#
# BioPerl module for Bio::SeqIO::genbank
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Bioperl project bioperl-l(at)bioperl.org
#
# Copyright Elia Stupka and contributors see AUTHORS section
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqIO::genbank - GenBank sequence input/output stream
=head1 SYNOPSIS
It is probably best not to use this object directly, but
rather go through the SeqIO handler:
$stream = Bio::SeqIO->new(-file => $filename,
-format => 'GenBank');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from GenBank flat
file databases.
There is some flexibility here about how to write GenBank output
that is not fully documented.
=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 ", $func($seq), "\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 Genbank 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 pulled from a
L<Bio::Annotation::Collection> object:
reference - Should contain Bio::Annotation::Reference objects
comment - Should contain Bio::Annotation::Comment objects
dblink - Should contain a Bio::Annotation::DBLink object
segment - Should contain a Bio::Annotation::SimpleValue object
origin - Should contain a Bio::Annotation::SimpleValue object
wgs - Should contain a Bio::Annotation::SimpleValue object
=back
=head1 Where does the data go?
Data parsed in Bio::SeqIO::genbank is stored in a variety of data
fields in the sequence object that is returned. Here is a partial list
of fields.
Items listed as RichSeq or Seq or PrimarySeq and then NAME() tell you
the top level object which defines a function called NAME() which
stores this information.
Items listed as Annotation 'NAME' tell you the data is stored the
associated Bio::AnnotationCollectionI object which is associated with
Bio::Seq objects. If it is explicitly requested that no annotations
should be stored when parsing a record of course they will not be
available when you try and get them. If you are having this problem
look at the type of SeqBuilder that is being used to contruct your
sequence object.
Comments Annotation 'comment'
References Annotation 'reference'
Segment Annotation 'segment'
Origin Annotation 'origin'
Dbsource Annotation 'dblink'
Accessions PrimarySeq accession_number()
Secondary accessions RichSeq get_secondary_accessions()
GI number PrimarySeq primary_id()
LOCUS PrimarySeq display_id()
Keywords RichSeq get_keywords()
Dates RichSeq get_dates()
Molecule RichSeq molecule()
Seq Version RichSeq seq_version()
PID RichSeq pid()
Division RichSeq division()
Features Seq get_SeqFeatures()
Alphabet PrimarySeq alphabet()
Definition PrimarySeq description() or desc()
Version PrimarySeq version()
Sequence PrimarySeq seq()
There is more information in the Feature-Annotation HOWTO about each
field and how it is mapped to the Sequence object
L<http://bioperl.open-bio.org/wiki/HOWTO:Feature-Annotation>.
=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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Bioperl Project
bioperl-l at bioperl.org
Original author Elia Stupka, elia -at- tigem.it
=head1 CONTRIBUTORS
Ewan Birney birney at ebi.ac.uk
Jason Stajich jason at bioperl.org
Chris Mungall cjm at fruitfly.bdgp.berkeley.edu
Lincoln Stein lstein at cshl.org
Heikki Lehvaslaiho, heikki at ebi.ac.uk
Hilmar Lapp, hlapp at gmx.net
Donald G. Jackson, donald.jackson at bms.com
James Wasmuth, james.wasmuth at ed.ac.uk
Brian Osborne, bosborne at alum.mit.edu
Chris Fields, cjfields at bioperl dot org
=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::genbank;
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;
use base qw(Bio::SeqIO);
# Note that a qualifier that exceeds one line (i.e. a long label) will
# automatically be quoted regardless:
our $FTQUAL_LINE_LENGTH = 60;
our %FTQUAL_NO_QUOTE = map {$_ => 1} qw(
anticodon citation
codon codon_start
cons_splice direction
evidence label
mod_base number
rpt_type rpt_unit
transl_except transl_table
usedin
);
our %DBSOURCE = map {$_ => 1} qw(
EchoBASE IntAct SWISS-2DPAGE ECO2DBASE ECOGENE TIGRFAMs
TIGR GO InterPro Pfam PROSITE SGD GermOnline
HSSP PhosSite Ensembl RGD AGD ArrayExpress KEGG
H-InvDB HGNC LinkHub PANTHER PRINTS SMART SMR
MGI MIM RZPD-ProtExp ProDom MEROPS TRANSFAC Reactome
UniGene GlycoSuiteDB PIRSF HSC-2DPAGE PHCI-2DPAGE
PMMA-2DPAGE Siena-2DPAGE Rat-heart-2DPAGE Aarhus/Ghent-2DPAGE
Biocyc MetaCyc Biocyc:Metacyc GenomeReviews FlyBase
TMHOBP COMPLUYEAST-2DPAGE OGP DictyBase HAMAP
PhotoList Gramene WormBase WormPep Genew ZFIN
PeroxiBase MaizeDB TAIR DrugBank REBASE HPA
swissprot GenBank GenPept REFSEQ embl PDB UniProtKB
DIP PeptideAtlas PRIDE CYGD HOGENOME Gene3D
Project);
our %VALID_MOLTYPE = map {$_ => 1} qw(NA DNA RNA tRNA rRNA cDNA cRNA ms-DNA
mRNA uRNA ss-RNA ss-DNA snRNA snoRNA PRT);
our %VALID_ALPHABET = (
'bp' => 'dna',
'aa' => 'protein',
'rc' => '' # rc = release candidate; file has no sequences
);
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(Bio::Seq::SeqFactory->new
(-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 %args = @args;
my $builder = $self->sequence_builder();
my $seq;
my %params;
RECORDSTART:
while (1) {
my $buffer;
my (@acc, @features);
my ($display_id, $annotation);
my $species;
# initialize; we may come here because of starting over
@features = ();
$annotation = undef;
@acc = ();
$species = undef;
%params = (-verbose => $self->verbose); # reset hash
local($/) = "\n";
while(defined($buffer = $self->_readline())) {
last if index($buffer,'LOCUS ') == 0;
}
return unless defined $buffer; # end of file
$buffer =~ /^LOCUS\s+(\S.*)$/o ||
$self->throw("GenBank stream with bad LOCUS line. Not GenBank in my book. Got '$buffer'");
my @tokens = split(' ', $1);
# this is important to have the id for display in e.g. FTHelper,
# otherwise you won't know which entry caused an error
$display_id = shift(@tokens);
$params{'-display_id'} = $display_id;
# may still be useful if we don't want the seq
my $seqlength = shift(@tokens);
