gffread

gff

conversion

validation

filtering

Description

Validate, filter, convert and perform various other operations on GFF files.

Inputs

Name	Type & Properties	Description
--input	file required	A reference file in either the GFF3, GFF2 or GTF format.
--chr_mapping -m	file	<chr_replace> is a name mapping table for converting reference sequence names, having this 2-column format: <original_ref_ID> <new_ref_ID>.
--seq_info -s	file	<seq_info.fsize> is a tab-delimited file providing this info for each of the mapped sequences: <seq-name> <seq-length> <seq-description> (useful for --description option with mRNA/EST/protein mappings).
--genome -g	file	Full path to a multi-fasta file with the genomic sequences for all input mappings, OR a directory with single-fasta files (one per genomic sequence, with file names matching sequence names).

Name

Type & Properties

--input

file

required

--chr_mapping

-m

file

--seq_info

-s

file

--genome

-g

file

Outputs

Name	Type & Properties	Description
--outfile -o	file required output	Write the output records into <outfile>.
--force_exons	boolean_true	Make sure that the lowest level GFF features are considered "exon" features.
--gene2exon	boolean_true	For single-line genes not parenting any transcripts, add an exon feature spanning the entire gene (treat it as a transcript).
--t_adopt	boolean_true	Try to find a parent gene overlapping/containing a transcript that does not have any explicit gene Parent.
--decode -D	boolean_true	Decode url encoded characters within attributes.
--merge_exons -Z	boolean_true	Merge very close exons into a single exon (when intron size<4).
--junctions -j	boolean_true	Output the junctions and the corresponding transcripts.
--spliced_exons -w	file output	Write a fasta file with spliced exons for each transcript.
--w_add	integer	For the --spliced_exons option, extract additional <N> bases both upstream and downstream of the transcript boundaries.
--w_nocds	boolean_true	For --spliced_exons, disable the output of CDS info in the FASTA file.
--spliced_cds -x	file	Write a fasta file with spliced CDS for each GFF transcript.
--tr_cds -y	file	Write a protein fasta file with the translation of CDS for each record.
--w_coords -W	boolean_true	For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline all the exon coordinates projected onto the spliced sequence.
--stop_dot -S	boolean_true	For --tr_cds option, use '*' instead of '.' as stop codon translation.
--id_version -L	boolean_true	Ensembl GTF to GFF3 conversion, adds version to IDs.
--trackname -t	string	Use <trackname> in the 2nd column of each GFF/GTF output line.
--gtf_output -T	boolean_true	Main output will be GTF instead of GFF3.
--bed	boolean_true	Output records in BED format instead of default GFF3.
--tlf	boolean_true	Output "transcript line format" which is like GFF but with exons and CDS related features stored as GFF attributes in the transcript feature line, like this: exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> <exons> is a comma-delimited list of exon_start-exon_end coordinates; <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>.
--table	string multiple	Output a simple tab delimited format instead of GFF, with columns having the values of GFF attributes given in <attrlist>; special pseudo-attributes (prefixed by @) are recognized: @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen If any of --spliced_exons/--tr_cds/--spliced_cds FASTA output files are enabled, the same fields (excluding @id) are appended to the definition line of corresponding FASTA records.
--expose_dups -E -v	boolean_true	Expose (warn about) duplicate transcript IDs and other potential problems with the given GFF/GTF records.

Name

Type & Properties

--outfile

-o

file

required

output

--force_exons

boolean_true

--gene2exon

boolean_true

--t_adopt

boolean_true

--decode

-D

boolean_true

--merge_exons

-Z

boolean_true

--junctions

-j

boolean_true

--spliced_exons

-w

file

output

--w_add

integer

--w_nocds

boolean_true

--spliced_cds

-x

file

--tr_cds

-y

file

--w_coords

-W

boolean_true

--stop_dot

-S

boolean_true

--id_version

-L

boolean_true

--trackname

-t

string

--gtf_output

-T

boolean_true

--bed

boolean_true

--tlf

boolean_true

--table

string

multiple

--expose_dups

-E

-v

boolean_true

Options

Name	Type & Properties	Description
--ids	file	Discard records/transcripts if their IDs are not listed in <IDs.lst>.
--nids	file	Discard records/transcripts if their IDs are listed in <IDs.lst>.
--maxintron -i	integer	Discard transcripts having an intron larger than <maxintron>.
--minlen -l	integer	Discard transcripts shorter than <minlen> bases.
--range -r	string	Only show transcripts overlapping coordinate range <start>..<end> (on chromosome/contig <chr>, strand <strand> if provided).
--strict_range -R	boolean_true	For --range option, discard all transcripts that are not fully contained within the given range.
--jmatch	string	Only output transcripts matching the given junction.
--no_single_exon -U	boolean_true	Discard single-exon transcripts.
--coding -C	boolean_true	Coding only: discard mRNAs that have no CDS features.
--nc	boolean_true	Non-coding only: discard mRNAs that have CDS features.
--ignore_locus	boolean_true	Discard locus features and attributes found in the input.
--description -A	boolean_true	Use the description field from <seq_info.fsize> and add it as the value for a 'descr' attribute to the GFF record.

