Raw content of Bio::SeqIO::embl
<![CDATA[# $Id: embl.pm,v 1.57.2.6 2003/09/14 19:06:51 jason Exp $
#
# BioPerl module for Bio::SeqIO::EMBL
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::embl - EMBL sequence input/output stream
=head1 SYNOPSIS
It is probably best not to use this object directly, but
rather go through the AnnSeqIO handler system. Go:
$stream = Bio::SeqIO->new(-file => $filename, -format => 'EMBL');
while ( (my $seq = $stream->next_seq()) ) {
# do something with $seq
}
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from EMBL flat
file databases.
There is alot of flexibility here about how to dump things which I need
to document fully.
There should be a common object that this and genbank share (probably
with swissprot). Too much of the magic is identical.
=head2 Optional functions
=over 3
=item _show_dna()
(output only) shows the dna or not
=item _post_sort()
(output only) provides a sorting func which is applied to the FTHelpers
before printing
=item _id_generation_func()
This is function which is called as
print "ID ", $func($annseq), "\n";
To generate the ID line. If it is not there, it generates a sensible ID
line using a number of tools.
If you want to output annotations in embl format they need to be
stored in a Bio::Annotation::Collection object which is accessible
through the Bio::SeqI interface method L<annotation()|annotation>.
The following are the names of the keys which are polled from a
L<Bio::Annotation::Collection> object.
reference - Should contain Bio::Annotation::Reference objects
comment - Should contain Bio::Annotation::Comment objects
dblink - Should contain Bio::Annotation::DBLink objects
=back
=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 one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.shtml - 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 - Ewan Birney
Email birney@ebi.ac.uk
Describe contact details here
=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::SeqIO::embl;
use vars qw(@ISA);
use strict;
use Bio::SeqIO::FTHelper;
use Bio::SeqFeature::Generic;
use Bio::Species;
use Bio::Seq::SeqFactory;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;
use Bio::Annotation::Reference;
use Bio::Annotation::DBLink;
@ISA = qw(Bio::SeqIO);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
# hash for functions for decoding keys.
$self->{'_func_ftunit_hash'} = {};
$self->_show_dna(1); # sets this to one by default. People can change it
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(new Bio::Seq::SeqFactory
(-verbose => $self->verbose(),
-type => 'Bio::Seq::RichSeq'));
}
}
=head2 next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
=cut
sub next_seq {
my ($self,@args) = @_;
my ($pseq,$c,$line,$name,$desc,$acc,$seqc,$mol,$div,
$date, $comment, @date_arr);
my ($annotation, %params, @features) = ( new Bio::Annotation::Collection);
$line = $self->_readline; # This needs to be before the first eof() test
if( !defined $line ) {
return undef; # no throws - end of file
}
if( $line =~ /^\s+$/ ) {
while( defined ($line = $self->_readline) ) {
$line =~/^\S/ && last;
}
}
if( !defined $line ) {
return undef; # end of file
}
$line =~ /^ID\s+\S+/ || $self->throw("EMBL stream with no ID. Not embl in my book");
$line =~ /^ID\s+(\S+)\s+\S+\;\s+([^;]+)\;\s+(\S+)\;/;
$name = $1;
$mol = $2;
$div = $3;
if(! $name) {
$name = "unknown id";
}
my $alphabet;
# this is important to have the id for display in e.g. FTHelper, otherwise
# you won't know which entry caused an error
if($mol) {
if ( $mol =~ /circular/ ) {