if (exists $VALID_ALPHABET{$seqlength}) {
# moved one token too far. No locus name?
$self->warn("Bad LOCUS name? Changing [$params{'-display_id'}] to 'unknown' and length to $display_id");
$params{'-display_id'} = 'unknown';
$params{'-length'} = $display_id;
# add token back...
unshift @tokens, $seqlength;
} else {
$params{'-length'} = $seqlength;
}
# the alphabet of the entry
# shouldn't assign alphabet unless one is specifically designated (such as for rc files)
my $alphabet = lc(shift @tokens);
$params{'-alphabet'} = (exists $VALID_ALPHABET{$alphabet}) ? $VALID_ALPHABET{$alphabet} :
$self->warn("Unknown alphabet: $alphabet");
# for aa there is usually no 'molecule' (mRNA etc)
if ($params{'-alphabet'} eq 'protein') {
$params{'-molecule'} = 'PRT'
} else {
$params{'-molecule'} = shift(@tokens);
}
# take care of lower case issues
if ($params{'-molecule'} eq 'dna' || $params{'-molecule'} eq 'rna') {
$params{'-molecule'} = uc $params{'-molecule'};
}
$self->debug("Unrecognized molecule type:".$params{'-molecule'}) if
!exists($VALID_MOLTYPE{$params{'-molecule'}});
my $circ = shift(@tokens);
if ($circ eq 'circular') {
$params{'-is_circular'} = 1;
$params{'-division'} = shift(@tokens);
} else {
# 'linear' or 'circular' may actually be omitted altogether
$params{'-division'} =
(CORE::length($circ) == 3 ) ? $circ : shift(@tokens);
}
my $date = join(' ', @tokens); # we lump together the rest
# this is per request bug #1513
# we can handle
# 9-10-2003
# 9-10-03
# 09-10-2003
# 09-10-03
if($date =~ s/\s*((\d{1,2})-(\w{3})-(\d{2,4})).*/$1/) {
if( length($date) < 11 ) {
# improperly formatted date
# But we'll be nice and fix it for them
my ($d,$m,$y) = ($2,$3,$4);
if( length($d) == 1 ) {
$d = "0$d";
}
# guess the century here
if( length($y) == 2 ) {
if( $y > 60 ) { # arbitrarily guess that '60' means 1960
$y = "19$y";
} else {
$y = "20$y";
}
$self->warn("Date was malformed, guessing the century for $date to be $y\n");
}
$params{'-dates'} = [join('-',$d,$m,$y)];
} else {
$params{'-dates'} = [$date];
}
}
# set them all at once
$builder->add_slot_value(%params);
%params = ();
# parse the rest if desired, otherwise start over
if(! $builder->want_object()) {
$builder->make_object();
next RECORDSTART;
}
# set up annotation depending on what the builder wants
if($builder->want_slot('annotation')) {
$annotation = Bio::Annotation::Collection->new();
}
$buffer = $self->_readline();
until( !defined ($buffer) ) {
$_ = $buffer;
# Description line(s)
if (/^DEFINITION\s+(\S.*\S)/) {
my @desc = ($1);
while ( defined($_ = $self->_readline) ) {
if( /^\s+(.*)/ ) { push (@desc, $1); next };
last;
}
$builder->add_slot_value(-desc => join(' ', @desc));
# we'll continue right here because DEFINITION always comes
# at the top of the entry
$buffer= $_;
}
# accession number (there can be multiple accessions)
if( /^ACCESSION\s+(\S.*\S)/ ) {
push(@acc, split(/\s+/,$1));
while( defined($_ = $self->_readline) ) {
/^\s+(.*)/ && do { push (@acc, split(/\s+/,$1)); next };
last;
}
$buffer = $_;
next;
}
# PID
elsif( /^PID\s+(\S+)/ ) {
$params{'-pid'} = $1;
}
# Version number
elsif( /^VERSION\s+(\S.+)$/ ) {
my ($acc,$gi) = split(' ',$1);
if($acc =~ /^\w+\.(\d+)/) {
$params{'-version'} = $1;
$params{'-seq_version'} = $1;
}
if($gi && (index($gi,"GI:") == 0)) {
$params{'-primary_id'} = substr($gi,3);
}
}
# Keywords
elsif( /^KEYWORDS\s+(\S.*)/ ) {
my @kw = split(/\s*\;\s*/,$1);
while( defined($_ = $self->_readline) ) {
chomp;
/^\s+(.*)/ && do { push (@kw, split(/\s*\;\s*/,$1)); next };
last;
}
@kw && $kw[-1] =~ s/\.$//;
$params{'-keywords'} = \@kw;
$buffer = $_;
next;
}
# Organism name and phylogenetic information
elsif (/^SOURCE\s+\S/) {
if($builder->want_slot('species')) {
$species = $self->_read_GenBank_Species(\$buffer);
$builder->add_slot_value(-species => $species);
} else {
while(defined($buffer = $self->_readline())) {
last if substr($buffer,0,1) ne ' ';
}
}
next;
}
# References
elsif (/^REFERENCE\s+\S/) {
if($annotation) {
my @refs = $self->_read_GenBank_References(\$buffer);
foreach my $ref ( @refs ) {
$annotation->add_Annotation('reference',$ref);
}
} else {
while(defined($buffer = $self->_readline())) {
last if substr($buffer,0,1) ne ' ';
}
}
next;
}
# Project
elsif (/^PROJECT\s+(\S.*)/) {
if ($annotation) {
my $project = Bio::Annotation::SimpleValue->new(-value => $1);
$annotation->add_Annotation('project',$project);
}
}
# Comments
elsif (/^COMMENT\s+(\S.*)/) {
if($annotation) {
my $comment = $1;
while (defined($_ = $self->_readline)) {
last if (/^\S/);
$comment .= $_;
}
$comment =~ s/\n/ /g;
$comment =~ s/ +/ /g;
$annotation->add_Annotation('comment',
Bio::Annotation::Comment->new(-text => $comment,
