From a5c5d208e51b9f38f307dd6243448722f6d9d3cd Mon Sep 17 00:00:00 2001
From: Eduardo Eyras <eae@sanger.ac.uk>
Date: Wed, 18 Jun 2003 13:24:44 +0000
Subject: [PATCH] module with some methods to convert gff into ensembl exons
---
modules/Bio/EnsEMBL/Utils/GFF2Exon.pm | 368 ++++++++++++++++++++++++++
1 file changed, 368 insertions(+)
create mode 100644 modules/Bio/EnsEMBL/Utils/GFF2Exon.pm
diff --git a/modules/Bio/EnsEMBL/Utils/GFF2Exon.pm b/modules/Bio/EnsEMBL/Utils/GFF2Exon.pm
new file mode 100644
index 0000000000..e54e7adfe7
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Utils/GFF2Exon.pm
@@ -0,0 +1,368 @@
+# You may distribute this module under the same terms as perl itself
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+GFF2Exon
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Utils::GFF2Exon;
+my $gff = GFF2Exon->new(-gff_version => 2);
+my $exon = $gff->exon_from_gff( $gff_string );
+
+=cut
+
+# Let the code begin...
+
+package Bio::EnsEMBL::Utils::GFF2Exon;
+
+use vars qw(@ISA);
+use strict;
+
+use Bio::EnsEMBL::Root;
+@ISA = qw(Bio::EnsEMBL::Root);
+
+
+sub new {
+ my ($class, @args) = @_;
+ my $self = $class->SUPER::new(@args);
+
+ my ($gff_version) = $self->_rearrange([qw(GFF_VERSION)],@args);
+
+ if(($gff_version != 1) && ($gff_version != 2)) {
+ $self->throw("unknown version: $gff_version");
+ }
+ $self->gff_version($gff_version);
+ return $self;
+}
+
+=head2 exon_from_gff
+
+ Usage : my $exon = $gff->exon_from_gff_string($gff_string);
+ Function: Sets properties of an exon object from a GFF-formatted
+ string. Interpretation of the string depends on the version
+ that has been specified at initialization.
+ Args : The GFF-formatted string
+
+=cut
+
+sub exon_from_gff {
+ my ($self, $gff_string, $trans_hash ) = @_;
+
+ if($self->gff_version() == 1) {
+ return $self->_from_gff1_string($gff_string, $trans_hash);
+ }
+ else{
+ return $self->_from_gff2_string($gff_string, $trans_hash);
+ }
+}
+
+=head2 _from_gff1_string
+
+ Returns : Exon
+ Args : The GFF-formatted string to initialize it from
+
+=cut
+
+sub _from_gff1_string {
+ my ($self, $gffstring, $trans_hash) = @_;
+
+ #print STDERR "gff_string: $gffstring\n";
+
+ #39896 human_cdna exon 1030942 1031591 100 + 0 6604
+ #39897 human_cdna exon 1034227 1034285 100 + 0 6604
+ #39898 human_cdna exon 1035280 1035339 100 + 0 6604
+ #39899 human_cdna exon 1035741 1035820 100 + 0 6604
+ #39900 human_cdna exon 1036477 1036629 100 + 0 6604
+ #243299 human_cdna exon 1037161 1037229 100 + 0 40150
+ #243301 human_cdna exon 1043180 1043315 100 + 0 40150
+ #243303 human_cdna exon 1048194 1048340 100 + 0 40150
+ #243305 human_cdna exon 1053724 1053855 100 + 0 40150
+ #243307 human_cdna exon 1054346 1054451 100 + 0 40150
+ #243309 human_cdna exon 1055667 1055833 100 + 0 40150
+ #243310 human_cdna exon 1057048 1057221 100 + 0 40150
+ #243311 human_cdna exon 1058529 1058630 100 + 0 40150
+ #243313 human_cdna exon 1061487 1062080 100 + 0 40150
+ my ($seqname,
+ $source,
+ $primary,
+ $start,
+ $end,
+ $score,
+ $strand,
+ $frame,
+ @group)
+ = split(/\s+/, $gffstring);
+
+ if ( !defined $frame ) {
+ $self->throw("[$gffstring] does not look like GFF to me");
+ }
+ $frame = 0 unless( $frame =~ /^\d+$/);
+
+ my $exon = Bio::EnsEMBL::Exon->new();
+ $exon->seqname($seqname);
+ #$exon->source_tag($source);
+ $exon->start($start);
+ $exon->end($end);
+ my $phase = ( 3 - $frame )%3;
+ $exon->phase($phase);
+ $exon->end_phase( ( $exon->phase + $exon->length)%3 );
+ if ( $score ){
+ $exon->score( $score );
+ }
