refeature - Read a file representing a set of features,
optionally
refeature [OPTIONS] <infile>
Read a file representing a set of features, optionally alter the
set in one or more of several possible ways, then output it in the desired
format. Input and output formats may be GFF, BED, or genepred.
The input format is recognized automatically, but autorecognition
requires a 'seekable' input stream (e.g., an actual file rather than a pipe
from stdin).
--include-only, -i <types> Include only
features of the specified types (comma-delimited list); filter out
everything else.
--include-groups, -l <file>
- Include only groups whose names are listed in the specified file. Group
names in file must be delimited by white-space (can be on any number of
lines).
--sort, -s
- Sort features primarily by start position and secondarily by end position
(usually has desired effect in case of short overlapping features, e.g.,
start & stop codons). Features will be sorted both across groups and
within groups, but members of a group will be kept together.
--unique, -u
- Ensures that output contains no overlapping groups (or subgroups, if
-e). If groups overlap, the one with the highest score (if
available) or longest length (if no score) is kept and others are
discarded. Warning: long UTRs can have undesirable results; filter out UTR
exons to avoid.
--groupby, -g <tag> Group features
according to specified tag (default "transcript_id")
--exongroup, -e <tag>
- Sub-group features into contiguous sets, and define sub-groups using
specified tag (e.g., "exon_id"). Can be used to group the
features describing individual exons, e.g., each CDS and its flanking
splice sites. Only features in the same major group will be included in
the same minor group (e.g., exons of the same transcript).
--fix-start-stop, -f
- Ensure that CDS features include start codons and exclude stop codons, as
required by the GTF2 standard. Assumes at most one start_codon and at most
one stop_codon per group.
--add-utrs, -U
- Create UTR features for portions of exons outside CDS (only useful with
GFF output; features must be grouped at level of transcript).
--add-introns, -I
- Create intron features between exons (only useful with GFF output;
features must be grouped at level of transcript).
--add-signals, -S Adds features for start and
stop codons and 3' and 5' splice sites (only useful with GFF output;
features must be grouped at level of transcript). Start and stop codons will
be added as required by the GTF2 standard (--fix-start-stop is not
necessary). Warning: does not correctly handle case of splice site in middle
of start or stop codon.
--output, -o gff|bed|genepred|wig Output format
(default gff). Note that wig output is fixedStep can only be used if all
elements have a score and are of equal length.
--simplebed, -b
- (for use with --output bed) Create a separate line for each feature
in bed output (by default, all features of a group are described by a
single line).
--discards, -d <fname>
- Write any discarded features to specified file.
--help, -h Print this help message.