-tagname => 'comment'));
$buffer = $_;
} else {
while(defined($buffer = $self->_readline())) {
last if substr($buffer,0,1) ne ' ';
}
}
next;
}
# Corresponding Genbank nucleotide id, Genpept only
elsif( /^DB(?:SOURCE|LINK)\s+(\S.+)/ ) {
if ($annotation) {
my $dbsource = $1;
while (defined($_ = $self->_readline)) {
last if (/^\S/);
$dbsource .= $_;
}
# deal with UniProKB dbsources
if( $dbsource =~ s/(UniProt(?:KB)?|swissprot):\s+locus\s+(\S+)\,.+\n// ) {
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $2,
-database => $1,
-tagname => 'dblink'));
if( $dbsource =~ s/\s+created:\s+([^\.]+)\.\n// ) {
$annotation->add_Annotation
('swissprot_dates',
Bio::Annotation::SimpleValue->new
(-tagname => 'date_created',
-value => $1));
}
while( $dbsource =~ s/\s+(sequence|annotation)\s+updated:\s+([^\.]+)\.\n//g ) {
$annotation->add_Annotation
('swissprot_dates',
Bio::Annotation::SimpleValue->new
(-tagname => 'date_updated',
-value => $2));
}
$dbsource =~ s/\n/ /g;
if( $dbsource =~ s/\s+xrefs:\s+((?:\S+,\s+)+\S+)\s+xrefs/xrefs/ ) {
# will use $i to determine even or odd
# for swissprot the accessions are paired
my $i = 0;
for my $dbsrc ( split(/,\s+/,$1) ) {
if( $dbsrc =~ /(\S+)\.(\d+)/ ||
$dbsrc =~ /(\S+)/ ) {
my ($id,$version) = ($1,$2);
$version ='' unless defined $version;
my $db;
if( $id =~ /^\d\S{3}/) {
$db = 'PDB';
} else {
$db = ($i++ % 2 ) ? 'GenPept' : 'GenBank';
}
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $id,
-version => $version,
-database => $db,
-tagname => 'dblink'));
}
}
} elsif( $dbsource =~ s/\s+xrefs:\s+(.+)\s+xrefs/xrefs/i ) {
# download screwed up and ncbi didn't put acc in for gi numbers
my $i = 0;
for my $id ( split(/\,\s+/,$1) ) {
my ($acc,$db);
if( $id =~ /gi:\s+(\d+)/ ) {
$acc= $1;
$db = ($i++ % 2 ) ? 'GenPept' : 'GenBank';
} elsif( $id =~ /pdb\s+accession\s+(\S+)/ ) {
$acc= $1;
$db = 'PDB';
} else {
$acc= $id;
$db = '';
}
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $acc,
-database => $db,
-tagname => 'dblink'));
}
} else {
$self->debug("Cannot match $dbsource\n");
}
if( $dbsource =~ s/xrefs\s+\(non\-sequence\s+databases\):\s+
((?:\S+,\s+)+\S+)//x ) {
for my $id ( split(/\,\s+/,$1) ) {
my $db;
# this is because GenBank dropped the spaces!!!
# I'm sure we're not going to get this right
##if( $id =~ s/^://i ) {
## $db = $1;
##}
$db = substr($id,0,index($id,':'));
if (! exists $DBSOURCE{ $db }) {
$db = ''; # do we want 'GenBank' here?
}
$id = substr($id,index($id,':')+1);
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $id,
-database => $db,
-tagname => 'dblink'));
}
}
} else {
if( $dbsource =~ /^(\S*?):?\s*accession\s+(\S+)\.(\d+)/ ) {
my ($db,$id,$version) = ($1,$2,$3);
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $id,
-version => $version,
-database => $db || 'GenBank',
-tagname => 'dblink'));
} elsif ( $dbsource =~ /^(\S*?):?\s*accession\s+(\S+)/ ) {
my ($db,$id) = ($1,$2);
$annotation->add_Annotation
('dblink',
Bio::Annotation::DBLink->new
(-primary_id => $id,
-database => $db || 'GenBank',
-tagname => 'dblink'));
} elsif ( $dbsource =~ /(\S+)([\.:])\s*(\S+)/ ) {
my ($db, $version);
my @ids = ();
if ($2 eq ':') {
$db = $1;
# Genbank 192 release notes say this: "The second field can consist of
# multiple comma-separated identifiers, if a sequence record has
# multiple DBLINK cross-references of a given type."
# For example: DBLINK Project:100,200,300"
@ids = split (/,/, $3);
} else {
($db, $version) = ('GenBank', $3);
$ids[0] = $1;
}
foreach my $id (@ids) {
$annotation->add_Annotation('dblink',
Bio::Annotation::DBLink->new(
-primary_id => $id,
-version => $version,
-database => $db,
-tagname => 'dblink')
);
}
} else {
$self->warn("Unrecognized DBSOURCE data: $dbsource\n");
}
}
$buffer = $_;
} else {
while(defined($buffer = $self->_readline())) {
last if substr($buffer,0,1) ne ' ';
}
}
next;
}
# Exit at start of Feature table, or start of sequence
last if( /^(FEATURES|ORIGIN)/ );
# Get next line and loop again
$buffer = $self->_readline;
}
return unless defined $buffer;
# add them all at once for efficiency
$builder->add_slot_value(-accession_number => shift(@acc),
-secondary_accessions => \@acc,
%params);
$builder->add_slot_value(-annotation => $annotation) if $annotation;
%params = (); # reset before possible re-use to avoid setting twice
# start over if we don't want to continue with this entry
if(! $builder->want_object()) {
$builder->make_object();
next RECORDSTART;
}
# some "minimal" formats may not necessarily have a feature table
if($builder->want_slot('features') && defined($_) && /^FEATURES/o) {
# need to read the first line of the feature table
$buffer = $self->_readline;