$params{'-is_circular'} = 1;
$mol =~ s|circular ||;
}
if (defined $mol ) {
if ($mol =~ /DNA/) {
$alphabet='dna';
}
elsif ($mol =~ /RNA/) {
$alphabet='rna';
}
elsif ($mol =~ /AA/) {
$alphabet='protein';
}
}
}
# $self->warn("not parsing upper annotation in EMBL file yet!");
my $buffer = $line;
local $_;
BEFORE_FEATURE_TABLE :
until( !defined $buffer ) {
$_ = $buffer;
# Exit at start of Feature table
last if /^F[HT]/;
# Description line(s)
if (/^DE\s+(\S.*\S)/) {
$desc .= $desc ? " $1" : $1;
}
#accession number
if( /^AC\s+(.*)?/ ) {
my @accs = split(/[; ]+/, $1); # allow space in addition
$params{'-accession_number'} = shift @accs
unless defined $params{'-accession_number'};
push @{$params{'-secondary_accessions'}}, @accs;
}
#version number
if( /^SV\s+\S+\.(\d+);?/ ) {
my $sv = $1;
#$sv =~ s/\;//;
$params{'-seq_version'} = $sv;
$params{'-version'} = $sv;
}
#date (NOTE: takes last date line)
if( /^DT\s+(.+)$/ ) {
my $date = $1;
push @{$params{'-dates'}}, $date;
}
#keywords
if( /^KW\s+(.*)\S*$/ ) {
my @kw = split(/\s*\;\s*/,$1);
push @{$params{'-keywords'}}, @kw;
}
# Organism name and phylogenetic information
elsif (/^O[SC]/) {
my $species = $self->_read_EMBL_Species(\$buffer);
$params{'-species'}= $species;
}
# References
elsif (/^R/) {
my @refs = $self->_read_EMBL_References(\$buffer);
foreach my $ref ( @refs ) {
$annotation->add_Annotation('reference',$ref);
}
}
# DB Xrefs
elsif (/^DR/) {
my @links = $self->_read_EMBL_DBLink(\$buffer);
foreach my $dblink ( @links ) {
$annotation->add_Annotation('dblink',$dblink);
}
}
# Comments
elsif (/^CC\s+(.*)/) {
$comment .= $1;
$comment .= " ";
while (defined ($_ = $self->_readline) ) {
if (/^CC\s+(.*)/) {
$comment .= $1;
$comment .= " ";
}
else {
last;
}
}
my $commobj = Bio::Annotation::Comment->new();
$commobj->text($comment);
$annotation->add_Annotation('comment',$commobj);
$comment = "";
}
# Get next line.
$buffer = $self->_readline;
}
while( defined ($_ = $self->_readline) ) {
/^FT \w/ && last;
/^SQ / && last;
/^CO / && last;
}
$buffer = $_;
if (defined($buffer) && $buffer =~ /^FT /) {
until( !defined ($buffer) ) {
my $ftunit = $self->_read_FTHelper_EMBL(\$buffer);
# process ftunit
push(@features,
$ftunit->_generic_seqfeature($self->location_factory(), $name));
if( $buffer !~ /^FT/ ) {
last;
}
}
}
# skip comments
while( defined ($buffer) && $buffer =~ /^XX/ ) {
$buffer = $self->_readline();
}
if( $buffer =~ /^CO/ ) {
until( !defined ($buffer) ) {
my $ftunit = $self->_read_FTHelper_EMBL(\$buffer);
# process ftunit
push(@features,
$ftunit->_generic_seqfeature($self->location_factory(),
$name));
if( $buffer !~ /^CO/ ) {
last;
}
}
}
if( $buffer !~ /^SQ/ ) {
while( defined ($_ = $self->_readline) ) {
/^SQ/ && last;
}
}
$seqc = "";
while( defined ($_ = $self->_readline) ) {
/^\/\// && last;
$_ = uc($_);
s/[^A-Za-z]//g;
$seqc .= $_;
}
my $seq = $self->sequence_factory->create
(-verbose => $self->verbose(),
-division => $div,
-seq => $seqc,
-desc => $desc,
-display_id => $name,
-annotation => $annotation,
-molecule => $mol,
-alphabet => $alphabet,
-features => \@features,
%params);
return $seq;
}
=head2 write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object (must be seq) to the stream
Returns : 1 for success and 0 for error
Args : array of 1 to n Bio::SeqI objects
=cut
sub write_seq {
my ($self,@seqs) = @_;
foreach my $seq ( @seqs ) {
$self->throw("Attempting to write with no seq!") unless defined $seq;
unless ( ref $seq && $seq->isa('Bio::SeqI' ) ) {
$self->warn("$seq is not a SeqI compliant sequence object!")
