation::IO::flat
<![CDATA[# $Id: flat.pm,v 1.12 2002/10/22 07:38:50 lapp Exp $
# BioPerl module for Bio::Variation::IO::flat
#
# Cared for by Heikki Lehvaslaiho <Heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Variation::IO::flat - flat file sequence variation input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::Variation::IO class.
=head1 DESCRIPTION
This object can transform Bio::Variation::SeqDiff objects to and from
flat file databases. The format used is EMBL like extension of what is
used by the "EBI Mutation Checker" at
http://www.ebi.ac.uk/cgi-bin/mutations/check.cgi and will eventually
replace it.
More information of the attributes and values use can be found at
http://www.ebi.ac.uk/mutations/recommendations/.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk
Address:
EMBL Outstation, European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambs. CB10 1SD, United Kingdom
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Variation::IO::flat;
my $VERSION=1.0;
use vars qw(@ISA);
use strict;
use Text::Wrap;
use Bio::Variation::IO;
use Bio::Variation::SeqDiff;
use Bio::Variation::DNAMutation;
use Bio::Variation::RNAChange;
use Bio::Variation::AAChange;
use Bio::Variation::Allele;
@ISA = qw(Bio::Variation::IO);
sub new {
my($class, @args) = @_;
my $self = bless {}, $class;
$self->_initialize(@args);
return $self;
}
sub _initialize {
my($self,@args) = @_;
return unless $self->SUPER::_initialize(@args);
}
=head2 next
Title : next
Usage : $haplo = $stream->next()
Function: returns the next seqDiff in the stream
Returns : Bio::Variation::SeqDiff object
Args : NONE
=cut
sub next {
my( $self ) = @_;
local $/ = '//';
return unless my $entry = $self->_readline;
return if $entry =~ /^\s+$/;
$entry =~ /\s*ID\s+\S+/ || $self->throw("We do need an ID!");
my ($id, $offset, $alphabet) = $entry =~ /\s*ID +([^:]+)..(\d+)[^\)]*.\[?([cg])?/
or $self->throw("Can't parse ID line");
# $self->throw("$1|$2|$3");
my $h =Bio::Variation::SeqDiff->new(-id => $id,
-offset => $offset,
);
if ($alphabet) {
if ($alphabet eq 'g') {
$alphabet = 'dna';
}
elsif ($alphabet eq 'c') {
$alphabet = 'rna';
}
$h->alphabet($alphabet);
}
#
# DNA
#
my @dna = split ( / DNA;/, $entry );
shift @dna;
my $prevdnaobj;
foreach my $dna (@dna) {
$dna =~ s/Feature[ \t]+//g;
($dna) = split "RNA; ", $dna;
#$self->warn("|$dna|") ;
#exit;
my ($mut_number, $proof, $location, $upflank, $change, $dnflank) =
$dna =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+).+/upflank: ([ \n\w]+).+/change: ([^ /]+).+/dnflank: ([ \n\w]+)|s;
$change =~ s/[ \n]//g;
my ($ori, $mut) = split /[>\|]/, $change;
my ($variation_number, $change_number) = split /\./, $mut_number;
#$self->warn("|$mut_number|>|$variation_number|$change_number|");
my $dnamut;
if ($change_number and $change_number > 1 ) {
my $a3 = Bio::Variation::Allele->new;
$a3->seq($mut) if $mut;
#$dnamut->add_Allele($a3);
$prevdnaobj->add_Allele($a3);
} else {
$upflank =~ s/[ \n]//g;
$dnflank =~ s/[ \n]//g;
my ($region, $junk, $region_value, $junk2, $region_dist) =
$dna =~ m|.+/region: ([\w\']+)(; )?(\w+)?( ?\(\+?)?(-?\d+)?|s;
#my $s = join ("|", $mut_number, $proof, $location, $upflank,
# $change, $dnflank, $region, $region_value, $region_dist, $1,$2,$3,$4,$5);
#$self->warn($s);
#exit;
my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/;
