[Bioperl-l] Re: Proposed GFF version 3
Lincoln Stein
lstein at cshl.org
Mon Feb 10 13:25:33 EST 2003
Hi Richard,
Do you mean that we should swap columns 9 and 10 entirely, or just swap their
names? I think you mean the former, but I want to be sure.
Lincoln
On Monday 10 February 2003 11:12 am, Richard Durbin wrote:
> Hello all,
>
> This looks very nice to me. Not surprising perhaps because I had an
> earlier involvement as Lincoln says.
>
> I have added gff-list at sanger.ac.uk to the mailing Cc: list because it is
> the "official" GFF mailing list, although it is very little used.
>
> I have one major comment, that columns 9 (group) and 10 (attributes)
> should be switched. Although GFF version 1 column 9 was called "group"
> in version 2, which is what has been current for over two years, this
> was renamed "attribute" and contains the attribute information. For
> consistency we should keep column 9 for the attributes. Also, in many
> cases there will be attributes but no group.
>
> I like ID and Target. I see the idea with hsp's for gapped alignments,
> though perhaps they could be called "match_block". But there is a case
> I think to also encode gapped alignments on one line, perhaps using the
> CIGAR encoding used by ENSEMBL (and BioPerl?), e.g. as
>
> Target=M1:1..1000;Align=xxxxxxx
>
> (sorry I don't know cigar format well enough to write a legal string.
>
> Richard
>
> Lincoln Stein wrote:
> > This letter is to discuss a proposed extension to GFF. It arises from
> > conversations with Richard Durbin during last fall's Hinxton genome
> > informatics meeting.
> >
> > Although there are many richer ways of representing genomic features
> > via XML, the stubborn persistence of a variety of ad-hoc tab-delimited
> > flat file formats declares the bioinformatics community's need for a
> > simple format that can be modified with a text editor and processed
> > with shell tools like grep. The GFF format, although widely used, has
> > fragmented into multiple incompatible dialects. When asked why they
> > have modified the published Sanger specification, bioinformaticists
> > frequently answer that the format was insufficient for their needs,
> > and they needed to extend it. The proposed GFF3 format addresses the
> > most common extensions to GFF, while preserving backward compatibility
> > with previous formats. The new format:
> >
> > 1) adds a mechanism for representing more than one level
> > of hierarchical grouping of features and subfeatures.
> > 2) separates the ideas of group membership and feature name/id
> > 3) constrains the feature type field to be taken from a controlled
> > vocabulary.
> > 4) allows a single feature, such as an exon, to belong to more than
> > one group at a time.
> > 5) one level of relative addressing for subfeatures (e.g. exons
> > can be expressed in transcript coordinates)
> > 6) an explicit convention for pairwise alignments
> > 7) an explicit convention for features that occupy disjunct regions
> >
> > The format consists of 10 columns, separated by spaces. The following
> > unescaped characters are allowed within fields:
> > [a-zA-Z0-9.:;=%^*$@!+_?-]. All other characters must must be escaped
> > using the URL escaping conventions. Unescaped quotation marks,
> > backslashes and other ad-hoc escaping conventions that have been added
> > to the GFF format are explicitly forbidden. The =, ; and % characters
> > have reserved meanings as described below.
> >
> > Undefined fields are replaced with the "." character, as described in
> > the original GFF spec.
> >
> > Column 1: "seqid"
> >
> > The ID of the landmark used to establish the coordinate system for the
> > current feature. IDs must contain alphanumeric characters.
> > Whitespace, if present, must be escaped using URL escaping rules
> > (e.g. space="%20").
> >
> > Column 2: "source"
> >
> > The source of the feature. This is unchanged from the older GFF specs
> > and is not part of a controlled vocabulary.
> >
> > Column 3: "type"
> >
> > The type of the feature (previously called the "method"). This is
> > constrained to be either: (a) a term from SOFA; or (b) a SOFA
> > accession number. The latter alternative is distinguished using the
> > syntax SOFA:000000.
> >
> > Columns 4 & 5: "start" and "end"
> >
> > The start and end of the feature, in 1-based integer coordinates,
> > relative to the landmark given in column 1. Start is less than end.
> >
> > Column 6: "score"
> >
> > The score of the feature, a floating point number. As in earlier
> > versions of the format, the semantics of the score are ill-defined.
> > It is strongly recommended that E-values be used for sequence
> > similarity features, and that P-values be used for ab initio gene
> > prediction features.
> >
> > Column 7: "strand"
> >
> > The strand of the feature. + for positive strand (relative to the
> > landmark), - for minus strand, and . for features that are not
> > stranded. In addition, ? can be used for features whose strandedness
> > is relevant, but unknown.
> >
> > Column 8: "phase"
> >
> > The phase of the feature, for protein-encoding featues (primarily
> > CDSs). This is an integer-valued field with the values 0, 1, or 2.