if $self->verbose >= 0;
unless ( ref $seq && $seq->isa('Bio::PrimarySeqI' ) ) {
$self->throw("$seq is not a PrimarySeqI compliant sequence object!");
}
}
my $str = $seq->seq || '';
my $mol;
my $div;
my $len = $seq->length();
if ($seq->can('division') && defined $seq->division) {
$div = $seq->division();
}
$div ||= 'UNK';
if ($seq->can('molecule')) {
$mol = $seq->molecule();
$mol = 'RNA' if defined $mol && $mol =~ /RNA/; # no 'mRNA'
}
elsif ($seq->can('primary_seq') && defined $seq->primary_seq->alphabet) {
my $alphabet =$seq->primary_seq->alphabet;
if ($alphabet eq 'dna') {
$mol ='DNA';
}
elsif ($alphabet eq 'rna') {
$mol='RNA';
}
elsif ($alphabet eq 'protein') {
$mol='AA';
}
}
$mol ||= 'XXX';
$mol = "circular $mol" if $seq->is_circular;
my $temp_line;
if( $self->_id_generation_func ) {
$temp_line = &{$self->_id_generation_func}($seq);
} else {
$temp_line = sprintf("%-11sstandard; $mol; $div; %d BP.", $seq->id(), $len);
}
$self->_print( "ID $temp_line\n","XX\n");
# Write the accession line if present
my( $acc );
{
if( my $func = $self->_ac_generation_func ) {
$acc = &{$func}($seq);
} elsif( $seq->isa('Bio::Seq::RichSeqI') &&
defined($seq->accession_number) ) {
$acc = $seq->accession_number;
$acc = join(";", $acc, $seq->get_secondary_accessions);
} elsif ( $seq->can('accession_number') ) {
$acc = $seq->accession_number;
}
if (defined $acc) {
$self->_print("AC $acc;\n",
"XX\n");
}
}
# Write the sv line if present
{
my( $sv );
if (my $func = $self->_sv_generation_func) {
$sv = &{$func}($seq);
} elsif($seq->isa('Bio::Seq::RichSeqI') &&
defined($seq->seq_version)) {
$sv = "$acc.". $seq->seq_version();
}
if (defined $sv) {
$self->_print( "SV $sv\n",
"XX\n");
}
}
# Date lines
my $switch=0;
if( $seq->can('get_dates') ) {
foreach my $dt ( $seq->get_dates() ) {
$self->_write_line_EMBL_regex("DT ","DT ",$dt,'\s+|$',80);#'
$switch=1;
}
if ($switch == 1) {
$self->_print("XX\n");
}
}
# Description lines
$self->_write_line_EMBL_regex("DE ","DE ",$seq->desc(),'\s+|$',80); #'
$self->_print( "XX\n");
# if there, write the kw line
{
my( $kw );
if( my $func = $self->_kw_generation_func ) {
$kw = &{$func}($seq);
} elsif( $seq->can('keywords') ) {
$kw = $seq->keywords;
if( ref($kw) =~ /ARRAY/i ) {
$kw = join("; ", @$kw);
}
$kw .= '.' if( defined $kw && $kw !~ /\.$/ );
}
if (defined $kw) {
$self->_write_line_EMBL_regex("KW ", "KW ",
$kw, '\s+|$', 80); #'
$self->_print( "XX\n");
}
}
# Organism lines
if ($seq->can('species') && (my $spec = $seq->species)) {
my($species, @class) = $spec->classification();
my $genus = $class[0];
my $OS = "$genus $species";
if (my $ssp = $spec->sub_species) {
$OS .= " $ssp";
}
if (my $common = $spec->common_name) {
$OS .= " ($common)";
}
$self->_print("OS $OS\n");
my $OC = join('; ', reverse(@class)) .'.';
$self->_write_line_EMBL_regex("OC ","OC ",$OC,'; |$',80); #'
if ($spec->organelle) {
$self->_write_line_EMBL_regex("OG ","OG ",$spec->organelle,'; |$',80); #'
}
$self->_print("XX\n");
}
# Reference lines
my $t = 1;
if ( $seq->can('annotation') && defined $seq->annotation ) {
foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
$self->_print( "RN [$t]\n");
# Having no RP line is legal, but we need both
# start and end for a valid location.
my $start = $ref->start;
my $end = $ref->end;
if ($start and $end) {
$self->_print( "RP $start-$end\n");
} elsif ($start or $end) {
$self->throw("Both start and end are needed for a valid RP line. Got: start='$start' end='$end'");
}
if (my $med = $ref->medline) {
$self->_print( "RX MEDLINE; $med.\n");
}
if (my $pm = $ref->pubmed) {
$self->_print( "RX PUBMED; $pm.\n");
}
$self->_write_line_EMBL_regex("RA ", "RA ",
$ref->authors . ";",
'\s+|$', 80); #'
