#!/usr/bin/perl -w =pod =head1 NAME genbank2owl.pl -- converts GenBank files to OWL =head1 SYNOPSIS genbank2owl.pl [options] filename(s) # process a directory containing GenBank flatfiles genbank2owl.pl --dir path_to_files --zip # process a single file, ignore explicit exons and introns perl genbank2owl.pl --filter exon --filter intron file.gbk.gz # process a list of files perl genbank2owl.pl *gbk.gz # process data from URL, with Chado GFF model (-noCDS), and pipe to database loader curl ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_X/NC_001142.gbk \ | perl genbank2owl.pl -noCDS -in stdin -out stdout \ | perl gmod_bulk_load_gff3.pl -dbname mychado -organism fromdata Options: --enumerate-junctions -j materialize individuals for all interbase junctions --dir -d path to a list of genbank flatfiles --outdir -o location to write GFF files (can be 'stdout' or '-' for pipe) --zip -z compress GFF3 output files with gzip --summary -s print a summary of the features in each contig --filter -x genbank feature type(s) to ignore --split -y split output to seperate GFF and fasta files for each genbank record --nolump -n seperate file for each reference sequence (default is to lump all records together into one output file for each input file) --ethresh -e error threshold for unflattener set this high (>2) to ignore all unflattener errors --[no]CDS -c Keep CDS-exons, or convert to alternate gene-RNA-protein-exon model. --CDS is default. Use --CDS to keep default GFF gene model, use --noCDS to convert to g-r-p-e. --format -f Input format (SeqIO types): GenBank, Swiss or Uniprot, EMBL work (GenBank is default) --GFF_VERSION 3 is default, 2 and 2.5 and other Bio::Tools::GFF versions available --quiet dont talk about what is being processed --typesource SO sequence type for source (e.g. chromosome; region; contig) --help -h display this message =head1 DESCRIPTION This script uses Bio::SeqFeature::Tools::Unflattener and Bio::Tools::GFF to convert GenBank flatfiles to GFF3 with gene containment hierarchies mapped for optimal display in gbrowse. The input files are assumed to be gzipped GenBank flatfiles for refseq contigs. The files may contain multiple GenBank records. Either a single file or an entire directory can be processed. By default, the DNA sequence is embedded in the GFF but it can be saved into seperate fasta file with the --split(-y) option. If an input file contains multiple records, the default behaviour is to dump all GFF and sequence to a file of the same name (with .gff appended). Using the 'nolump' option will create a seperate file for each genbank record. Using the 'split' option will create seperate GFF and Fasta files for each genbank record. =head2 Notes =head3 'split' and 'nolump' produce many files In cases where the input files contain many GenBank records (for example, the chromosome files for the mouse genome build), a very large number of output files will be produced if the 'split' or 'nolump' options are selected. If you do have lists of files E 6000, use the --long_list option in bp_bulk_load_gff.pl or bp_fast_load_gff.pl to load the gff and/ or fasta files. =head3 Designed for RefSeq This script is designed for RefSeq genomic sequence entries. It may work for third party annotations but this has not been tested. But see below, Uniprot/Swissprot works, EMBL and possibly EMBL/Ensembl if you don't mind some gene model unflattener errors (dgg). =head3 G-R-P-E Gene Model Don Gilbert worked this over with needs to produce GFF3 suited to loading to GMOD Chado databases. Most of the changes I believe are suited for general use. One main chado-specific addition is the --[no]cds2protein flag My favorite GFF is to set the above as ON by default (disable with --nocds2prot) For general use it probably should be OFF, enabled with --cds2prot. This writes GFF with an alternate, but useful Gene model, instead of the consensus model for GFF3 [ gene > mRNA> (exon,CDS,UTR) ] This alternate is gene > mRNA > polypeptide > exon means the only feature with dna bases is the exon. The others specify only location ranges on a genome. Exon of course is a child of mRNA and protein/peptide. The protein/polypeptide feature is an important one, having all the annotations of the GenBank CDS feature, protein ID, translation, GO terms, Dbxrefs to other proteins. UTRs, introns, CDS-exons are all inferred from the primary exon bases inside/outside appropriate higher feature ranges. Other special gene model features remain the same. Several other improvements and bugfixes, minor but useful are included * IO pipes now work: curl ftp://ncbigenomes/... | genbank2owl --in stdin --out stdout | gff2chado ... * GenBank main record fields are added to source feature, e.g. organism, date, and the sourcetype, commonly chromosome for genomes, is used. * Gene Model handling for ncRNA, pseudogenes are added. * GFF header is cleaner, more informative. --GFF_VERSION flag allows choice of v2 as well as default v3 * GFF ##FASTA inclusion is improved, and CDS translation sequence is moved to FASTA records. * FT -> GFF attribute mapping is improved. * --format choice of SeqIO input formats (GenBank default). Uniprot/Swissprot and EMBL work and produce useful GFF. * SeqFeature::Tools::TypeMapper has a few FT -> SOFA additions and more flexible usage. =head1 TODO =head2 Are these additions desired? * filter input records by taxon (e.g. keep only organism=xxx or taxa level = classYYY * handle Entrezgene, other non-sequence SeqIO structures (really should change those parsers to produce consistent annotation tags). =head2 Related bugfixes/tests These items from Bioperl mail were tested (sample data generating errors), and found corrected: From: Ed Green eva.mpg.de> Subject: genbank2owl.pl on new human RefSeq Date: 2006-03-13 21:22:26 GMT -- unspecified errors (sample data works now). From: Eric Just northwestern.edu> Subject: bp_genbank2owl.pl Date: 2007-01-26 17:08:49 GMT -- bug fixed in genbank2owl for multi-record handling This error is for a /trans_splice gene that is hard to handle, and unflattner/genbank2 doesn't From: Chad Matsalla dieselwurks.com> Subject: genbank2owl.PLS and the unflatenner - Inconsistent order? Date: 2005-07-15 19:51:48 GMT =head1 AUTHOR Sheldon McKay (mckays@cshl.edu) Copyright (c) 2004 Cold Spring Harbor Laboratory. =head2 AUTHOR of hacks for GFF2Chado loading Don Gilbert (gilbertd@indiana.edu) =cut use strict; use lib "$ENV{HOME}/bioperl-live"; # chad put this here to enable situations when this script is tested # against bioperl compiled into blib along with other programs using blib BEGIN { unshift(@INC,'blib/lib'); }; use Pod::Usage; use Bio::Root::RootI; use Bio::SeqIO; use File::Spec; use Bio::SeqFeature::Tools::Unflattener; use Bio::SeqFeature::Tools::TypeMapper; use Bio::SeqFeature::Tools::IDHandler; use Bio::Location::SplitLocationI; use Bio::Location::Simple; use Bio::Tools::GFF; use Getopt::Long; use vars qw/$split @filter $zip $outdir $help $ethresh $file @files $dir $summary $nolump $source_type %proteinfa %exonpar $didheader $verbose $DEBUG $GFF_VERSION $gene_id $rna_id $tnum $ncrna_id $rnum %method %id %seen/; use constant GM_NEW_TOPLEVEL => 2; use constant GM_NEW_PART => 1; use constant GM_DUP_PART => 0; use constant GM_NOT_PART => -1; $GFF_VERSION = 3; # allow v2 ... $verbose = 1; # right default? -nov to turn off # dgg: change the gene model to Gene/mRNA/Polypeptide/exons... my $CDSkeep= 1; # default should be ON (prior behavior), see gene_features() my $PROTEIN_TYPE = 'polypeptide'; # for noCDSkeep; # protein = flybase chado usage; GMOD Perls use 'polypeptide' with software support my $FORMAT="GenBank"; # swiss ; embl; genbank ; ** guess from SOURCEID ** my $SOURCEID= $FORMAT; # "UniProt" "GenBank" "EMBL" should work # other Bio::SeqIO formats may work. TEST: EntrezGene < problematic tags; InterPro KEGG my %TAG_MAP = ( db_xref => 'Dbxref', name => 'Name', note => 'Note', # also pull GO: ids into Ontology_term synonym => 'Alias', symbol => 'Alias', # is symbol still used? # protein_id => 'Dbxref', also seen Dbxref tags: EC_number # translation: handled in gene_features ); $| = 1; my $quiet= !