# DO NOT read lines in the while condition -- this is done as a side
# effect in _read_FTHelper_GenBank!
# part of new circular spec:
# commented out for now until kinks worked out
#my $sourceEnd = 0;
#$sourceEnd = $2 if ($buffer =~ /(\d+?)\.\.(\d+?)$/);
while( defined($buffer) ) {
# check immediately -- not at the end of the loop
# note: GenPept entries obviously do not have a BASE line
last if( $buffer =~ /^BASE|ORIGIN|CONTIG|WGS/o);
# slurp in one feature at a time -- at return, the start of
# the next feature will have been read already, so we need
# to pass a reference, and the called method must set this
# to the last line read before returning
my $ftunit = $self->_read_FTHelper_GenBank(\$buffer);
# implement new circular spec: features that cross the origin are now
# seamless instead of being 2 separate joined features
# commented out until kinks get worked out
#if ((! $args{'-nojoin'}) && $ftunit->{'loc'} =~ /^join\((\d+?)\.\.(\d+?),(\d+?)..(\d+?)\)$/
#&& $sourceEnd == $2 && $3 == 1) {
#my $start = $1;
#my $end = $2 + $4;
#$ftunit->{'loc'} = "$start..$end";
#}
# fix suggested by James Diggans
if( !defined $ftunit ) {
# GRRRR. We have fallen over. Try to recover
$self->warn("Unexpected error in feature table for ".$params{'-display_id'}." Skipping feature, attempting to recover");
unless( ($buffer =~ /^\s{5,5}\S+/o) or
($buffer =~ /^\S+/o)) {
$buffer = $self->_readline();
}
next; # back to reading FTHelpers
}
# process ftunit
my $feat =
$ftunit->_generic_seqfeature($self->location_factory(),
$display_id);
# add taxon_id from source if available
if($species && ($feat->primary_tag eq 'source') &&
$feat->has_tag('db_xref') && (! $species->ncbi_taxid() ||
($species->ncbi_taxid && $species->ncbi_taxid =~ /^list/))) {
foreach my $tagval ($feat->get_tag_values('db_xref')) {
if(index($tagval,"taxon:") == 0) {
$species->ncbi_taxid(substr($tagval,6));
last;
}
}
}
# add feature to list of features
push(@features, $feat);
}
$builder->add_slot_value(-features => \@features);
$_ = $buffer;
}
if( defined ($_) ) {
if( /^CONTIG/o ) {
my @contig;
my $ctg = '';
while($_ !~ m{^//}) { # end of file
$_ =~ /^(?:CONTIG)?\s+(.*)/;
$ctg .= $1;
$_ = $self->_readline;
}
if ($ctg) {
$annotation->add_Annotation(
Bio::Annotation::SimpleValue->new(-tagname => 'contig',
-value => $ctg )
);
}
$self->_pushback($_);
} elsif( /^WGS|WGS_SCAFLD\s+/o ) { # catch WGS/WGS_SCAFLD lines
while($_ =~ s/(^WGS|WGS_SCAFLD)\s+//){ # gulp lines
chomp;
$annotation->add_Annotation(
Bio::Annotation::SimpleValue->new(-value => $_,
-tagname => lc($1)));
$_ = $self->_readline;
}
} elsif(! m{^(ORIGIN|//)} ) { # advance to the sequence, if any
while (defined( $_ = $self->_readline) ) {
last if m{^(ORIGIN|//)};
}
}
}
if(! $builder->want_object()) {
$builder->make_object(); # implicit end-of-object
next RECORDSTART;
}
if($builder->want_slot('seq')) {
# the fact that we want a sequence does not necessarily mean that
# there also is a sequence ...
if(defined($_) && s/^ORIGIN\s+//) {
chomp;
if( $annotation && length($_) > 0 ) {
$annotation->add_Annotation('origin',
Bio::Annotation::SimpleValue->new(-tagname => 'origin',
-value => $_));
}
my $seqc = '';
while( defined($_ = $self->_readline) ) {
m{^//} && last;
$_ = uc($_);
s/[^A-Za-z]//g;
$seqc .= $_;
}
#$self->debug("sequence length is ". length($seqc) ."\n");
$builder->add_slot_value(-seq => $seqc);
}
} elsif ( defined($_) && (substr($_,0,2) ne '//')) {
# advance to the end of the record
while( defined($_ = $self->_readline) ) {
last if substr($_,0,2) eq '//';
}
}
# Unlikely, but maybe the sequence is so weird that we don't want it
# anymore. We don't want to return undef if the stream's not exhausted
# yet.
$seq = $builder->make_object();
next RECORDSTART unless $seq;
last RECORDSTART;
} # end while RECORDSTART
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;
if( ! ref $seq || ! $seq->isa('Bio::SeqI') ) {
$self->warn(" $seq is not a SeqI compliant module. Attempting to dump, but may fail!");
}
my $str = $seq->seq;
my ($div, $mol);
my $len = $seq->length();
if ( $seq->can('division') ) {
$div = $seq->division;
}
if( !defined $div || ! $div ) { $div = 'UNK'; }
my $alpha = $seq->alphabet;
if( !$seq->can('molecule') || ! defined ($mol = $seq->molecule()) ) {
$mol = $alpha || 'DNA';
}
my $circular = 'linear ';
$circular = 'circular' if $seq->is_circular;
local($^W) = 0; # supressing warnings about uninitialized fields.