# If there is no title to the reference, it appears
# as a single semi-colon. All titles must end in
# a semi-colon.
my $ref_title = $ref->title || '';
$ref_title =~ s/[\s;]*$/;/;
$self->_write_line_EMBL_regex("RT ", "RT ", $ref_title, '\s+|$', 80); #'
$self->_write_line_EMBL_regex("RL ", "RL ", $ref->location, '\s+|$', 80); #'
if ($ref->comment) {
$self->_write_line_EMBL_regex("RC ", "RC ", $ref->comment, '\s+|$', 80); #'
}
$self->_print("XX\n");
$t++;
}
# DB Xref lines
if (my @db_xref = $seq->annotation->get_Annotations('dblink') ) {
foreach my $dr (@db_xref) {
my $db_name = $dr->database;
my $prim = $dr->primary_id;
my $opt = $dr->optional_id || '';
my $line = "$db_name; $prim; $opt.";
$self->_write_line_EMBL_regex("DR ", "DR ", $line, '\s+|$', 80); #'
}
$self->_print("XX\n");
}
# Comment lines
foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
$self->_write_line_EMBL_regex("CC ", "CC ", $comment->text, '\s+|$', 80); #'
$self->_print("XX\n");
}
}
# "\\s\+\|\$"
## FEATURE TABLE
$self->_print("FH Key Location/Qualifiers\n");
$self->_print("FH\n");
my @feats = $seq->can('top_SeqFeatures') ? $seq->top_SeqFeatures : ();
if ($feats[0]) {
if( defined $self->_post_sort ) {
# we need to read things into an array.
# Process. Sort them. Print 'em
my $post_sort_func = $self->_post_sort();
my @fth;
foreach my $sf ( @feats ) {
push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq));
}
@fth = sort { &$post_sort_func($a,$b) } @fth;
foreach my $fth ( @fth ) {
$self->_print_EMBL_FTHelper($fth);
}
} else {
# not post sorted. And so we can print as we get them.
# lower memory load...
foreach my $sf ( @feats ) {
my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq);
foreach my $fth ( @fth ) {
if( $fth->key eq 'CONTIG') {
$self->_show_dna(0);
}
$self->_print_EMBL_FTHelper($fth);
}
}
}
}
if( $self->_show_dna() == 0 ) {
$self->_print( "//\n");
return;
}
$self->_print( "XX\n");
# finished printing features.
$str =~ tr/A-Z/a-z/;
# Count each nucleotide
my $alen = $str =~ tr/a/a/;
my $clen = $str =~ tr/c/c/;
my $glen = $str =~ tr/g/g/;
my $tlen = $str =~ tr/t/t/;
my $olen = $len - ($alen + $tlen + $clen + $glen);
if( $olen < 0 ) {
$self->warn("Weird. More atgc than bases. Problem!");
}
$self->_print("SQ Sequence $len BP; $alen A; $clen C; $glen G; $tlen T; $olen other;\n");
my $nuc = 60; # Number of nucleotides per line
my $whole_pat = 'a10' x 6; # Pattern for unpacking a whole line
my $out_pat = 'A11' x 6; # Pattern for packing a line
my $length = length($str);
# Calculate the number of nucleotides which fit on whole lines
my $whole = int($length / $nuc) * $nuc;
# Print the whole lines
my( $i );
for ($i = 0; $i < $whole; $i += $nuc) {
my $blocks = pack $out_pat,
unpack $whole_pat,
substr($str, $i, $nuc);
$self->_print(sprintf(" $blocks%9d\n", $i + $nuc));
}
# Print the last line
if (my $last = substr($str, $i)) {
