NAME

       refeature - Read a file representing a set of features, optionally

SYNOPSIS

       refeature [OPTIONS] <infile>

DESCRIPTION

       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).

OPTIONS

       --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.

refeature 1.4                                       May 2016                                        REFEATURE(1)