my $temp_line;
if( $self->_id_generation_func ) {
$temp_line = &{$self->_id_generation_func}($seq);
} else {
my $date = '';
if( $seq->can('get_dates') ) {
($date) = $seq->get_dates();
}
$self->warn("No whitespace allowed in GenBank display id [". $seq->display_id. "]")
if $seq->display_id =~ /\s/;
$temp_line = sprintf ("%-12s%-15s%13s %s%4s%-8s%-8s %3s %-s\n",
'LOCUS', $seq->id(),$len,
(lc($alpha) eq 'protein') ? ('aa','', '') :
('bp', '',$mol),$circular,$div,$date);
}
$self->_print($temp_line);
$self->_write_line_GenBank_regex("DEFINITION ", " ",
$seq->desc(),"\\s\+\|\$",80);
# if there, write the accession line
if( $self->_ac_generation_func ) {
$temp_line = &{$self->_ac_generation_func}($seq);
$self->_print("ACCESSION $temp_line\n");
} else {
my @acc = ();
push(@acc, $seq->accession_number());
if( $seq->isa('Bio::Seq::RichSeqI') ) {
push(@acc, $seq->get_secondary_accessions());
}
$self->_print("ACCESSION ", join(" ", @acc), "\n");
# otherwise - cannot print <sigh>
}
# if PID defined, print it
if($seq->isa('Bio::Seq::RichSeqI') && $seq->pid()) {
$self->_print("PID ", $seq->pid(), "\n");
}
# if there, write the version line
if( defined $self->_sv_generation_func() ) {
$temp_line = &{$self->_sv_generation_func}($seq);
if( $temp_line ) {
$self->_print("VERSION $temp_line\n");
}
} else {
if($seq->isa('Bio::Seq::RichSeqI') && defined($seq->seq_version)) {
my $id = $seq->primary_id(); # this may be a GI number
$self->_print("VERSION ",
$seq->accession_number(), ".", $seq->seq_version,
($id && ($id =~ /^\d+$/) ? " GI:".$id : ""),
"\n");
}
}
# if there, write the PROJECT line
for my $proj ( $seq->annotation->get_Annotations('project') ) {
$self->_print("PROJECT ".$proj->value."\n");
}
# if there, write the DBSOURCE line
foreach my $ref ( $seq->annotation->get_Annotations('dblink') ) {
my ($db, $id) = ($ref->database, $ref->primary_id);
my $prefix = $db eq 'Project' ? 'DBLINK' : 'DBSOURCE';
my $text = $db eq 'GenBank' ? '' :
$db eq 'Project' ? "$db:$id" : "$db accession $id";
$self->_print(sprintf ("%-11s %s\n",$prefix, $text));
}
# if there, write the keywords line
if( defined $self->_kw_generation_func() ) {
$temp_line = &{$self->_kw_generation_func}($seq);
$self->_print("KEYWORDS $temp_line\n");
} else {
if( $seq->can('keywords') ) {
my $kw = $seq->keywords;
$kw .= '.' if( $kw !~ /\.$/ );
$self->_print("KEYWORDS $kw\n");
}
}
# SEGMENT if it exists
foreach my $ref ( $seq->annotation->get_Annotations('segment') ) {
$self->_print(sprintf ("%-11s %s\n",'SEGMENT',
$ref->value));
}
# Organism lines
if (my $spec = $seq->species) {
my ($on, $sn, $cn) = ($spec->can('organelle') ? $spec->organelle : '',
$spec->scientific_name,
$spec->common_name);
my @classification;
if ($spec->isa('Bio::Species')) {
@classification = $spec->classification;
shift(@classification);
} else {
# Bio::Taxon should have a DB handle of some type attached, so
# derive the classification from that
my $node = $spec;
while ($node) {
$node = $node->ancestor || last;
unshift(@classification, $node->node_name);
#$node eq $root && last;
}
@classification = reverse @classification;
}
my $abname = $spec->name('abbreviated') ? # from genbank file
$spec->name('abbreviated')->[0] : $sn;
my $sl = $on ? "$on " : '';
$sl .= $cn ? $abname." ($cn)" : "$abname";
$self->_write_line_GenBank_regex("SOURCE ", ' 'x12, $sl, "\\s\+\|\$",80);
$self->_print(" ORGANISM ", $spec->scientific_name, "\n");
my $OC = join('; ', (reverse(@classification))) .'.';
$self->_write_line_GenBank_regex(' 'x12,' 'x12,
$OC,"\\s\+\|\$",80);
}
# Reference lines
my $count = 1;
foreach my $ref ( $seq->annotation->get_Annotations('reference') ) {
$temp_line = "REFERENCE $count";
if ($ref->start) {
$temp_line .= sprintf (" (%s %d to %d)",
($seq->alphabet() eq "protein" ?
"residues" : "bases"),
$ref->start,$ref->end);
} elsif ($ref->gb_reference) {
$temp_line .= sprintf (" (%s)", $ref->gb_reference);
}
$self->_print("$temp_line\n");
$self->_write_line_GenBank_regex(" AUTHORS ",' 'x12,
$ref->authors,"\\s\+\|\$",80);
$self->_write_line_GenBank_regex(" CONSRTM ",' 'x12,
$ref->consortium,"\\s\+\|\$",80) if $ref->consortium;
$self->_write_line_GenBank_regex(" TITLE "," "x12,
$ref->title,"\\s\+\|\$",80);
$self->_write_line_GenBank_regex(" JOURNAL "," "x12,
$ref->location,"\\s\+\|\$",80);
if( $ref->medline) {
$self->_write_line_GenBank_regex(" MEDLINE "," "x12,
$ref->medline, "\\s\+\|\$",80);
# I am assuming that pubmed entries only exist when there
# are also MEDLINE entries due to the indentation
}
# This could be a wrong assumption
if( $ref->pubmed ) {
$self->_write_line_GenBank_regex(" PUBMED "," "x12,
$ref->pubmed, "\\s\+\|\$",
80);
}
# put remark at the end
if ($ref->comment) {
$self->_write_line_GenBank_regex(" REMARK "," "x12,
$ref->comment,"\\s\+\|\$",80);
}
$count++;
}
# Comment lines
foreach my $comment ( $seq->annotation->get_Annotations('comment') ) {
$self->_write_line_GenBank_regex("COMMENT "," "x12,
$comment->text,"\\s\+\|\$",80);
}
$self->_print("FEATURES Location/Qualifiers\n");
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 ( $seq->top_SeqFeatures ) {
push(@fth,Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq));
}
@fth = sort { &$post_sort_func($a,$b) } @fth;
foreach my $fth ( @fth ) {
$self->_print_GenBank_FTHelper($fth);