Name

Type & Properties

--ids

file

--nids

file

--maxintron

-i

integer

--minlen

-l

integer

--range

-r

string

--strict_range

-R

boolean_true

--jmatch

string

--no_single_exon

-U

boolean_true

--coding

-C

boolean_true

--nc

boolean_true

--ignore_locus

boolean_true

--description

-A

boolean_true

Sorting

Name	Type & Properties	Description
--sort_alpha	boolean_true	Chromosomes (reference sequences) are sorted alphabetically.
--sort_by	file	Sort the reference sequences by the order in which their names are given in the <refseq.lst> file.

Name

Type & Properties

--sort_alpha

boolean_true

--sort_by

file

Misc options

Name	Type & Properties	Description
--keep_attrs -F	boolean_true	Keep all GFF attributes (for non-exon features).
--keep_exon_attrs	boolean_true	For -F option, do not attempt to reduce redundant exon/CDS attributes.
--no_exon_attrs -G	boolean_true	Do not keep exon attributes, move them to the transcript feature (for GFF3 output).
--attrs	string	Only output the GTF/GFF attributes listed in <attr-list> which is a comma delimited list of attribute names to.
--keep_genes	boolean_true	In transcript-only mode (default), also preserve gene records.
--keep_comments	boolean_true	For GFF3 input/output, try to preserve comments.
--process_other -O	boolean_true	process other non-transcript GFF records (by default non-transcript records are ignored).
--rm_stop_codons -V	boolean_true	Discard any mRNAs with CDS having in-frame stop codons (requires --genome).
--adj_cds_start -H	boolean_true	For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon.
--opposite_strand -B	boolean_true	For -V option, single-exon transcripts are also checked on the opposite strand (requires --genome).
--coding_status -P	boolean_true	Add transcript level GFF attributes about the coding status of each transcript, including partialness or in-frame stop codons (requires --genome).
--add_hasCDS	boolean_true	Add a "hasCDS" attribute with value "true" for transcripts that have CDS features.
--adj_stop	boolean_true	Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop coordinate if premature or downstream.
--rm_noncanon -N	boolean_true	Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus (i.e. not GT-AG, GC-AG or AT-AC).
--complete_cds -J	boolean_true	Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (i.e. only print mRNAs with a complete CDS).
--no_pseudo	boolean_true	Filter out records matching the 'pseudo' keyword.
--in_bed	boolean_true	Input should be parsed as BED format (automatic if the input filename ends with .bed*).
--in_tlf	boolean_true	Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option below); automatic if the input filename ends with .tlf).
--stream	boolean_true	Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must be grouped by transcript in the input data).

Name

Type & Properties

--keep_attrs

-F

boolean_true

--keep_exon_attrs

boolean_true

--no_exon_attrs

-G

boolean_true

--attrs

string

--keep_genes

boolean_true

--keep_comments

boolean_true

--process_other

-O

boolean_true

--rm_stop_codons

-V

boolean_true

--adj_cds_start

-H

boolean_true

--opposite_strand

-B

boolean_true

--coding_status

-P

boolean_true

--add_hasCDS

boolean_true

--adj_stop

boolean_true

--rm_noncanon

-N

boolean_true

--complete_cds

-J

boolean_true

--no_pseudo

boolean_true

--in_bed

boolean_true

--in_tlf

boolean_true

--stream

boolean_true

Clustering

Name	Type & Properties	Description
--merge -M	boolean_true	Cluster the input transcripts into loci, discarding "redundant" transcripts (those with the same exact introns and fully contained or equal boundaries).
--dupinfo -d	file	For --merge option, write duplication info to file <dupinfo>.
--cluster_only	boolean_true	Same as --merge but without discarding any of the "duplicate" transcripts, only create "locus" features.
--rm_redundant -K	boolean_true	For --merge option: also discard as redundant the shorter, fully contained transcripts (intron chains matching a part of the container).
--no_boundary -Q	boolean_true	For --merge option, no longer require boundary containment when assessing redundancy (can be combined with --rm_redundant); only introns have to match for multi-exon transcripts, and >=80% overlap for single-exon transcripts.
--no_overlap -Y	boolean_true	For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts, even on the opposite strand (can be combined with --rm_redudant).

Name

Type & Properties

--merge

-M

boolean_true

--dupinfo

-d

file

--cluster_only

boolean_true

--rm_redundant

-K

boolean_true

--no_boundary

-Q

boolean_true

--no_overlap

-Y

boolean_true

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
outfile: "$id.$key.outfile.gff"  
spliced_exons: "$id.$key.spliced_exons.fa"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.1 \  
  -main-script target/nextflow/gffread/main.nf \  
  -params-file params.yaml

gffread

Inputs

Outputs

Options

Sorting

Misc options

Clustering

Run this component

Relationships

Used by

Uses