$verbose; my $ok= GetOptions( 'd|dir|input:s' => \$dir, 'z|zip' => \$zip, 'h|help' => \$help, 's|summary' => \$summary, 'o|outdir|output:s'=> \$outdir, 'x|filter:s'=> \@filter, 'y|split' => \$split, "ethresh|e=s"=>\$ethresh, 'c|CDS!' => \$CDSkeep, 'f|format=s' => \$FORMAT, 'typesource=s' => \$source_type, 'GFF_VERSION=s' => \$GFF_VERSION, 'quiet!' => \$quiet, # swap quiet to verbose 'DEBUG!' => \$DEBUG, 'n|nolump' => \$nolump); my $lump = 1 unless $nolump || $split; $verbose= !$quiet; # look for help request pod2usage(2) if $help || !$ok; # keep SOURCEID as-is and change FORMAT for SeqIO types; # note SeqIO uses file.suffix to guess type; not useful here $SOURCEID= $FORMAT; $FORMAT = "swiss" if $FORMAT =~/UniProt|trembl/; $verbose =1 if($DEBUG); # initialize handlers my $unflattener = Bio::SeqFeature::Tools::Unflattener->new; # for ensembl genomes (-trust_grouptag=>1); $unflattener->error_threshold($ethresh) if $ethresh; $unflattener->verbose(1) if($DEBUG); # $unflattener->group_tag('gene') if($FORMAT =~ /embl/i) ; #? ensembl only? # ensembl parsing is still problematic, forget this my $tm = Bio::SeqFeature::Tools::TypeMapper->new; my $idh = Bio::SeqFeature::Tools::IDHandler->new; # dgg $source_type ||= "region"; # should really parse from FT.source contents below my $FTSOmap = $tm->FT_SO_map(); # #convert $FTSOmap undefined to valid SO : moved to TypeMapper->map_types( -undefined => "region") # stringify filter list if applicable my $filter = join ' ', @filter if @filter; # determine input files my $stdin=0; # dgg: let dir == stdin == '-' for pipe use if ($dir && ($dir eq '-' || $dir eq 'stdin')) { $stdin=1; $dir=''; @files=('stdin'); } elsif ( $dir ) { if ( -d $dir ) { opendir DIR, $dir or die "could not open $dir for reading: $!"; @files = map { "$dir/$_";} grep { /\.gb.*/ } readdir DIR; closedir DIR; } else { die "$dir is not a directory\n"; } } else { @files = @ARGV; $dir = ''; } # we should have some files by now pod2usage(2) unless @files; my $stdout=0; # dgg: let outdir == stdout == '-' for pipe use if($outdir && ($outdir eq '-' || $outdir eq 'stdout')) { warn("std. output chosen: cannot split\n") if($split); warn("std. output chosen: cannot zip\n") if($zip); warn("std. output chosen: cannot nolump\n") if($nolump); $stdout=1; $lump=1; $split= 0; $zip= 0; # unless we pipe stdout thru gzip } elsif ( $outdir && !-e $outdir ) { mkdir($outdir) or die "could not create directory $outdir: $!\n"; } elsif ( !$outdir ) { $outdir = $dir || '.'; } $outdir .= '/' unless $outdir =~ m|/$|; for my $file ( @files ) { # dgg ; allow 'stdin' / '-' input ? chomp $file; die "$! $file" unless($stdin || -e $file); print "# Input: $file\n" if($verbose); my ($lump_fh, $lumpfa_fh, $outfile, $outfa); if ($stdout) { $lump_fh= *STDOUT; $lump="stdout$$"; $outfa= "stdout$$.fa"; # this is a temp file ... see below open $lumpfa_fh, ">$outfa" or die "Could not create a lump outfile called ($outfa) because ($!)\n"; } elsif ( $lump ) { # this is better, but still should use catfile my ($vol,$dirs,$fileonly) = File::Spec->splitpath($file); $lump = $outdir . $fileonly . '.owl'; ($outfa= $lump) =~ s/\.gff/\.fa/; open $lump_fh, ">$lump" or die "Could not create a lump outfile called ($lump) because ($!)\n"; open $lumpfa_fh, ">$outfa" or die "Could not create a lump outfile called ($outfa) because ($!)