$end = $start if not $end ;
my ($len) = $end - $start +1;
$len = 0, $start = $end if defined $sep and $sep eq '^';
my $ismut = 0;
$ismut = 1 if $change =~ m/>/;
$dnamut = Bio::Variation::DNAMutation->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-upStreamSeq' => $upflank,
'-dnStreamSeq' => $dnflank,
'-proof' => $proof,
'-mut_number' => $mut_number
);
$prevdnaobj = $dnamut;
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$dnamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$dnamut->add_Allele($a2);
if ($ismut) {
$dnamut->isMutation(1);
$dnamut->allele_mut($a2);
}
$dnamut->region($region) if defined $region;
$dnamut->region_value($region_value) if defined $region_value;
$dnamut->region_dist($region_dist) if defined $region_dist;
$h->add_Variant($dnamut);
$dnamut->SeqDiff($h);
}
}
#
# RNA
#
my @rna = split ( / RNA;/, $entry );
shift @rna;
my $prevrnaobj;
foreach my $rna (@rna) {
$rna = substr ($rna, 0, index($rna, 'Feature AA'));
$rna =~ s/Feature[ \t]+//g;
($rna) = split "DNA; ", $rna;
#$self->warn("|$rna|") ;
my ($mut_number, $proof, $location, $upflank, $change, $dnflank) =
$rna =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+).+/upflank: (\w+).+/change: ([^/]+).+/dnflank: (\w+)|s ;#'
my ($region, $junk, $region_value, $junk2, $region_dist) =
$rna =~ m|.+/region: ([\w\']+)(; )?(\w+)?( ?\(\+?)?(-?\d+)?|s;
#my $s = join ("|", $mut_number, $proof, $location, $upflank,
# $change, $dnflank, $region, $region_value, $region_dist, $1,$2,$3,$4,$5);
#$self->warn($s);
#exit;
$change =~ s/[ \n]//g;
my ($ori, $mut) = split /[>\|]/, $change;
my $rnamut;
my ($variation_number, $change_number) = split /\./, $mut_number;
if ($change_number and $change_number > 1 ) {
my $a3 = Bio::Variation::Allele->new;
$a3->seq($mut) if $mut;
#$rnamut->add_Allele($a3);
$prevrnaobj->add_Allele($a3);
} else {
my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/;
$end = $start if not $end ;
my ($len) = $end - $start + 1;
$len = 0, $start = $end if defined $sep and $sep eq '^';
my $ismut;
$ismut = 1 if $change =~ m/>/;
my ($codon_table) = $rna =~ m|.+/codon_table: (\d+)|s;
my ($codon_pos) = $rna =~ m|.+/codon:[^;]+; ([123])|s;
$rnamut = Bio::Variation::RNAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-upStreamSeq' => $upflank,
'-dnStreamSeq' => $dnflank,
'-proof' => $proof,
'-mut_number' => $mut_number
);
$prevrnaobj = $rnamut;
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$rnamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$rnamut->add_Allele($a2);
if ($ismut) {
$rnamut->isMutation(1);
$rnamut->allele_mut($a2);
}
$rnamut->region($region) if defined $region;
$rnamut->region_value($region_value) if defined $region_value;
$rnamut->region_dist($region_dist) if defined $region_dist;
$rnamut->codon_table($codon_table) if $codon_table;
$rnamut->codon_pos($codon_pos) if $codon_pos;
$h->add_Variant($rnamut);
foreach my $mut ($h->each_Variant) {
if ($mut->isa('Bio::Variation::DNAMutation') ) {
if ($mut->mut_number == $rnamut->mut_number) {
$rnamut->DNAMutation($mut);
$mut->RNAChange($rnamut);
}
}
}
}
}
#
# AA
#
my @aa = split ( / AA;/, $entry );
shift @aa;
my $prevaaobj;
foreach my $aa (@aa) {
$aa = substr ($aa, 0, index($aa, 'Feature AA'));
$aa =~ s/Feature[ \t]+//g;
($aa) = split "DNA; ", $aa;
#$self->warn("|$aa|") ;
