ORFtrack parameters#
Mandatory
-fna
nucleotide fasta file of the genome whose ORFs are to annotate
-gff
gff annotation file
Optional
-h, --help
shows the help and exits
--show-types
prints all genomic features annotated in the input gff file
--show-chrs
prints all the seqID (usually corresponding to chromosome or contig ID) present in the input gff file
-chr
list of seqID to be treated by ORFtrack (i.e. column #1
of the gff file - generally chromosome or contig ID).
ID must be separated by a space: -chr NC_001148.4 NC_001139.3
In this case, ORFtrack will not treat the entire genome, but
the following seqID NC_001148.4 NC_001139.3. We recommend using this option
when dealing with large genomes in order to distribute the calculations on
several CPUs (one per (subset of) seqID).
-orf_len
Minimal number of nucleotides between two
consecutive STOP codons to define an ORF (default: 60 nucleotides)
(see the ORF definition section for more details).
-co_ovp
Minimal fraction of the ORF length that overlaps a genomic feature
to annotate the ORF as overlapping it
(default: 0.70). (see the Overlap section for more details).
-types_only
Genomic feature(s) considered for the annotation step ('CDS' is
included by default). If there are several genomic features
to be considered, they must be given separated by a space. Noncoding ORFs are annotated as
intergenic (when they do not overlap any feature) or overlapping (when
they overlap a given genomic feature). The "overlapping" status
directly derives from the genomic features considered for the annotation
step. For example, if the user specifies with the "types_only" option, the features
"tRNA" and "rRNA" (CDS are included by default), all ORFs that overlap another
genomic feature (i.e. different from tRNA, rRNA, or CDS) will be annotated as
noncoding intergenic ORFs. If no genomic feature is indicated, noncoding ORFs that overlap
any genomic feature annotated in the original gff file will be annotated
as noncoding ORF overlapping the corresponding genomic feature. Nevertheless,
the resulting ORFs can be treated specifically (grouped according to their annotation
for example) with ORFget afterwards
(see the ORFget section for more details).
-types_except
Genomic feature(s) not to be considered for the annotation step
('gene' and 'exon' not considered by default). If there are several genomic features
to be considered, they must be given separated by a space. Noncoding ORFs are annotated as
intergenic (when they do not overlap any feature) or overlapping (when
they overlap a given genomic feature). The "overlapping" status
directly derives from the genomic features considered for the annotation
step. For example, when specifying with the "types_except" option,
the features "telomer" and "centromer" ('gene' and 'exon' not considered by
default), if an ORF overlaps a "telomer", "centromer", "gene" and/or "exon",
the overlap will not be considered and the ORF will be annotated as intergenic or
overalapping another genomic feature if there is another genomic feature
in the same region (e.g. an ORF that overlaps at the same time a gene and a
tRNA will be annotated as overlapping a tRNA since the gene is not considered
for the ORF annotation). If no genomic feature is indicated, noncoding ORFs that overlap
any genomic feature annotated in the original gff file will be annotated
as noncoding ORF overlapping the corresponding genomic feature. Nevertheless,
the resulting ORFs can be treated specifically (grouped according to their annotation
for example) with ORFget afterwards
(see the ORFget section for more details).