my $last_len = length($last);
my $last_pat = 'a10' x int($last_len / 10) .'a'. $last_len % 10;
my $blocks = pack $out_pat,
unpack($last_pat, $last);
$self->_print(sprintf(" $blocks%9d\n", $length)); # Add the length to the end
}
$self->_print( "//\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
}
=head2 _print_EMBL_FTHelper
Title : _print_EMBL_FTHelper
Usage :
Function: Internal function
Returns :
Args :
=cut
sub _print_EMBL_FTHelper {
my ($self,$fth,$always_quote) = @_;
$always_quote ||= 0;
if( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) {
$fth->warn("$fth is not a FTHelper class. Attempting to print, but there could be tears!");
}
#$self->_print( "FH Key Location/Qualifiers\n");
#$self->_print( sprintf("FT %-15s %s\n",$fth->key,$fth->loc));
# let
if( $fth->key eq 'CONTIG' ) {
$self->_print("XX\n");
$self->_write_line_EMBL_regex("CO ",
"CO ",$fth->loc,
'\,|$',80); #'
return;
}
$self->_write_line_EMBL_regex(sprintf("FT %-15s ",$fth->key),
"FT ",$fth->loc,
'\,|$',80); #'
foreach my $tag ( keys %{$fth->field} ) {
if( ! defined $fth->field->{$tag} ) { next; }
foreach my $value ( @{$fth->field->{$tag}} ) {
$value =~ s/\"/\"\"/g;
if ($value eq "_no_value") {
$self->_write_line_EMBL_regex("FT ",
"FT ",
"/$tag",'.|$',80); #'
}
elsif( $always_quote == 1 || $value !~ /^\d+$/ ) {
my $pat = $value =~ /\s/ ? '\s|$' : '.|$';
$self->_write_line_EMBL_regex("FT ",
"FT ",
"/$tag=\"$value\"",$pat,80);
}
else {
$self->_write_line_EMBL_regex("FT ",
"FT ",
"/$tag=$value",'.|$',80); #'
}
# $self->_print( "FT /", $tag, "=\"", $value, "\"\n");
}
}
}
#'
=head2 _read_EMBL_References
Title : _read_EMBL_References
Usage :
Function: Reads references from EMBL format. Internal function really
Example :
Returns :
Args :
=cut
sub _read_EMBL_References {
my ($self,$buffer) = @_;
my (@refs);
# assumme things are starting with RN
if( $$buffer !~ /^RN/ ) {
warn("Not parsing line '$$buffer' which maybe important");
}
my $b1;
my $b2;
my $title;
my $loc;
my $au;
my $med;
my $pm;
my $com;
while( defined ($_ = $self->_readline) ) {
/^R/ || last;
/^RP (\d+)-(\d+)/ && do {$b1=$1;$b2=$2;};
/^RX MEDLINE;\s+(\d+)/ && do {$med=$1};
/^RX PUBMED;\s+(\d+)/ && do {$pm=$1};
/^RA (.*)/ && do {
$au = $self->_concatenate_lines($au,$1); next;
};
/^RT (.*)/ && do {
$title = $self->_concatenate_lines($title,$1); next;
};
/^RL (.*)/ && do {
$loc = $self->_concatenate_lines($loc,$1); next;
};
/^RC (.*)/ && do {
$com = $self->_concatenate_lines($com,$1); next;
};
}
my $ref = new Bio::Annotation::Reference;
$au =~ s/;\s*$//g;
$title =~ s/;\s*$//g;
$ref->start($b1);
$ref->end($b2);
$ref->authors($au);
$ref->title($title);
$ref->location($loc);
$ref->medline($med);
$ref->comment($com);
$ref->pubmed($pm);
push(@refs,$ref);
$$buffer = $_;
return @refs;
}
=head2 _read_EMBL_Species
Title : _read_EMBL_Species
Usage :
Function: Reads the EMBL Organism species and classification
lines.