my ($mut_number, $proof, $location, $change) =
$aa =~ m|\W+([\d\.]+).+/proof: (\w+).+/location: ([^ \n]+)./change: ([^/;]+)|s;
$change =~ s/[ \n]//g;
#my $s = join ("|", $mut_number, $proof, $location, $change);
#$self->warn($s);
#exit;
$change =~ s/[ \n]//g;
$change =~ s/DNA$//;
my ($ori, $mut) = split /[>\|]/, $change;
#print "------$location----$ori-$mut-------------\n";
my ($variation_number, $change_number) = split /\./, $mut_number;
my $aamut;
if ($change_number and $change_number > 1 ) {
my $a3 = Bio::Variation::Allele->new;
$a3->seq($mut) if $mut;
$prevaaobj->add_Allele($a3);
} else {
my ($start, $sep, $end) = $location =~ /(-?\d+)(.)?\D?(-?\d+)?/;
$end = $start if not $end ;
my ($len) = $end - $start + 1;
$len = 0, $start = $end if defined $sep and $sep eq '^';
my $ismut;
$ismut = 1 if $change =~ m/>/;
my ($region) = $aa =~ m|.+/region: (\w+)|s ;
$aamut = Bio::Variation::AAChange->new
('-start' => $start,
'-end' => $end,
'-length' => $len,
'-proof' => $proof,
'-mut_number' => $mut_number
);
$prevaaobj = $aamut;
my $a1 = Bio::Variation::Allele->new;
$a1->seq($ori) if $ori;
$aamut->allele_ori($a1);
my $a2 = Bio::Variation::Allele->new;
$a2->seq($mut) if $mut;
$aamut->add_Allele($a2);
if ($ismut) {
$aamut->isMutation(1);
$aamut->allele_mut($a2);
}
$region && $aamut->region($region);
$h->add_Variant($aamut);
foreach my $mut ($h->each_Variant) {
if ($mut->isa('Bio::Variation::RNAChange') ) {
if ($mut->mut_number == $aamut->mut_number) {
$aamut->RNAChange($mut);
$mut->AAChange($aamut);
}
}
}
}
}
return $h;
}
=head2 write
Title : write
Usage : $stream->write(@seqDiffs)
Function: writes the $seqDiff object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Variation::SeqDiff object
=cut
sub write {
my ($self,@h) = @_;
#$columns = 75; #default for Text::Wrap
my %tag =
(
'ID' => 'ID ',
'Description' => 'Description ',
'FeatureKey' => 'Feature ',
'FeatureQual' => "Feature ",
'FeatureWrap' => "Feature ",
'ErrorComment' => 'Comment '
#'Comment' => 'Comment -!-',
#'CommentLine' => 'Comment ',
);
if( !defined $h[0] ) {
$self->throw("Attempting to write with no information!");
}
foreach my $h (@h) {
my @entry =();
my ($text, $tmp, $tmp2, $sep);
my ($count) = 0;
$text = $tag{ID};
$text .= $h->id;
$text .= ":(". $h->offset;
$text .= "+1" if $h->sysname =~ /-/;
$text .= ")". $h->sysname;
$text .= "; ". $h->trivname if $h->trivname;
push (@entry, $text);
#Variants need to be ordered accoding to mutation_number attribute
#put them into a hash of arrays holding the Variant objects
#This is necessary for cases like several distict mutations present
# in the same sequence.
my @allvariants = $h->each_Variant;
my %variants = ();
foreach my $mut ($h->each_Variant) {
push @{$variants{$mut->mut_number} }, $mut;
}
#my ($variation_number, $change_number) = split /\./, $mut_number;
foreach my $var (sort keys %variants) {
#print $var, ": ", join (" ", @{$variants{$var}}), "\n";
foreach my $mut (@{$variants{$var}}) {
#
# DNA
#
if ( $mut->isa('Bio::Variation::DNAMutation') ) {
#collect all non-reference alleles
$self->throw("allele_ori needs to be defined in [$mut]")
if not $mut->allele_ori;
if ($mut->isMutation) {
$sep = '>';
} else {
$sep = '|';
}
my @alleles = $mut->each_Allele;
#push @alleles, $mut->allele_mut if $mut->allele_mut;