\n"; } # open input file, unzip if req'd if ($stdin) { *FH= *STDIN; } elsif ( $file =~ /\.gz/ ) { open FH, "gunzip -c $file |"; } else { open FH, "<$file"; } my $in = Bio::SeqIO->new(-fh => \*FH, -format => $FORMAT, -debug=>$DEBUG); my $gffio = Bio::Tools::GFF->new( -noparse => 1, -gff_version => $GFF_VERSION ); while ( my $seq = $in->next_seq ) { my $seq_name = $seq->accession_number; my $end = $seq->length; my @to_print; # arrange disposition of GFF output $outfile = $lump || $outdir . $seq_name . ".gff"; my $out; if ( $lump ) { $outfile = $lump; $out = $lump_fh; } else { $outfile = $outdir . $seq_name . ".gff"; open $out, ">$outfile"; } # filter out unwanted features my $source_feat= undef; my @source= filter($seq); $source_feat= $source[0]; ($source_type,$source_feat)= getSourceInfo( $seq, $source_type, $source_feat ) ; # always; here we build main prot $source_feat; # if @source; # abort if there are no features warn "$seq_name has no features, skipping\n" and next if !$seq->all_SeqFeatures; $FTSOmap->{'source'}= $source_type; ## $FTSOmap->{'CDS'}= $PROTEIN_TYPE; # handle this in gene_features # construct a GFF header # add: get source_type from attributes of source feature? chromosome=X tag # also combine 1st ft line here with source ft from $seq .. my($header,$info)= gff_header($seq_name, $end, $source_type, $source_feat); print $out $header; print "# working on $info\n" if($verbose); # unflatten gene graphs, apply SO types, etc; this also does TypeMapper .. unflatten_seq($seq); # Note that we use our own get_all_SeqFeatures function # to rescue cloned exons for my $feature ( get_all_SeqFeatures($seq) ) { my $method = $feature->primary_tag; next if($SOURCEID =~/UniProt|swiss|trembl/i && $method ne $source_type); $feature->seq_id($seq->id) unless($feature->seq_id); $feature->source_tag($SOURCEID); # dgg; need to convert some Genbank to GFF tags: note->Note; db_xref->Dbxref; ## also, pull any GO:000 ids from /note tag and put into Ontology_term maptags2gff($feature); # current gene name. The unflattened gene features should be in order so any # exons, CDSs, etc that follow will belong to this gene my $gene_name; if ( $method eq 'gene' || $method eq 'pseudogene' ) { @to_print= print_held($out, $gffio, \@to_print); $gene_id = $gene_name= gene_name($feature); } else { $gene_name= gene_name($feature); } #?? should gene_name from /locus_tag,/gene,/product,/transposon=xxx # be converted to or added as Name=xxx (if not ID= or as well) ## problematic: convert_to_name ($feature); # drops /locus_tag,/gene, tags ## dgg: extended to protein|polypeptide ## this test ($feature->has_tag('gene') ||) is not good: repeat_regions over genes ## in yeast have that genbank tag; why? ## these include pseudogene ... ## Note we also have mapped types to SO, so these RNA's are now transcripts: # pseudomRNA => "pseudogenic_transcript", # pseudotranscript" => "pseudogenic_transcript", # misc_RNA=>'processed_transcript', warn "#at: $method $gene_id/$gene_name\n" if $DEBUG; if ( $method =~ /(gene|RNA|CDS|exon|UTR|protein|polypeptide|transcript)/ || ( $gene_id && $gene_name eq $gene_id ) ) { my $action = gene_features($feature, $gene_id, $gene_name); # -1, 0, 1, 2 result if ($action == GM_DUP_PART) { # ignore, this is dupl. exon with new parent ... } elsif ($action == GM_NOT_PART) { add_generic_id( $feature, $gene_name, "nocount"); my $gff= $gffio->gff_string($feature); print $out "$gff\n" if $gff; } elsif ($action > 0) { # hold off print because exon etc. may get 2nd, 3rd parents @to_print= print_held($out, $gffio, \@to_print) if ($action == GM_NEW_TOPLEVEL); push(@to_print, $feature); } } # otherwise handle as generic feats with IDHandler labels else { add_generic_id( $feature, $gene_name, ""); my $gff= $gffio->gff_string($feature); print $out "$gff\n" if $gff; } } # dont like doing this after others; do after each new gene id? @to_print= print_held($out, $gffio, \@to_print); # deal with the corresponding DNA my ($fa_out,$fa_outfile); my $dna = $seq->seq; if($dna || %proteinfa) { $method{'RESIDUES'} += length($dna); $dna =~ s/(\S{60})/$1\n/g; $dna .