Example :
Returns : A Bio::Species object
Args : a reference to the current line buffer
=cut
sub _read_EMBL_Species {
my( $self, $buffer ) = @_;
my $org;
$_ = $$buffer;
my( $sub_species, $species, $genus, $common, @class );
while (defined( $_ ||= $self->_readline )) {
if (/^OS\s+(\S+)(?:\s+([^\(]\S*))?(?:\s+([^\(]\S*))?(?:\s+\((.*)\))?/) {
$genus = $1;
$species = $2 || 'sp.';
$sub_species = $3 if $3;
$common = $4 if $4;
}
elsif (s/^OC\s+//) {
# only split on ';' or '.' so that
# classification that is 2 words will
# still get matched
# use map to remove trailing/leading spaces
chomp;
push(@class, map { s/^\s+//; s/\s+$//; $_; } split /[;\.]+/);
}
elsif (/^OG\s+(.*)/) {
$org = $1;
}
else {
last;
}
$_ = undef; # Empty $_ to trigger read of next line
}
$$buffer = $_;
# Don't make a species object if it is "Unknown" or "None"
return if $genus =~ /^(Unknown|None)$/i;
# Bio::Species array needs array in Species -> Kingdom direction
if ($class[$#class] eq $genus) {
push( @class, $species );
} else {
push( @class, $genus, $species );
}
@class = reverse @class;
my $make = Bio::Species->new();
$make->classification( \@class, "FORCE" ); # no name validation please
$make->common_name( $common ) if $common;
$make->sub_species( $sub_species ) if $sub_species;
$make->organelle ( $org ) if $org;
return $make;
}
=head2 _read_EMBL_DBLink
Title : _read_EMBL_DBLink
Usage :
Function: Reads the EMBL database cross reference ("DR") lines
Example :
Returns : A list of Bio::Annotation::DBLink objects
Args :
=cut
sub _read_EMBL_DBLink {
my( $self,$buffer ) = @_;
my( @db_link );
$_ = $$buffer;
while (defined( $_ ||= $self->_readline )) {
if (my($databse, $prim_id, $sec_id)
= /^DR ([^\s;]+);\s*([^\s;]+);\s*([^\s;]+)?\.$/) {
my $link = Bio::Annotation::DBLink->new();
$link->database ( $databse );
$link->primary_id ( $prim_id );
$link->optional_id( $sec_id ) if $sec_id;
push(@db_link, $link);
}
else {
last;
}
$_ = undef; # Empty $_ to trigger read of next line
}
$$buffer = $_;
return @db_link;
}
=head2 _filehandle
Title : _filehandle
Usage : $obj->_filehandle($newval)
Function:
Example :
Returns : value of _filehandle
Args : newvalue (optional)
=cut
sub _filehandle{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_filehandle'} = $value;
}
return $obj->{'_filehandle'};
}
=head2 _read_FTHelper_EMBL
Title : _read_FTHelper_EMBL
Usage : _read_FTHelper_EMBL($buffer)
Function: reads the next FT key line
Example :
Returns : Bio::SeqIO::FTHelper object
Args : filehandle and reference to a scalar
=cut
sub _read_FTHelper_EMBL {
my ($self,$buffer) = @_;
my ($key, # The key of the feature
$loc, # The location line from the feature
@qual, # An arrray of lines making up the qualifiers
);
if ($$buffer =~ /^FT\s{3}(\S+)\s+(\S+)/) {
$key = $1;
$loc = $2;
# Read all the lines up to the next feature
while ( defined($_ = $self->_readline) ) {
if (/^FT(\s+)(.+?)\s*$/) {
# Lines inside features are preceeded by 19 spaces
# A new feature is preceeded by 3 spaces
if (length($1) > 4) {
# Add to qualifiers if we're in the qualifiers
if (@qual) {
push(@qual, $2);
}
# Start the qualifier list if it's the first qualifier
elsif (substr($2, 0, 1) eq '/') {
@qual = ($2);
}
# We're still in the location line, so append to location
else {
$loc .= $2;
}
} else {
# We've reached the start of the next feature
last;
}
} else {
# We're at the end of the feature table
last;
}
}
} elsif( $$buffer =~ /^CO\s+(\S+)/) {
$key = 'CONTIG';
$loc = $1;
# Read all the lines up to the next feature
while ( defined($_ = $self->_readline) ) {
if (/^CO\s+(\S+)\s*$/) {
$loc .= $1;
} else {
# We've reached the start of the next feature
last;
}
}
} else {
# No feature key
return;
}
# Put the first line of the next feature into the buffer
$$buffer = $_;
# Make the new FTHelper object
my $out = new Bio::SeqIO::FTHelper();
$out->verbose($self->verbose());
$out->key($key);
$out->loc($loc);
