[Bioperl-l] Re: Proposed GFF version 3

Jim Kent jim_kent at pacbell.net
Tue Feb 11 10:40:09 EST 2003


Everywhere outside of WormBase and DAS I've personally seen
uses '&'.  We had to implement ';' to cope with DAS.

----- Original Message -----
From: "Richard Durbin" <rd at sanger.ac.uk>
To: <lstein at cshl.org>
Cc: <bioperl-l at bioperl.org>; <suzi at fruitfly.org>; <gff-list at sanger.ac.uk>
Sent: Tuesday, February 11, 2003 4:54 AM
Subject: Re: Proposed GFF version 3


> Swap them entirely.  i.e. put the attributes in column 9 and call that
> "attributes" and put the new hierarchical group term in column 10 and
> call that "group".  Or perhaps it would be better to call it something
> else to minimise confusion, because in gff version 1 column 9 was called
> group.  What about calling column 10 "cluster"?
>
> I see you have switched to URL type format for the attributes, away from
> acedb.  That's fine - URL format is much more universal.  But is ';' a
> standard separator in URLS?  I just looked and see that Ensembl uses '&'
> and WormBase uses ';' and I think I have seen '+' somewhere, so maybe
> there is no standard.
>
> Richard
>
> Lincoln Stein wrote:
> > 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
> >>
> >
>
>



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