> > The integer indicates the offset from the start of the feature to the
> > first base of the first codon in the reading frame. "." is used for
> > features that do not corresponding to a reading frame.
> >
> > Column 9: "group"
> >
> > A list of the immediate parents of the current feature. Multiple
> > parents are allowed (example: one exon shared by multiple
> > transcripts). Multiple parents are separated by a semicolon.
> > Parentless features have a dot in this field.
> >
> > Column 10: "attributes"
> >
> > A list of feature attributes in the format tag=value. Multiple
> > tag=value pairs are separated by semicolons. URL escaping rules are
> > used for tags or values containing whitespace, "=" characters and
> > semicolons.
> >
> > Two tags are special:
> >
> > ID Indicates the name of the feature. IDs must be unique
> > within the scope of the GFF file.
> >
> > Target Indicates the target of a nucleotide to nucleotide or
> > nucleotide to protein alignment. The format of the
> > value is "target_id:start..end" Start may be greater
> > than end to indicate a + strand alignment to the
> > reverse complement of a target nucleotide sequence.
> >
> > In the example GFF3 file given below, the first column contains line
> > numbers that I have added for the purposes of the narrative. Here are
> > some common scenarios that I have attempted to illustrate:
> >
> > A) a simple feature, no public ID
> >
> > Line 2 in the example is a feature of type "repeat". It has a start
> > and an end and no ID, but it does have an attribute named "Note."
> >
> > B) a simple feature with a public ID
> >
> > Line 3 is a feature of type clone. It has a start and an end. Its
> > parent is undefined (empty column 9), but it has an attribute of type
> > ID with value "cTel33B."
> >
> > C) a feature with multiple attributes
> >
> > Line 5 is a feature of type "gene." It has no parent, and has
> > attributes of type ID, Note, and GO_term.
> >
> > D) a hierarchical grouping of features
> >
> > Lines 5-13 demonstrate a hierarchical grouping. At the top level is
> > line 5, which defines the extent of a "gene" with ID Y74C9A.1. Below
> > this are two features of type mRNA (lines 6 and 7). Their group
> > fields contain the ID of Y74C9A.1, indicating that this feature is
> > their immediate parent. In the 10th column, the mRNA features have
> > their own IDs independent of the ID of the parent gene.
> >
> > This pattern is repeated for the exons listed on lines 8-11. Exons
> > e1, e2, and e4 belong to both of the transcripts. Therefore, both
> > transcript IDs are listed in the group column, separated by
> > semicolons.
> >
> > Exon e3 belongs only to one of the transcripts, and therefore only
> > that transcript's ID is listed in the group column.
> >
> > Lines 12 and 13 indicate coding_start and coding_end features. These
> > subfeatures are hierarchically grouped underneath their corresponding
> > exons, but they do not have independent public IDs.
> >
> > E) Disjunct coordinates
> >
> > Lines 14-16 illustrates a single feature -- the CDS corresponding to
> > mRNA Y74C9A.1a -- which occupies multiple disjunct regions. The group
> > column indicates that the CDS belongs to mRNA Y74C9A.1a. However, the
> > attribute column assigns each of lines 14-16 the same ID. Because the
> > ID is the same, this is to be interpreted as a single feature that
> > spans multiple locations.
> >
> > F) Alignments
> >
> > Lines 17-19 demonstrate a gapped alignment of two sequences using the
> > reserved Target attribute. Each non-gapped segment becomes a line in
> > the GFF3 file. The segments each share the same ID, thereby
> > indicating that the segments are disjunct regions of the same feature.
> > The Target attribute indicates the ID of the target sequence (which
> > does not have to be represented in the GFF3 file) and the start and
> > end coordinates of the aligned target.
> >
> > Unlike the GFF1 and GFF2 formats, the group field for gapped
> > alignments can be empty. However, a valid alternative representation
> > is to create a single "match" feature, and a series of "hsp" features
> > underneath it via the group field. Lines 20-22 show this alternative
> > representation.
> >
> > G) Relative coordinates
> >
> > Lines 23-26 illustrate using relative coordinate addressing in
> > feature/subfeature relationships. Line 23 defines an mRNA that is
> > positioned on sequence landmark "I" from positions 5000 to 6000. Its
> > ID field indicates that it is M7.3. Lines 24-26 are exon subfeatures
> > of M7.3 as indicated by their group field. However, the seqid field
> > specifies M7.3 as the parent coordinate system, thereby allowing the
> > exons to begin at position 1.
> >
> > 0 ##gff-version 3
> > 1 ##sequence-region I:1..14972282
> > 2 I wormbase repeat 5000 5100 . . .
> > . Note=ALU3 3 I wormbase clone 1 2679 .
> > + . . ID=cTel33B 4 I wormbase
> > contig 1 14972282 . + . .
> > ID=CHROMOSOME_I 5 I wormbase gene 43733 44677 .