+ if ( $strand eq '-' ) { $exon->strand(-1); }
+ if ( $strand eq '+' ) { $exon->strand(1); }
+ if ( $strand eq '.' ) { $exon->strand(0); }
+
+ ############################################################
+ # warning: it parses only the first element of the group
+
+ $trans_hash->{ $exon } = $group[0];
+ return $exon;
+}
+
+=head2 _from_gff2_string
+
+ Returns : Exon
+ Args : The GFF2-formatted string to initialize it from
+
+=cut
+
+sub _from_gff2_string {
+ my ($self, $gffstring) = @_;
+ chomp($gffstring);
+
+ # according to the Sanger website, GFF2 should be single-tab separated elements, and the
+ # free-text at the end should contain text-translated tab symbols but no "real" tabs,
+ # so splitting on \t is safe, and $attribs gets the
+ # entire attributes field to be parsed later
+
+ my ($seqname, $source, $primary, $start, $end, $score, $strand, $frame, @attribs)
+ = split(/\t+/, $gffstring);
+
+ # just in case the rule against tab characters has been broken
+ my $attribs = join '', @attribs;
+
+ if ( !defined $frame ) {
+ $self->throw("[$gffstring] does not look like GFF2 to me");
+ }
+ my $exon = Bio::EnsEMBL::Exon->new();
+ $exon->seqname($seqname);
+ $exon->source_tag($source);
+ $exon->analysis->gff_feature($primary);
+ $exon->start($start);
+ $exon->end($end);
+ $exon->phase($frame);
+ $exon->end_phase( ( $exon->phase + $exon->length)%3 );
+ if ( $score eq '.' ) {
+ #$exon->score(undef);
+ } else {
+ $exon->score($score);
+ }
+ if ( $strand eq '-' ) { $exon->strand(-1); }
+ if ( $strand eq '+' ) { $exon->strand(1); }
+ if ( $strand eq '.' ) { $exon->strand(0); }
+
+ # <Begin Inefficient Code from Mark Wilkinson>
+ # this routine is necessay to allow the presence of semicolons in quoted text
+ # Semicolons are the delimiting character for new tag/value attributes.
+ # it is more or less a "state" machine, with the "quoted" flag going up and down
+ # as we pass thorugh quotes to distinguish free-text semicolon and hash
+ # symbols from GFF control characters
+
+ # remove comments field (format: #blah blah blah... at the end of the GFF line)
+ #$attribs =~ s/\#(.*)$//;
+ #my @att = split //, $attribs; # split into individual characters
+ #my $num = $#att; # count them
+ #my $flag = 0;
+ #my @parsed; # this is needed to hold the characters that have been parsed
+
+ # run through each character one at a time and check it
+ #for (my $a = 0; $a <= $num ; $a +=1){
+ # if ($att[$a] eq "\""){$flag=($flag==0)?1:0} # flag up on entering quoted text, down on leaving it
+ # if (($att[$a] eq ";") && $flag){$att[$a] = "INSERT_SEMICOLON_HERE"} # replace semicolon with an unusual message if the quoted text flag is up
+ # if (($att[$a] eq "#") && !$flag){last} # an unquoted hash symbol means the beginning of the comments field - discard
+ # push @parsed, $att[$a] # take the parsed character and push it onto the parsed list
+ # }
+
+ #$attribs = join "", @parsed; # rejoin into a single string
+
+ # <End Inefficient Code> Please feel free to fix this and make it more "perlish"
+
+ # my @key_vals = split /;/, $attribs; # attributes are semicolon-delimited
+
+ # foreach my $pair ( @key_vals ) {
+ # $pair =~ s/INSERT_SEMICOLON_HERE/;/g; # replace semicolons that were removed from free-text above.
+ # my ($blank, $key, $values) = split /^\s*([\w\d]+)\s/, $pair; # separate the key from the value
+
+ # my @values;
+
+ # while ($values =~ s/"(.*?)"//){ # free text is quoted, so match each free-text block
+ # if ($1){push @values, $1}; # and push it on to the list of values (tags may have more than one value...)
