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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/manual/source/Tutorial/InputOutput/
H A DGffAndGtfIO.rst7 GFF and GTF I/O
11 In this tutorial, you will learn how to read and write GFF and GTF files.
23 …ith a quick reminder on the structure of GFF and GTF files and will then continue with how to read…
26 GFF exists in versions 2 and 3 and GTF is sometimes called "GFF 2.5".
41 For writing, :dox:`GffFileOut` supports only GFF 3 and GTF.
43 GFF Format
46 The following is an example of a GFF 3 file:
79 For GTF and GFF 2, this is a list of tuples, separated by semicolon.
116 …Create a file with the sample GFF content from above and adjust the path ``"example.gff"`` to the …
167 Generating GFF From Scratch
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/data/
H A DEfeatures.emboss2 # === From release 5.0.0 based on the GFF standard 3.0
5 # Note: GFF includes SO numbers with defined relations to most of the
8 # === Originally Based on the GFF standard 2.0 ===
9 # Note: GFF includes EMBL/Genbank/DDBJ feature keys and tags
17 # GFF 2.0 feature keys
23 # GFF 3.0 feature keys
H A DEtags.emboss1 # === Based on the GFF standard 3.0 and EMBL ===
2 # Note: GFF includes EMBL/Genbank/DDBJ feature keys and tags
9 # === end of GFF tags
/dports/biology/py-gffutils/gffutils-0.10.1/gffutils/test/data/
H A DFBgn0031208.gtf2 # same isoform model as the same gene in the test GFF file.
23 # start_codons not listed in GFF
30 # same as unnamed_exon:1 in GFF,but in GTF format, constitutive exons are listed once for each isof…
38 # same as CDS_FBgn0031208:1_737 in GFF
48 # exon FBgn0031208:3 in GFF -- these two exons imply different-length introns
55 # CDS_FBgn0031208:3_737 in GFF
62 # CDS_FBgn0031208:2_737 in GFF
85 # CDS_FBgn0031208:4_737 in GFF
/dports/biology/jalview/jalview/examples/testdata/
H A Dexonerateoutput.gff1 # (exonerate delimits GFF with [START|END] OF GFF DUMP)
2 # --- START OF GFF DUMP ---
16 #TODO need to understand why GFF features is from 11269 but Align is from 11270
20 # --- END OF GFF DUMP ---
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/
H A DREADME.mason_splicing22 Mason Splicing allows one to construct transcripts from a GFF/GTF file, a
46 We can use mason_splicing to simulate the transcript from a GFF file and its
64 Besides the path to the input FASTA and GFF file and the output FASTA file, we
67 The GFF type is the value of the third column (in both GFF and GTF) to filter
70 The GFF group-by key is the name of a key/tag from the last column of the
74 mason_splicing will read in the reference FASTA file and the GFF file. For
75 each group of GFF/GTF records with the same "group-by" key, it will generate
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Tools/
H A DGFF.t11 use_ok('Bio::Tools::GFF');
26 my $gff1out = Bio::Tools::GFF->new(-gff_version => 1, -file => ">$out1");
28 my $gff2out = Bio::Tools::GFF->new(-gff_version => 2, -file => ">$out2");
37 my $gff1in = Bio::Tools::GFF->new(-gff_version => 1, -file => "$out1");
39 my $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => "$out2");
58 $gff2in = Bio::Tools::GFF->new(-gff_version => 2, -file => test_input_file('hg16_chroms.gff'));
70 my $gffout = Bio::Tools::GFF->new(-fh => $str, -gff_version => 3);
86 my $in = Bio::Tools::GFF->new(-fh => $str,
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/SearchIO/Writer/
H A DGbrowseGFF.pm177 my $gffio = Bio::Tools::GFF->new(-gff_version => $format); # try to set it
183 my ($GFF,$cigar,$score);
288 my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
289 $GFF .= $feat->gff_string($formatter)."\n";
314 my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
315 $GFF .= $feat->gff_string($formatter)."\n";
354 my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
355 $GFF .= $feat->gff_string($formatter)."\n";
393 my $formatter = Bio::Tools::GFF->new(-gff_version => $format);
394 $GFF .= $feat->gff_string($formatter) ."\n";
[all …]
/dports/biology/biolibc/biolibc-0.2.1/Man/
H A Dbl_bed_gff_cmp.332 Compare the position of a BED feature to that of a GFF feature.
34 of the GFF feature, > 0 if the BED feature is downstream of the GFF
46 A value < 0 if the BED feature is upstream of the GFF feature
47 A value > 0 if the BED feature is downstream of the GFF feature
48 0 if the BED feature overlaps the GFF feature
/dports/news/husky-areafix/husky-areafix-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky/husky-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-fidoconf/husky-fidoconf-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-hpt/husky-hpt-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-huskylib/husky-huskylib-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-htick/husky-htick-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-sqpack/husky-sqpack-1.9.20191207/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/news/husky-smapi/husky-smapi-1.9.20191207,1/gff/
H A DREADME1 GFF - Graphical FIDO Front-end for GNU/Linux (Perl script)
2 Really GFF uses pseudo-graphic features of text console, not graphics.
5 GFF do not supported after 1999.
/dports/biology/velvet/velvet_1.2.10/contrib/columbus_scripts/
H A Denlarge_exons.pl5 use Bio::Tools::GFF;
7 my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
8 my $out = Bio::Tools::GFF->new(-fh => \*STDOUT, -gff_version => 2);
H A Dmerge_gtf_exons.pl5 use Bio::Tools::GFF;
7 my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
8 my $out = Bio::Tools::GFF->new(-fh => \*STDOUT, -gff_version => 2);
/dports/graphics/py-gdal/gdal-3.3.3/doc/source/drivers/raster/
H A Dgff.rst4 GFF -- Sandia National Laboratories GSAT File Format
7 .. shortname:: GFF
17 The GFF format was implemented based on the Matlab code provided by
25 The extension for GFF formats is .gff.
/dports/graphics/p5-Geo-GDAL/gdal-3.3.3/doc/source/drivers/raster/
H A Dgff.rst4 GFF -- Sandia National Laboratories GSAT File Format
7 .. shortname:: GFF
17 The GFF format was implemented based on the Matlab code provided by
25 The extension for GFF formats is .gff.
/dports/graphics/gdal/gdal-3.3.3/doc/source/drivers/raster/
H A Dgff.rst4 GFF -- Sandia National Laboratories GSAT File Format
7 .. shortname:: GFF
17 The GFF format was implemented based on the Matlab code provided by
25 The extension for GFF formats is .gff.
/dports/biology/gffread/gffread-0.12.7/examples/
H A DREADME.md3 GffRead can be used to simply read an annotation file in a GFF format, and print it in either GFF3 …
5 …so report some potential issues found in the input GFF records. The command line for such a quick …
20 GffRead can be used to generate a FASTA file with the DNA sequences for all transcripts in a GFF fi…
26 This also requires that every contig or chromosome name found in the 1st column of the input GFF fi…
/dports/biology/p5-BioPerl/BioPerl-1.7.7/examples/tools/
H A Dgb_to_gff.pl4 use Bio::Tools::GFF;
17 my $gffout = new Bio::Tools::GFF(-file => ">$fname" ,
/dports/biology/bedtools/bedtools2-2.30.0/docs/content/tools/
H A Dcomplement.rst16 covered by at least one interval in the input BED/GFF/VCF file.
30 bedtools complement -i <BED/GFF/VCF> -g <GENOME>
35 complementBed -i <BED/GFF/VCF> -g <GENOME>

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