= "\n"; if ($split) { $fa_outfile = $outfile; $fa_outfile =~ s/gff$/fa/; open $fa_out, ">$fa_outfile" or die $!; print $fa_out ">$seq_name\n$dna" if $dna; foreach my $aid (sort keys %proteinfa) { my $aa= delete $proteinfa{$aid}; $method{'RESIDUES(tr)'} += length($aa); $aa =~ s/(\S{60})/$1\n/g; print $fa_out ">$aid\n$aa\n"; } } else { ## problem here when multiple GB Seqs in one file; all FASTA needs to go at end of $out ## see e.g. Mouse: mm_ref_chr19.gbk has NT_082868 and NT_039687 parts in one .gbk ## maybe write this to temp .fa then cat to end of lumped gff $out print $lumpfa_fh ">$seq_name\n$dna" if $dna; foreach my $aid (sort keys %proteinfa) { my $aa= delete $proteinfa{$aid}; $method{'RESIDUES(tr)'} += length($aa); $aa =~ s/(\S{60})/$1\n/g; print $lumpfa_fh ">$aid\n$aa\n"; } } %proteinfa=(); } if ( $zip && !$lump ) { system "gzip -f $outfile"; system "gzip -f $fa_outfile" if($fa_outfile); $outfile .= '.gz'; $fa_outfile .= '.gz' if $split; } # print "\n>EOF\n" if($stdout); #?? need this if summary goes to stdout after FASTA print "# GFF3 saved to $outfile" unless( !$verbose || $stdout || $lump); print ($split ? "; DNA saved to $fa_outfile\n" : "\n") unless($stdout|| $lump); # dgg: moved to after all inputs; here it prints cumulative sum for each record # if ( $summary ) { # print "# Summary:\n# Feature\tCount\n# -------\t-----\n"; # # for ( keys %method ) { # print "# $_ $method{$_}\n"; # } # print "# \n"; # } } print "# GFF3 saved to $outfile\n" if( $verbose && $lump); if ( $summary ) { print "# Summary:\n# Feature\tCount\n# -------\t-----\n"; for ( keys %method ) { print "# $_ $method{$_}\n"; } print "# \n"; } ## FIXME for piped output w/ split FA files ... close($lumpfa_fh); if (!$split && $outfa && $lump_fh) { print $lump_fh "##FASTA\n"; # GFF3 spec open $lumpfa_fh, $outfa or warn "reading FA $outfa: $!"; while( <$lumpfa_fh>) { print $lump_fh $_; } # is $lump_fh still open? close($lumpfa_fh); unlink($outfa); } if ( $zip && $lump ) { system "gzip -f $lump"; } close FH; } sub typeorder { return 1 if ($_[0] =~ /gene/); return 2 if ($_[0] =~ /RNA|transcript/); return 3 if ($_[0] =~ /protein|peptide/); return 4 if ($_[0] =~ /exon|CDS/); return 3; # default before exon (smallest part) } sub sort_by_feattype { my($at,$bt)= ($a->primary_tag, $b->primary_tag); return (typeorder($at) <=> typeorder($bt)) or ($at cmp $bt); ## or ($a->name() cmp $b->name()); } sub print_held { my($out,$gffio,$to_print)= @_; return unless(@$to_print); @$to_print = sort sort_by_feattype @$to_print; # put exons after mRNA, otherwise chado loader chokes while ( my $feature = shift @$to_print) { my $gff= $gffio->gff_string($feature); # $gff =~ s/\'/./g; # dang bug in encode print $out "$gff\n"; } return (); # @to_print } sub maptags2gff { my $f = shift; ## should copy/move locus_tag to Alias, if not ID/Name/Alias already # but see below /gene /locus_tag usage foreach my $tag (keys %TAG_MAP) { if ($f->has_tag($tag)) { my $newtag= $TAG_MAP{$tag}; my @v= $f->get_tag_values($tag); $f->remove_tag($tag); $f->add_tag_value($newtag,@v); ## also, pull any GO:000 ids from /note tag and put into Ontology_term ## ncbi syntax in CDS /note is now '[goid GO:0005886]' OR '[goid 0005624]' if ($tag eq 'note') { map { s/\[goid (\d+)/\[goid GO:$1/g; } @v; my @go= map { m/(GO:\d+)/g } @v; $f->add_tag_value('Ontology_term',@go) if(@go); } } } } sub getSourceInfo { my ($seq, $source_type, $sf) = @_; my $is_swiss= ($SOURCEID =~/UniProt|swiss|trembl/i); my $is_gene = ($SOURCEID =~/entrezgene/i); my $is_rich = (ref($seq) =~ /RichSeq/); my $seq_name= $seq->accession_number(); unless($sf) { # make one $source_type= $is_swiss ? $PROTEIN_TYPE : $is_gene ? "eneg" # "gene" # "region" # : $is_rich ? $seq->molecule : $source_type; $sf = Bio::SeqFeature::Generic->direct_new(); my $len = $seq->length(); $len=1 if($len<1); my $start = 1; ##$start= $len if ($len<1); my $loc= $seq->can('location') ? $seq->location() : new Bio::Location::Simple( -start => $start, -end => $len); $sf->location( $loc ); $sf->primary_tag($source_type); $sf->source_tag($SOURCEID); $sf->seq_id( $seq_name); #? $sf->display_name($seq->id()); ## Name or Alias ? $sf->add_tag_value( Alias => $seq->id()); # unless id == accession $seq->add_SeqFeature($sf); ## $source_feat= $sf; } if ($sf->has_tag("chromosome")) { $source_type= "chromosome"; my ($chrname) = $sf->get_tag_values("chromosome"); ## PROBLEM with Name <> ID, RefName for Gbrowse; use Alias instead ## e.g. Mouse chr 19 has two IDs in NCBI genbank now $sf->add_tag_value( Alias => $chrname ); } # pull GB Comment, Description for source ft ... # add reference - can be long, not plain string... warn "# $SOURCEID:$seq_name fields = ", join(",", $seq->annotation->get_all_annotation_keys()),"\n" if $DEBUG; # GenBank fields: keyword,comment,reference,date_changed # Entrezgene fields 850293 =ALIAS_SYMBOL,RefSeq status,chromosome,SGD,dblink,Entrez Gene Status,OntologyTerm,LOCUS_SYNONYM # is this just for main $seq object or for all seqfeatures ? my %AnnotTagMap= ( 'gene_name' => 'Alias', 'ALIAS_SYMBOL' => 'Alias', # Entrezgene 'LOCUS_SYNONYM' => 'Alias', #? 'symbol' => 'Alias', 'synonym' => 'Alias', 'dblink' => 'Dbxref', 'product' => 'product', 'Reference' => 'reference', 'OntologyTerm' => 'Ontology_term', 'comment' => 'Note', 'comment1' => 'Note', # various map-type locations # gene accession tag is named per source db !?? # 'Index terms' => keywords ?? ); my ($desc)= $seq->annotation->get_Annotations("desc") || ( $seq->desc() ); my ($date)= $seq->annotation->get_Annotations("dates") || $seq->annotation->get_Annotations("update-date") || $is_rich ? $seq->get_dates() : (); my ($comment)= $seq->annotation->get_Annotations("comment"); my ($species)= $seq->annotation->get_Annotations("species"); if (!$species && $seq->can('species') && defined $seq->species() && $seq->species()->can('binomial') ) { $species= $seq->species()->binomial(); } # update source feature with main GB fields $sf->add_tag_value( ID => $seq_name ) unless $sf->has_tag('ID'); $sf->add_tag_value( Note => $desc ) if($desc && ! $sf->has_tag('Note')); $sf->add_tag_value( organism => $species ) if($species && ! $sf->has_tag('organism')); $sf->add_tag_value( comment1 => $comment ) if(!$is_swiss && $comment && ! $sf->has_tag('comment1')); $sf->add_tag_value( date => $date ) if($date && ! $sf->has_tag('date')); $sf->add_tag_value( Dbxref => $SOURCEID.':'.$seq_name ) if $is_swiss || $is_gene; foreach my $atag (sort keys %AnnotTagMap) { my $gtag= $AnnotTagMap{$atag}; next unless($gtag); my @anno = map{ if (ref $_ && $_->can('get_all_values')) { split( /[,;] */, join ";", $_->get_all_values) } elsif (ref $_ && $_->can('display_text')) { split( /[,;] */, $_->display_text) } elsif (ref $_ && $_->can('value')) { split( /[,;] */, $_->value) } else { (); } } $seq->annotation->get_Annotations($atag); foreach(@anno) { $sf->add_tag_value( $gtag => $_ ); } } # my @genes = map{ split( /[,;] */, "$_"); } $seq->annotation->get_Annotations('gene_name'); # $sf->add_tag_value( Alias => $_ ) foreach(@genes); # # my @dblink= map { "$_"; } $seq->annotation->get_Annotations("dblink"); # add @all # $sf->add_tag_value( Dbxref => $_ ) foreach(@dblink); return (wantarray)? ($source_type,$sf) : $source_type; #? } sub gene_features { my ($f, $gene_id, $genelinkID) = @_; local $_ = $f->primary_tag; $method{$_}++; if ( /gene/ ) { $f->add_tag_value( ID => $gene_id ) unless($f->has_tag('ID')); # check is same value!? $tnum = $rnum= 0; $ncrna_id= $rna_id = ''; return GM_NEW_TOPLEVEL; } elsif ( /mRNA/ ) { return GM_NOT_PART unless $gene_id; return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id); ($rna_id = $gene_id ) =~ s/gene/mRNA/; $rna_id .= '.t0' . ++$tnum; $f->add_tag_value( ID => $rna_id ); $f->add_tag_value( Parent => $gene_id ); } elsif ( /RNA|transcript/) { ## misc_RNA here; missing exons ... flattener problem? # all of {t,nc,sn}RNA can have gene models now ## but problem in Worm chr: mRNA > misc_RNA > CDS with same locus tag ## CDS needs to use mRNA, not misc_RNA, rna_id ... ## also need to fix cases where tRNA,... lack a 'gene' parent: make this one top-level if($gene_id) { return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id); ($ncrna_id = $gene_id) =~ s/gene/ncRNA/; $ncrna_id .