my $count = 0; # two alleles
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
push (@entry,
$tag{FeatureKey}. 'DNA'. "; ". $mut->mut_number
);
#label
$text=$tag{FeatureQual}. '/label: '. $mut->label;
push (@entry, $text);
#proof
if ($mut->proof) {
$text = $tag{FeatureQual}. '/proof: '. $mut->proof;
push (@entry, $text) ;
}
#location
$text = $tag{FeatureQual}. '/location: ';
#$mut->id. '; '. $mut->start;
if ($mut->length > 1 ) {# if ($mut->end - $mut->start ) {
my $l = $mut->start + $mut->length -1;
$text .= $mut->start. '..'. $l;
}
elsif ($mut->length == 0) {
my $tmp_start = $mut->start - 1;
$tmp_start-- if $tmp_start == 0;
$text .= $tmp_start. '^'. $mut->end;
} else {
$text .= $mut->start;
}
if ($h->alphabet && $h->alphabet eq 'dna') {
$tmp = $mut->start + $h->offset;
$tmp-- if $tmp <= 0;
$mut->start < 1 && $tmp++;
#$text.= ' ('. $h->id. '::'. $tmp;
$tmp2 = $mut->end + $h->offset;
if ( $mut->length > 1 ) {
$mut->end < 1 && $tmp2++;
$text.= ' ('. $h->id. '::'. $tmp. "..". $tmp2;
}
elsif ($mut->length == 0) {
$tmp--;
$tmp-- if $tmp == 0;
$text .= ' ('. $h->id. '::'. $tmp. '^'. $tmp2;
} else {
$text.= ' ('. $h->id. '::'. $tmp;
}
$text .= ')';
}
push (@entry, $text);
#sequence
push (@entry,
$tag{FeatureQual}. '/upflank: '. $mut->upStreamSeq
);
$text = '';
$text = $mut->allele_ori->seq if $mut->allele_ori->seq;
$text .= $sep;
$text .= $mut->allele_mut->seq if $mut->allele_mut->seq;
push (@entry,
wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap},
$text)
);
push (@entry,
$tag{FeatureQual}. '/dnflank: '. $mut->dnStreamSeq
);
#restriction enzyme
if ($mut->restriction_changes ne '') {
$text = $mut->restriction_changes;
$text = wrap($tag{FeatureQual}. '/re_site: ', $tag{FeatureWrap}, $text);
push (@entry,
$text
);
}
#region
if ($mut->region ) {
$text = $tag{FeatureQual}. '/region: '. $mut->region;
$text .= ';' if $mut->region_value or $mut->region_dist;
$text .= ' '. $mut->region_value if $mut->region_value;
if ($mut->region_dist ) {
$tmp = '';
$tmp = '+' if $mut->region_dist > 1;
$text .= " (". $tmp. $mut->region_dist. ')';
}
push (@entry, $text);
}
#CpG
if ($mut->CpG) {
push (@entry,
$tag{FeatureQual}. "/CpG"
);
}
}
}
#
# RNA
#
elsif ($mut->isa('Bio::Variation::RNAChange') ) {
#collect all non-reference alleles
$self->throw("allele_ori needs to be defined in [$mut]")
if not $mut->allele_ori;
my @alleles = $mut->each_Allele;
#push @alleles, $mut->allele_mut if $mut->allele_mut;
if ($mut->isMutation) {
$sep = '>';
} else {
$sep = '|';
}
my $count = 0; # two alleles
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
push (@entry,
$tag{FeatureKey}. 'RNA'. "; ". $mut->mut_number
);
#label
$text=$tag{FeatureQual}. '/label: '. $mut->label;
push (@entry, $text);
#proof
if ($mut->proof) {
$text = $tag{FeatureQual}. '/proof: '. $mut->proof;
push (@entry, $text) ;
}
#location
$text = $tag{FeatureQual}. '/location: ' ;
if ($mut->length > 1 ) {
$text .= $mut->start. '..'. $mut->end;
$tmp2 = $mut->end + $h->offset;
}
elsif ($mut->length == 0) {
my $tmp_start = $mut->start;
$tmp_start--;
$tmp_start-- if $tmp_start == 0;
$text .= $tmp_start. '^'. $mut->end;
} else {
$text .= $mut->start;
}
if ($h->alphabet && $h->alphabet eq 'rna') {
$tmp = $mut->start + $h->offset;
$tmp-- if $tmp <= 0;
#$mut->start < 1 && $tmp++;
#$text.= ' ('. $h->id. '::'. $tmp;