+ #}
+
+ # my @othervals = split /\s+/, $values; # and what is left over should be space-separated non-free-text values
+ # foreach my $othervalue(@othervals){
+# if (CORE::length($othervalue) > 0){push @values, $othervalue} # get rid of any empty strings which might result from the split
+# }
+
+# foreach my $value(@values){
+# $exon->add_tag_value($key, $value);
+# }
+ # }
+
+ return $exon;
+}
+
+=head2 gff_string
+
+=cut
+
+sub gff_string{
+ my ($self, $exon,$transcript) = @_;
+
+ if($self->gff_version() == 1) {
+ return $self->_gff1_string($exon,$transcript);
+ } else {
+ return $self->_gff2_string($exon,$transcript);
+ }
+}
+
+=head2 _gff1_string
+
+=cut
+
+sub _gff1_string{
+ my ($self, $exon, $transcript) = @_;
+ my ($str,$source,$primary_tag,$score,$frame,$name,$strand);
+
+ if( $exon->can('score') ) {
+ $score = $exon->score();
+ }
+ $score = '.' unless defined $score;
+
+ if( $exon->can('frame') ) {
+ $frame = $exon->frame();
+ }
+ $frame = '.' unless defined $frame;
+
+ $strand = $exon->strand();
+ if(! $strand) {
+ $strand = ".";
+ } elsif( $strand == 1 ) {
+ $strand = '+';
+ } elsif ( $exon->strand == -1 ) {
+ $strand = '-';
+ }
+
+ $name = $exon->seqname();
+ $source = "merged";
+ $primary_tag = "exon";
+
+ $str = join("\t",
+ $name,
+ $source,
+ $primary_tag,
+ $exon->start(),
+ $exon->end(),
+ $score,
+ $strand,
+ $frame);
+
+ my $tag_str = $transcript->type;
+ $str .= "\t$tag_str";
+ return $str;
+}
+
+=head2 _gff2_string
+
+=cut
+
+sub _gff2_string{
+ my ($gff, $exon) = @_;
+ my ($str,$score,$frame,$name,$strand);
+
+ if( $exon->can('score') ) {
+ $score = $exon->score();
+ }
+ $score = '.' unless defined $score;
+
+ if( $exon->can('frame') ) {
+ $frame = $exon->frame();
+ }
+ $frame = '.' unless defined $frame;
+
+ $strand = $exon->strand();
+ if(! $strand) {
+ $strand = ".";
+ } elsif( $strand == 1 ) {
+ $strand = '+';
+ } elsif ( $exon->strand == -1 ) {
+ $strand = '-';
+ }
+
+ if( $exon->can('seqname') ) {
+ $name = $exon->seqname();
+ $name ||= 'SEQ';
+ } else {
+ $name = 'SEQ';
+ }
+
+
+ $str = join("\t",
+ $name,
+ $exon->source_tag(),
+ $exon->analysis->gff_feature(),
+ $exon->start(),
+ $exon->end(),
+ $score,
+ $strand,
+ $frame);
+
+ # the routine below is the only modification I made to the original
+ # ->gff_string routine (above) as on November 17th, 2000, the
+ # Sanger webpage describing GFF2 format reads: "From version 2
+ # onwards, the attribute field must have a tag value structure
+ # following the syntax used within objects in a .ace file,
+ # flattened onto one line by semicolon separators. Tags must be
+ # standard identifiers ([A-Za-z][A-Za-z0-9_]*). Free text values
+ # must be quoted with double quotes".
+
+ # MW
+
+ #my $valuestr;
+ #if ($exon->all_tags){ # only play this game if it is worth playing...
+ # $str .= "\t"; # my interpretation of the GFF2 specification suggests the need for this additional TAB character...??
+ # foreach my $tag ( $exon->all_tags ) {
+ # my $valuestr; # a string which will hold one or more values for this tag, with quoted free text and space-separated individual values.
+ # foreach my $value ( $exon->each_tag_value($tag) ) {
+ # if ($value =~ /[^A-Za-z0-9_]/){
+ # $value =~ s/\t/\\t/g; # substitute tab and newline characters
+ # $value =~ s/\n/\\n/g; # to their UNIX equivalents
+ # $value = '"' . $value . '" '} # if the value contains anything other than valid tag/value characters, then quote it
+ # $valuestr .= $value . " "; # with a trailing space in case there are multiple values
+ # # for this tag (allowed in GFF2 and .ace format)
+ # }
+ # $str .= "$tag $valuestr ; "; # semicolon delimited with no '=' sign
+ # }
+ # chop $str; chop $str # remove the trailing semicolon and space
+ # }
+ return $str;
+}
+
+=head2 gff_version
+
+=cut
+
+sub gff_version {
+ my ($self, $value) = @_;
+ if(defined $value && (($value == 1) || ($value == 2))) {
+ $self->{'GFF_VERSION'} = $value;
+ }
+ return $self->{'GFF_VERSION'};
+}
+
+
+1;
+
--
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