= '.r0' . ++$rnum; $f->add_tag_value( Parent => $gene_id ); $f->add_tag_value( ID => $ncrna_id ); } else { unless ($f->has_tag('ID')) { if($genelinkID) { $f->add_tag_value( ID => $genelinkID ) ; } else { $idh->generate_unique_persistent_id($f); } } ($ncrna_id)= $f->get_tag_values('ID'); return GM_NEW_TOPLEVEL; # this feat now acts as gene-top-level; need to print @to_print to flush prior exons? } } elsif ( /exon/ ) { # can belong to any kind of RNA return GM_NOT_PART unless ($rna_id||$ncrna_id); return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id); ## we are getting duplicate Parents here, which chokes chado loader, with reason... ## problem is when mRNA and ncRNA have same exons, both ids are active, called twice ## check all Parents for my $expar ($rna_id, $ncrna_id) { next unless($expar); if ( $exonpar{$expar} and $f->has_tag('Parent') ) { my @vals = $f->get_tag_values('Parent'); next if (grep {$expar eq $_} @vals); } $exonpar{$expar}++; $f->add_tag_value( Parent => $expar); # last; #? could be both } # now we can skip cloned exons # dgg note: multiple parents get added and printed for each unique exon return GM_DUP_PART if ++$seen{$f} > 1; } elsif ( /CDS|protein|polypeptide/ ) { return GM_NOT_PART unless $rna_id; ## ignore $ncrna_id ?? return GM_NOT_PART if($genelinkID && $genelinkID ne $gene_id); #?? (my $pro_id = $rna_id) =~ s/\.t/\.p/; if( ! $CDSkeep && /CDS/) { $f->primary_tag($PROTEIN_TYPE); ## duplicate problem is Location .. if ($f->location->isa("Bio::Location::SplitLocationI")) { # my($b,$e)=($f->start, $f->end); # is this all we need? my($b,$e)=(-1,0); foreach my $l ($f->location->each_Location) { $b = $l->start if($b<0 || $b > $l->start); $e = $l->end if($e < $l->end); } $f->location( Bio::Location::Simple->new( -start => $b, -end => $e, -strand => $f->strand) ); } $f->add_tag_value( Derives_from => $rna_id ); } else { $f->add_tag_value( Parent => $rna_id ); } $f->add_tag_value( ID => $pro_id ); move_translation_fasta($f, $pro_id); # if( $f->has_tag('translation')) { # my ($aa) = $f->get_tag_values("translation"); # $proteinfa{$pro_id}= $aa; # $f->remove_tag("translation"); # $f->add_tag_value("translation","length.".length($aa)); # hack for odd chado gbl problem # } } elsif ( /region/ ) { $f->primary_tag('gene_component_region'); $f->add_tag_value( Parent => $gene_id ); } else { return GM_NOT_PART unless $gene_id; $f->add_tag_value( Parent => $gene_id ); } ## return GM_DUP_PART if /exon/ && ++$seen{$f} > 1; return GM_NEW_PART; } ## was generic_features > add_generic_id sub add_generic_id { my ($f, $ft_name, $flags) = @_; my $method = $f->primary_tag; $method{$method}++ unless($flags =~ /nocount/); ## double counts GM_NOT_PART from above if ($f->has_tag('ID')) { } elsif ( $f->has_tag($method) ) { my ($name) = $f->get_tag_values($method); $f->add_tag_value( ID => "$method:$name" ); } elsif($ft_name) { # is this unique ? $f->add_tag_value( ID => $ft_name ); } else { $idh->generate_unique_persistent_id($f); } move_translation_fasta( $f, ($f->get_tag_values("ID"))[0] ) if($method =~ /CDS/); # return $io->gff_string($f); } sub move_translation_fasta { my ($f, $ft_id) = @_; if( $ft_id && $f->has_tag('translation') ) { my ($aa) = $f->get_tag_values("translation"); if($aa && $aa !~ /^length/) { $proteinfa{$ft_id}= $aa; $f->remove_tag("translation"); $f->add_tag_value("translation","length.".length($aa)); # hack for odd chado gbl problem } } } sub gff_header { my ($name, $end, $source_type, $source_feat) = @_; $source_type ||= "region"; my $info= "$source_type:$name"; my $head= "##gff-version $GFF_VERSION\n# sequence-region $name 1 $end\n"; $head .= "# conversion-by bp_genbank2owl.pl\n"; if($source_feat) { ## dgg: these header comment fields are not useful when have multi-records, diff organisms for my $key (qw(organism date Note)) { my($value) = $source_feat->get_tag_values($key); $head .= "# $key $value\n" if($value); $info .= ", $value" if($value); } $head="" if($didheader); } else { $head .= "$name\t$SOURCEID\t$source_type\t1\t$end\t.