$tmp2 = $mut->end + $h->offset;
#$mut->end < 1 && $tmp2++;
if ( $mut->length > 1 ) {
$text.= ' ('. $h->id. '::'. $tmp. "..". $tmp2;
}
elsif ($mut->length == 0) {
$tmp--;
$text .= ' ('. $h->id. '::'. $tmp. '^'. $tmp2;
} else {
$text.= ' ('. $h->id. '::'. $tmp;
}
$text .= ')';
}
push (@entry, $text);
#sequence
push (@entry,
$tag{FeatureQual}. '/upflank: '. $mut->upStreamSeq
);
$text = '';
$text = $mut->allele_ori->seq if $mut->allele_ori->seq;
$text .= $sep;
$text .= $mut->allele_mut->seq if $mut->allele_mut->seq;
push (@entry,
wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap},
$text)
);
push (@entry,
$tag{FeatureQual}. '/dnflank: '. $mut->dnStreamSeq
);
#restriction
if ($mut->restriction_changes ne '') {
$text = $mut->restriction_changes;
$text = wrap($tag{FeatureQual}. '/re_site: ', $tag{FeatureWrap}, $text);
push (@entry,
$text
);
}
#coding
if ($mut->region eq 'coding') {
#codon table
$text = $tag{FeatureQual}. '/codon_table: ';
$text .= $mut->codon_table;
push (@entry, $text);
#codon
$text = $tag{FeatureQual}. '/codon: '. $mut->codon_ori. $sep;
if ($mut->DNAMutation->label =~ /.*point/) {
$text .= $mut->codon_mut;
}
else {
$text .= '-';
}
$text .= "; ". $mut->codon_pos;
push (@entry, $text);
}
#region
if ($mut->region ) {
$text = $tag{FeatureQual}. '/region: '. $mut->region;
$text .= ';' if $mut->region_value or $mut->region_dist;
$text .= ' '. $mut->region_value if $mut->region_value;
if ($mut->region_dist ) {
$tmp = '';
$tmp = '+' if $mut->region_dist > 1;
$text .= " (". $tmp. $mut->region_dist. ')';
}
push (@entry, $text);
}
}
}
#
# AA
#
elsif ($mut->isa('Bio::Variation::AAChange')) {
#collect all non-reference alleles
$self->throw("allele_ori needs to be defined in [$mut]")
if not $mut->allele_ori;
if ($mut->isMutation) {
$sep = '>';
} else {
$sep = '|';
}
my @alleles = $mut->each_Allele;
#push @alleles, $mut->allele_mut if $mut->allele_mut;
my $count = 0; # two alleles
foreach my $allele (@alleles) {
$count++;
my ($variation_number, $change_number) = split /\./, $mut->mut_number;
if ($change_number and $change_number != $count){
$mut->mut_number("$change_number.$count");
}
$mut->allele_mut($allele);
push (@entry,
$tag{FeatureKey}. 'AA'. "; ". $mut->mut_number
);
#label
$text=$tag{FeatureQual}. '/label: '. $mut->label;
push (@entry, $text) ;
#proof
if ($mut->proof) {
$text = $tag{FeatureQual}. '/proof: '. $mut->proof;
push (@entry, $text) ;
}
#location
$text = $tag{FeatureQual}. '/location: '.
#$mut->id. '; '. $mut->start;
$mut->start;
if ($mut->length > 1 ) {
$tmp = $mut->start + $mut->length -1;
$text .= '..'. $tmp;
}
push (@entry, $text);
#sequence
$text = '';
$text = $mut->allele_ori->seq if $mut->allele_ori->seq;
$text .= $sep;
$text .= $mut->allele_mut->seq if $mut->allele_mut->seq;
push (@entry,
wrap($tag{FeatureQual}. '/change: ', $tag{FeatureWrap},
$text)
);
#region
if ($mut->region ) {
$text = $tag{FeatureQual}. '/region: '. $mut->region;
$text .= ';' if $mut->region_value or $mut->region_dist;
$text .= ' '. $mut->region_value if $mut->region_value;
if ($mut->region_dist ) {
$tmp = '';
$tmp = '+' if $mut->region_dist > 1;
$text .= " (". $tmp. $mut->region_dist. ')';
}
push (@entry, $text);
}
}
}
}
}
push (@entry,
"//"
);
my $str = join ("\n", @entry). "\n";
$str =~ s/\t/ /g;
$self->_print($str);
}
return 1;
}
1;
]]>