> > + . . ID=Y74C9A.1;Note=unc-3;GO_term=GO:12345
> > 6 I wormbase mRNA 43733 44677 . + .
> > Y74C9A.1 ID=Y74C9A.1a 7 I wormbase mRNA 43733
> > 44677 . + . Y74C9A.1 ID=Y74C9A.1b 8 I
> > wormbase exon 43733 43961 . + .
> > Y74C9A.1a;Y74C9A.1b ID=e1 9 I wormbase exon 44030
> > 44234 . + . Y74C9A.1a;T:Y74C9A.1b ID=e2 10 I
> > wormbase exon 44281 44328 . + . Y74C9A.1b
> > ID=e3 11 I wormbase exon 44521 44677 . +
> > . Y74C9A.1a;T:Y74C9A.1b ID=e4 12 I wormbase
> > coding_start 43740 43740 . + . e1 13 I
> > wormbase coding_end 44677 44677 . + .
> > e4 14 I wormbase cds 43740 43961 . + 0
> > Y74C9A.1a 15 I wormbase cds 44030 44234 .
> > + 1 Y74C9A.1a 16 I wormbase cds 44521
> > 44677 . + 1 Y74C9A.1a 17 I wormbase
> > match 1 100 100 . . .
> > ID=12345.s;Target=cb123:1001..1100 18 I wormbase match
> > 101 500 20 . . .
> > ID=12345.s;Target=cb123:1101..1500 19 I wormbase match
> > 501 1000 80 . . .
> > ID=12345.s;Target=cb123:1501..2000 20 I wormbase match
> > 5001 6000 100 . . . ID=abc;Target=M1:1..1000
> > 21 I wormbase hsp 5001 5500 . . .
> > abc Target=M1:1..500 22 I wormbase hsp 5501
> > 6000 . . . abc Target=M1:501..100 23 I
> > wormbase mRNA 5000 6000 + . . .
> > ID=M7.3 24 M7.3 wormbase exon 1 300 + .
> > . M7.3 ID=M7.3.1 25 M7.3 wormbase exon 301
> > 400 + . . M7.3 ID=M7.3.2 26 M7.3 wormbase
> > exon 401 1000 + . . M7.3 ID=M7.3.3
> >
> > =================================================================
> >
> > I have extended (in an experimental way), the Bio::Tools::GFF module
> > to accomodate this new format. Here is a test script and its output
> > when run on the above file.
> >
> > 0 #!/usr/bin/perl -w
> > 1 use strict;
> > 2 use lib '.';
> >
> > 3 use Bio::Tools::GFF;
> > 4 my $gffio = Bio::Tools::GFF->new(-fh=>\*STDIN,-gff_version=>3);
> > 5 my @f = $gffio->features;
> > 6 format_features(\@f);
> >
> > 7 sub format_features {
> > 8 my $features = shift;
> > 9 my $tabs = shift || 0;
> > 10 for my $f (@$features) {
> > 11 my $type = $f->primary_tag;
> > 12 my $id = $f->unique_id;
> > 13 $id ||= '(no id)';
> > 14 my ($start,$end) = ($f->start,$f->end);
> > 15 my $alt = ($f->alternative_locations)[0];
> > 16 my ($target,$tstart,$tend) =
> > ($alt->seq_id,$alt->start,$alt->end) if $alt;
> >
> > 17 print
> > "\t"x$tabs,join("\t",$id,$type,$f->location->to_FTstring,eval{$alt->locat
> >ion->seq_id,$alt->location->to_FTstring}),"\n"; 18
> > format_features([$f->sub_SeqFeature],$tabs+1);
> > 19 }
> > 20 }
> >
> > 21 1;
> >
> > OUTPUT:
> >
> > cTel33B clone 1..2679
> > CHROMOSOME_I contig 1..14972282
> > 12345.s match join(101..500,1..100,501..1000)
> > M7.3 mRNA 5000..6000
> > M7.3.1 exon 5000..5299
> > M7.3.2 exon 5300..5399
> > M7.3.3 exon 5400..5999
> > abc match 5001..6000
> > (no id) hsp 5001..5500
> > (no id) hsp 5501..6000
> > (no id) repeat 5000..5100
> > Y74C9A.1 gene 43733..44677
> > Y74C9A.1a mRNA 43733..44677
> > e1 exon 43733..43961
> > (no id) coding_start 43740
> > e2 exon 44030..44234
> > e4 exon 44521..44677
> > (no id) coding_end 44677
> > (no id) cds 43740..43961
> > (no id) cds 44030..44234
> > (no id) cds 44521..44677
> > Y74C9A.1b mRNA 43733..44677
> > e1 exon 43733..43961
> > (no id) coding_start 43740
> > e3 exon 44281..44328
--
========================================================================
Lincoln D. Stein Cold Spring Harbor Laboratory
lstein at cshl.org Cold Spring Harbor, NY
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