\t.\t.\tID=$name\n"; } $didheader++; return (wantarray) ? ($head,$info) : $head; } sub unflatten_seq { my $seq = shift; ## print "# working on $source_type:", $seq->accession, "\n"; my $uh_oh = "Possible gene unflattening error with" . $seq->accession_number . ": consult STDERR\n"; eval { $unflattener->unflatten_seq( -seq => $seq, -use_magic => 1 ); }; # deal with unflattening errors if ( $@ ) { warn $seq->accession_number . " Unflattening error:\n"; warn "Details: $@\n"; print "# ".$uh_oh; } return 0 if !$seq || !$seq->all_SeqFeatures; # map feature types to the sequence ontology ## $tm->map_types_to_SO( -seq => $seq ); $tm->map_types( -seq => $seq, -type_map => $FTSOmap, -undefined => "region" ); #dgg 1; } sub filter { my $seq = shift; ## return unless $filter; my @feats; my @sources; # dgg; pick source features here; only 1 always? if ($filter) { for my $f ( $seq->remove_SeqFeatures ) { my $m = $f->primary_tag; push @sources, $f if ($m eq 'source'); # dgg? but leave in @feats ? push @feats, $f unless $filter =~ /$m/i; } $seq->add_SeqFeature(@feats) if @feats; } else { for my $f ( $seq->get_SeqFeatures ){ my $m = $f->primary_tag; push @sources, $f if ($m eq 'source'); # dgg? but leave in @feats ? } } return @sources; } # The default behaviour of Bio::FeatureHolderI:get_all_SeqFeatures # changed to filter out cloned features. We have to implement the old # method. These two subroutines were adapted from the v1.4 Bio::FeatureHolderI sub get_all_SeqFeatures { my $seq = shift; my @flatarr; foreach my $feat ( $seq->get_SeqFeatures ){ push(@flatarr,$feat); _add_flattened_SeqFeatures(\@flatarr,$feat); } return @flatarr; } sub gene_name { my $g = shift; my $gene_id = ''; # zero it; if ($g->has_tag('gene')) { ($gene_id) = $g->get_tag_values('gene'); } elsif ($g->has_tag('locus_tag')) { ($gene_id) = $g->get_tag_values('locus_tag'); } elsif ($g->has_tag('ID')) { # for non-Genbank > Entrezgene ($gene_id) = $g->get_tag_values('ID'); } ## See Unflattener comment: # on rare occasions, records will have no /gene or /locus_tag # but it WILL have /product tags. These serve the same purpose # for grouping. For an example, see AY763288 (also in t/data) # eg. product=tRNA-Asp ; product=similar to crooked neck protein elsif ($g->has_tag('product')) { my ($name)= $g->get_tag_values('product'); ($gene_id) = $name unless($name =~ / /); # a description not name } ## dgg; also handle transposon=xxxx ID/name # ID=GenBank:repeat_region:NC_004353:1278337:1281302;transposon=HeT-A{}1685;Dbxref=FLYBASE:FBti0059746 elsif ($g->has_tag('transposon')) { my ($name)= $g->get_tag_values('transposon'); ($gene_id) = $name unless($name =~ / /); # a description not name } return $gene_id; } # same list as gene_name .. change tag to generic Name sub convert_to_name { my $g = shift; my $gene_id = ''; # zero it; if ($g->has_tag('gene')) { ($gene_id) = $g->get_tag_values('gene'); $g->remove_tag('gene'); $g->add_tag_value('Name', $gene_id); } elsif ($g->has_tag('locus_tag')) { ($gene_id) = $g->get_tag_values('locus_tag'); $g->remove_tag('locus_tag'); $g->add_tag_value('Name', $gene_id); } elsif ($g->has_tag('product')) { my ($name)= $g->get_tag_values('product'); ($gene_id) = $name unless($name =~ / /); # a description not name ## $g->remove_tag('product'); $g->add_tag_value('Name', $gene_id); } elsif ($g->has_tag('transposon')) { my ($name)= $g->get_tag_values('transposon'); ($gene_id) = $name unless($name =~ / /); # a description not name ## $g->remove_tag('transposon'); $g->add_tag_value('Name', $gene_id); } return $gene_id; } sub _add_flattened_SeqFeatures { my ($arrayref,$feat) = @_; my @subs = (); if ($feat->isa("Bio::FeatureHolderI")) { @subs = $feat->get_SeqFeatures; } elsif ($feat->isa("Bio::SeqFeatureI")) { @subs = $feat->sub_SeqFeature; } else { warn ref($feat)." is neither a FeatureHolderI nor a SeqFeatureI. ". "Don't know how to flatten."; } for my $sub (@subs) { push(@$arrayref,$sub); _add_flattened_SeqFeatures($arrayref,$sub); } }