}
} else {
# not post sorted. And so we can print as we get them.
# lower memory load...
foreach my $sf ( $seq->top_SeqFeatures ) {
my @fth = Bio::SeqIO::FTHelper::from_SeqFeature($sf,$seq);
foreach my $fth ( @fth ) {
if( ! $fth->isa('Bio::SeqIO::FTHelper') ) {
$sf->throw("Cannot process FTHelper... $fth");
}
$self->_print_GenBank_FTHelper($fth);
}
}
}
# deal with WGS; WGS_SCAFLD present only if WGS is also present
if($seq->annotation->get_Annotations('wgs')) {
foreach my $wgs
(map {$seq->annotation->get_Annotations($_)} qw(wgs wgs_scaffold)) {
$self->_print(sprintf ("%-11s %s\n",uc($wgs->tagname),
$wgs->value));
}
$self->_show_dna(0);
}
if($seq->annotation->get_Annotations('contig')) {
my $ct = 0;
my $cline;
foreach my $contig ($seq->annotation->get_Annotations('contig')) {
unless ($ct) {
$cline = uc($contig->tagname)." ".$contig->value."\n";
} else {
$cline = " ".$contig->value."\n";
}
$self->_print($cline);
$ct++;
}
$self->_show_dna(0);
}
if( $seq->length == 0 ) { $self->_show_dna(0) }
if( $self->_show_dna() == 0 ) {
$self->_print("\n//\n");
return;
}
# finished printing features.
$str =~ tr/A-Z/a-z/;
my ($o) = $seq->annotation->get_Annotations('origin');
$self->_print(sprintf("%-12s%s\n",
'ORIGIN', $o ? $o->value : ''));
# print out the sequence
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);
chop $blocks;
$self->_print(sprintf("%9d $blocks\n", $i + $nuc - 59));
}
# 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);
$blocks =~ s/ +$//;
$self->_print(sprintf("%9d $blocks\n",
$length - $last_len + 1));
}
$self->_print("//\n");
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
}
=head2 _print_GenBank_FTHelper
Title : _print_GenBank_FTHelper
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _print_GenBank_FTHelper {
my ($self,$fth) = @_;
if( ! ref $fth || ! $fth->isa('Bio::SeqIO::FTHelper') ) {
$fth->warn("$fth is not a FTHelper class. Attempting to print, but there could be tears!");
}
my $spacer = (length $fth->key >= 15) ? ' ' : '';
$self->_write_line_GenBank_regex(sprintf(" %-16s%s",$fth->key,$spacer),
" "x21,
$fth->loc,"\,\|\$",80);
foreach my $tag ( keys %{$fth->field} ) {
foreach my $value ( @{$fth->field->{$tag}} ) {
$value =~ s/\"/\"\"/g;
if ($value eq "_no_value") {
$self->_write_line_GenBank_regex(" "x21,
" "x21,
"/$tag","\.\|\$",80);
}
# there are almost 3x more quoted qualifier values and they
# are more common too so we take quoted ones first
#
# Long qualifiers, that will be line wrapped, are always quoted
elsif (!$FTQUAL_NO_QUOTE{$tag} or length("/$tag=$value") >= $FTQUAL_LINE_LENGTH) {
my ($pat) = ($value =~ /\s/ ? '\s|$' : '.|$');
$self->_write_line_GenBank_regex(" "x21,
" "x21,
"/$tag=\"$value\"",$pat,80);
} else {
$self->_write_line_GenBank_regex(" "x21,
" "x21,
"/$tag=$value","\.\|\$",80);
}
}
}
}
=head2 _read_GenBank_References
Title : _read_GenBank_References
Usage :
Function: Reads references from GenBank format. Internal function really
Returns :
Args :
=cut
sub _read_GenBank_References {
my ($self,$buffer) = @_;
my (@refs);
my $ref;
# assumme things are starting with RN
if( $$buffer !~ /^REFERENCE/ ) {
warn("Not parsing line '$$buffer' which maybe important");
}
$_ = $$buffer;
my (@title,@loc,@authors,@consort,@com,@medline,@pubmed);
REFLOOP: while( defined($_) || defined($_ = $self->_readline) ) {
if (/^\s{2}AUTHORS\s+(.*)/o) {
push (@authors, $1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/o && do { push (@authors, $1);next;};
last;
}
$ref->authors(join(' ', @authors));
}
if (/^\s{2}CONSRTM\s+(.*)/o) {
push (@consort, $1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/o && do { push (@consort, $1);next;};
last;
}
$ref->consortium(join(' ', @consort));
}
if (/^\s{2}TITLE\s+(.*)/o) {
push (@title, $1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/o && do { push (@title, $1);
next;
};
last;
}
$ref->title(join(' ', @title));
}
if (/^\s{2}JOURNAL\s+(.*)/o) {
push(@loc, $1);
while ( defined($_ = $self->_readline) ) {
# we only match when there are at least 4 spaces
# there is probably a better way to match this
# as it assumes that the describing tag is short enough
/^\s{9,}(.*)/o && do { push(@loc, $1);
next;
};
last;
}
$ref->location(join(' ', @loc));
redo REFLOOP;
}
if (/^\s{2}REMARK\s+(.*)/o) {
push (@com, $1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/o && do { push(@com, $1);
next;
};
last;
}
$ref->comment(join(' ', @com));
redo REFLOOP;
}
if( /^\s{2}MEDLINE\s+(.*)/ ) {
push(@medline,$1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/ && do { push(@medline, $1);
next;
};
last;
}
$ref->medline(join(' ', @medline));
redo REFLOOP;
}
if( /^\s{3}PUBMED\s+(.*)/ ) {
push(@pubmed,$1);
while ( defined($_ = $self->_readline) ) {
/^\s{9,}(.*)/ && do { push(@pubmed, $1);
next;
};
last;
}
$ref->pubmed(join(' ', @pubmed));
redo REFLOOP;
}
/^REFERENCE/o && do {
# store current reference
$self->_add_ref_to_array(\@refs,$ref) if defined $ref;
# reset
@authors = ();
@title = ();
@loc = ();
@com = ();
@pubmed = ();
@medline = ();
# create the new reference object
$ref = Bio::Annotation::Reference->new(-tagname => 'reference');
# check whether start and end base is given
if (/^REFERENCE\s+\d+\s+\([a-z]+ (\d+) to (\d+)\)/){
$ref->start($1);
$ref->end($2);
} elsif (/^REFERENCE\s+\d+\s+\((.*)\)/) {
$ref->gb_reference($1);
}
};
/^(FEATURES)|(COMMENT)/o && last;
$_ = undef; # Empty $_ to trigger read of next line
}
# store last reference
$self->_add_ref_to_array(\@refs,$ref) if defined $ref;
$$buffer = $_;
#print "\nnumber of references found: ", $#refs+1,"\n";
return @refs;