# Now parse and add any qualifiers. (@qual is kept
# intact to provide informative error messages.)
QUAL: for (my $i = 0; $i < @qual; $i++) {
$_ = $qual[$i];
my( $qualifier, $value ) = m{^/([^=]+)(?:=(.+))?}
or $self->throw("Can't see new qualifier in: $_\nfrom:\n"
. join('', map "$_\n", @qual));
if (defined $value) {
# Do we have a quoted value?
if (substr($value, 0, 1) eq '"') {
# Keep adding to value until we find the trailing quote
# and the quotes are balanced
while ($value !~ /"$/ or $value =~ tr/"/"/ % 2) { #"
$i++;
my $next = $qual[$i];
unless (defined($next)) {
warn("Unbalanced quote in:\n", map("$_\n", @qual),
"No further qualifiers will be added for this feature");
last QUAL;
}
# Join to value with space if value or next line contains a space
$value .= (grep /\s/, ($value, $next)) ? " $next" : $next;
}
# Trim leading and trailing quotes
$value =~ s/^"|"$//g;
# Undouble internal quotes
$value =~ s/""/"/g; #"
}
} else {
$value = '_no_value';
}
# Store the qualifier
$out->field->{$qualifier} ||= [];
push(@{$out->field->{$qualifier}},$value);
}
return $out;
}
=head2 _write_line_EMBL
Title : _write_line_EMBL
Usage :
Function: internal function
Example :
Returns :
Args :
=cut
sub _write_line_EMBL {
my ($self,$pre1,$pre2,$line,$length) = @_;
$length || die "Miscalled write_line_EMBL without length. Programming error!";
my $subl = $length - length $pre2;
my $linel = length $line;
my $i;
my $sub = substr($line,0,$length - length $pre1);
$self->_print( "$pre1$sub\n");
for($i= ($length - length $pre1);$i < $linel;) {
$sub = substr($line,$i,($subl));
$self->_print( "$pre2$sub\n");
$i += $subl;
}
}
=head2 _write_line_EMBL_regex
Title : _write_line_EMBL_regex
Usage :
Function: internal function for writing lines of specified
length, with different first and the next line
left hand headers and split at specific points in the
text
Example :
Returns : nothing
Args : file handle, first header, second header, text-line, regex for line breaks, total line length
=cut
sub _write_line_EMBL_regex {
my ($self,$pre1,$pre2,$line,$regex,$length) = @_;
#print STDOUT "Going to print with $line!\n";
$length || die "Programming error - called write_line_EMBL_regex without length.";
my $subl = $length - (length $pre1) -1 ;
my( @lines );
while(defined $line &&
$line =~ m/(.{1,$subl})($regex)/g) {
push(@lines, $1.$2);
}
foreach (@lines) { s/\s+$//; }
# Print first line
my $s = shift(@lines) || '';
$self->_print( "$pre1$s\n");
# Print the rest
foreach my $s ( @lines ) {
$s = '' if( !defined $s );
$self->_print( "$pre2$s\n");
}
}
=head2 _post_sort
Title : _post_sort
Usage : $obj->_post_sort($newval)
Function:
Returns : value of _post_sort
Args : newvalue (optional)
=cut
sub _post_sort{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_post_sort'} = $value;
}
return $obj->{'_post_sort'};
}
=head2 _show_dna
Title : _show_dna
Usage : $obj->_show_dna($newval)
Function:
Returns : value of _show_dna
Args : newvalue (optional)
=cut
sub _show_dna{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_show_dna'} = $value;
}
return $obj->{'_show_dna'};
}
=head2 _id_generation_func
Title : _id_generation_func
Usage : $obj->_id_generation_func($newval)
Function:
Returns : value of _id_generation_func
Args : newvalue (optional)
=cut
sub _id_generation_func{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_id_generation_func'} = $value;
}
return $obj->{'_id_generation_func'};
}
=head2 _ac_generation_func
Title : _ac_generation_func
Usage : $obj->_ac_generation_func($newval)
Function:
Returns : value of _ac_generation_func
Args : newvalue (optional)
=cut
sub _ac_generation_func{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_ac_generation_func'} = $value;
}
return $obj->{'_ac_generation_func'};
}
=head2 _sv_generation_func
Title : _sv_generation_func
Usage : $obj->_sv_generation_func($newval)
Function:
Returns : value of _sv_generation_func
Args : newvalue (optional)
=cut
sub _sv_generation_func{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_sv_generation_func'} = $value;
}
return $obj->{'_sv_generation_func'};
}
=head2 _kw_generation_func
Title : _kw_generation_func
Usage : $obj->_kw_generation_func($newval)
Function:
Returns : value of _kw_generation_func
Args : newvalue (optional)
=cut
sub _kw_generation_func{
my $obj = shift;
if( @_ ) {
my $value = shift;
$obj->{'_kw_generation_func'} = $value;
}
return $obj->{'_kw_generation_func'};
}
1;
]]>