}
#
# This is undocumented as it shouldn't be called by anywhere else as
# read_GenBank_References. For those who still want to know:
#
# Purpose: adds a Reference object to an array of Reference objects, takes
# care of possible cleanups to be done (currently, only author and title
# will be chopped of trailing semicolons).
# Parameters:
# a reference to an array of Reference objects
# the Reference object to be added
# Returns: nothing
#
sub _add_ref_to_array {
my ($self, $refs, $ref) = @_;
# first, polish author and title by removing possible trailing semicolons
my $au = $ref->authors();
my $title = $ref->title();
$au =~ s/;\s*$//g if $au;
$title =~ s/;\s*$//g if $title;
$ref->authors($au);
$ref->title($title);
# the rest should be clean already, so go ahead and add it
push(@{$refs}, $ref);
}
=head2 _read_GenBank_Species
Title : _read_GenBank_Species
Usage :
Function: Reads the GenBank Organism species and classification
lines. Able to deal with unconvential Organism naming
formats, and varietas in plants
Example : ORGANISM unknown marine gamma proteobacterium NOR5
$genus = undef
$species = unknown marine gamma proteobacterium NOR5
ORGANISM Drosophila sp. 'white tip scutellum'
$genus = Drosophila
$species = sp. 'white tip scutellum'
(yes, this really is a species and that is its name)
$subspecies = undef
ORGANISM Ajellomyces capsulatus var. farciminosus
$genus = Ajellomyces
$species = capsulatus
$subspecies = var. farciminosus
ORGANISM Hepatitis delta virus
$genus = undef (though this virus has a genus in its lineage, we
cannot know that without a database lookup)
$species = Hepatitis delta virus
Returns : A Bio::Species object
Args : A reference to the current line buffer
=cut
sub _read_GenBank_Species {
my ($self, $buffer) = @_;
my @unkn_names = ('other', 'unknown organism', 'not specified', 'not shown',
'Unspecified', 'Unknown', 'None', 'unclassified',
'unidentified organism', 'not supplied');
# dictionary of synonyms for taxid 32644
my @unkn_genus = ('unknown','unclassified','uncultured','unidentified');
# all above can be part of valid species name
my $line = $$buffer;
my( $sub_species, $species, $genus, $sci_name, $common, $class_lines,
$source_flag, $abbr_name, $organelle, $sl );
my %source = map { $_ => 1 } qw(SOURCE ORGANISM CLASSIFICATION);
# upon first entering the loop, we must not read a new line -- the SOURCE
# line is already in the buffer (HL 05/10/2000)
my ($ann, $tag, $data);
while (defined($line) || defined($line = $self->_readline())) {
# de-HTMLify (links that may be encountered here don't contain
# escaped '>', so a simple-minded approach suffices)
$line =~ s{<[^>]+>}{}g;
if ($line =~ m{^(?:\s{0,2})(\w+)\s+(.+)?$}ox) {
($tag, $data) = ($1, $2 || '');
last if ($tag && !exists $source{$tag});
} else {
return unless $tag;
($data = $line) =~ s{^\s+}{};
chomp $data;
$tag = 'CLASSIFICATION' if ($tag ne 'CLASSIFICATION' && $tag eq 'ORGANISM' && $line =~ m{[;\.]+});
}
(exists $ann->{$tag}) ? ($ann->{$tag} .= ' '.$data) : ($ann->{$tag} .= $data);
$line = undef;
}
($sl, $class_lines, $sci_name) = ($ann->{SOURCE}, $ann->{CLASSIFICATION}, $ann->{ORGANISM});
$$buffer = $line;
$sci_name || return;
# parse out organelle, common name, abbreviated name if present;
# this should catch everything, but falls back to
# entire SOURCE line just in case
if ($sl =~ m{^
(mitochondrion|chloroplast|plastid)?
\s*(.*?)
\s*(?: \( (.*?) \) )?\.?
$
}xms ){
($organelle, $abbr_name, $common) = ($1, $2, $3); # optional
} else {
$abbr_name = $sl; # nothing caught; this is a backup!
}
# Convert data in classification lines into classification array.
# only split on ';' or '.' so that classification that is 2 or more words will
# still get matched, use map() to remove trailing/leading/intervening spaces
my @class = map { s/^\s+//; s/\s+$//; s/\s{2,}/ /g; $_; } split /(?<!subgen)[;\.]+/, $class_lines;
# do we have a genus?
my $possible_genus = quotemeta($class[-1])
. ($class[-2] ? "|" . quotemeta($class[-2]) : '');
if ($sci_name =~ /^($possible_genus)/) {
$genus = $1;
($species) = $sci_name =~ /^$genus\s+(.+)/;
}
else {
$species = $sci_name;
}
# is this organism of rank species or is it lower?
# (we don't catch everything lower than species, but it doesn't matter -
# this is just so we abide by previous behaviour whilst not calling a
# species a subspecies)
if ($species && $species =~ /(.+)\s+((?:subsp\.|var\.).+)/) {
($species, $sub_species) = ($1, $2);
}
# Don't make a species object if it's empty or "Unknown" or "None"
# return unless $genus and $genus !~ /^(Unknown|None)$/oi;
# Don't make a species object if it belongs to taxid 32644
# my $unkn = grep { $_ =~ /^\Q$sl\E$/; } @unkn_names;
my $unkn = grep { $_ eq $sl } @unkn_names;
return unless ($species || $genus) and $unkn == 0;
# Bio::Species array needs array in Species -> Kingdom direction
push(@class, $sci_name);
@class = reverse @class;
my $make = Bio::Species->new();
$make->scientific_name($sci_name);
$make->classification(@class) if @class > 0;
$make->common_name( $common ) if $common;
$make->name('abbreviated', $abbr_name) if $abbr_name;
$make->organelle($organelle) if $organelle;
#$make->sub_species( $sub_species ) if $sub_species;
return $make;
}
=head2 _read_FTHelper_GenBank
Title : _read_FTHelper_GenBank
Usage : _read_FTHelper_GenBank($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_GenBank {
my ($self,$buffer) = @_;
my ($key, # The key of the feature
$loc # The location line from the feature
);
my @qual = (); # An array of lines making up the qualifiers
if ($$buffer =~ /^\s{5}(\S+)\s+(.+?)\s*$/o) {
$key = $1;
$loc = $2;
# Read all the lines up to the next feature
while ( defined($_ = $self->_readline) ) {
if (/^(\s+)(.+?)\s*$/o) {
# Lines inside features are preceded by 21 spaces
# A new feature is preceded by 5 spaces
if (length($1) > 6) {
# Add to qualifiers if we're in the qualifiers, or if it's
# the first qualifier
if (@qual || (index($2,'/') == 0)) {
push(@qual, $2);
}
# We're still in the location line, so append to location
else {
$loc .= $2;
}
} else {
# We've reached the start of the next feature
last;
}
} else {
# We're at the end of the feature table
last;
}
}
} else {
# No feature key
$self->debug("no feature key!\n");
# change suggested by JDiggans to avoid infinite loop-
# see bugreport 1062.
# reset buffer to prevent infinite loop
$$buffer = $self->_readline();
return;
}
# Put the first line of the next feature into the buffer
$$buffer = $_;
# Make the new FTHelper object
my $out = Bio::SeqIO::FTHelper->new();
$out->verbose($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->warn("cannot see new qualifier in feature $key: ".
$qual[$i]);
$qualifier = '' unless( defined $qualifier);
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 $value =~ tr/"/"/ % 2) {
if($i >= $#qual) {
$self->warn("Unbalanced quote in:\n" .
join("\n", @qual) .
"No further qualifiers will " .
"be added for this feature");
last QUAL;
}
$i++; # modifying a for-loop variable inside of the loop
# is not the best programming style ...
my $next = $qual[$i];
# add to value with a space unless the value appears
# to be a sequence (translation for example)
# if(($value.$next) =~ /[^A-Za-z\"\-]/o) {
# changed to explicitly look for translation tag - cjf 06/8/29
if ($qualifier !~ /^translation$/i ) {
$value .= " ";
}
$value .= $next;
}
# Trim leading and trailing quotes
$value =~ s/^"|"$//g;
# Undouble internal quotes
$value =~ s/""/\"/g;
} elsif ( $value =~ /^\(/ ) { # values quoted by ()s
# Keep adding to value until we find the trailing bracket
# and the ()s are balanced
my $left = ($value =~ tr/\(/\(/); # count left parens
my $right = ($value =~ tr/\)/\)/); # count right parens
while( $left != $right ) { # was "$value !~ /\)$/ or $left != $right"
if( $i >= $#qual) {
$self->warn("Unbalanced parens in:\n".
join("\n", @qual).
"\nNo further qualifiers will ".
"be added for this feature");
last QUAL;
}
$i++;
my $next = $qual[$i];
$value .= $next;
$left += ($next =~ tr/\(/\(/);
$right += ($next =~ tr/\)/\)/);
}
}
} else {
$value = '_no_value';
}
# Store the qualifier
$out->field->{$qualifier} ||= [];
push(@{$out->field->{$qualifier}},$value);
}
return $out;
}
=head2 _write_line_GenBank
Title : _write_line_GenBank
Usage :
Function: internal function
Example :
Returns :
Args :
=cut
sub _write_line_GenBank {
my ($self,$pre1,$pre2,$line,$length) = @_;
$length || $self->throw("Miscalled write_line_GenBank without length. Programming error!");
my $subl = $length - length $pre2;
my $linel = length $line;
my $i;
my $subr = substr($line,0,$length - length $pre1);
$self->_print("$pre1$subr\n");
for($i= ($length - length $pre1);$i < $linel; $i += $subl) {
$subr = substr($line,$i,$subl);
$self->_print("$pre2$subr\n");
}
}
=head2 _write_line_GenBank_regex
Title : _write_line_GenBank_regex
Usage :
Function: internal function for writing lines of specified
length, with different first and the next line
left hand headers and split at specific points in the
text
Example :
Returns : nothing
Args : file handle,
first header,
second header,
text-line,
regex for line breaks,
total line length
=cut
sub _write_line_GenBank_regex {
my ($self,$pre1,$pre2,$line,$regex,$length) = @_;
#print STDOUT "Going to print with $line!\n";
$length || $self->throw( "Miscalled write_line_GenBank without length. Programming error!");
my $subl = $length - (length $pre1) - 2;
my @lines = ();
CHUNK: while($line) {
foreach my $pat ($regex, '[,;\.\/-]\s|'.$regex, '[,;\.\/-]|'.$regex) {
if($line =~ m/^(.{0,$subl})($pat)(.*)/ ) {
my $l = $1.$2;
$line = substr($line,length($l));
# be strict about not padding spaces according to
# genbank format
$l =~ s/\s+$//;
next CHUNK if ($l eq '');
push(@lines, $l);
next CHUNK;
}
}
# if we get here none of the patterns matched $subl or less chars
$self->warn("trouble dissecting \"$line\"\n into chunks ".
"of $subl chars or less - this tag won't print right");
# insert a space char to prevent infinite loops
$line = substr($line,0,$subl) . " " . substr($line,$subl);
}
my $s = shift @lines;
$self->_print("$pre1$s\n") if $s;
foreach my $s ( @lines ) {
$self->_print("$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 ($obj,$value) = @_;
if( defined $value) {
$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 ($obj,$value) = @_;
if( defined $value) {
$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 ($obj,$value) = @_;
if( defined $value ) {
$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 ($obj,$value) = @_;
if( defined $value ) {
$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 ($obj,$value) = @_;
if( defined $value ) {
$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 ($obj,$value) = @_;
if( defined $value ) {
$obj->{'_kw_generation_func'} = $value;
}
return $obj->{'_kw_generation_func'};
}
1;