NAME
tofasta
USAGE
Usage: recs-tofasta <options> [files]
Outputs a FASTA-formatted sequence for each record.
By default the keys "id", "description", and "sequence" are used to build the
FASTA format. These defaults match up with what recs-fromfasta produces. The
special key name "NONE" may be used to indicate that no key should be used,
disabling the defaults. Note that specifying NONE for --id will cause any --
description to appear with a space between it and the line's ">", unless --
passthru is also used.
Arguments:
--id|-i <keyspec> Record field to use for the sequence id
--description|-d <keyspec> Record field to use for the sequence description
--sequence|-s <keyspec> Record field to use for the sequence itself
--width|w <#> Format sequence blocks to # characters wide
--oneline Format sequences on a single long line
--passthru Pass through nucleotides unformatted
--filename-key|fk <keyspec> Add a key with the source filename (if no
filename is applicable will put NONE)
Help Options:
--help-all Output all help for this script
--help This help screen
--help-keys Help on keygroups and keyspecs
--help-keyspecs Help on keyspecs, a way to index deeply and with regexes
Examples:
# Remove gaps from a fasta file
recs-fromfasta seqs.fa | recs-xform '{{sequence}} =~ s/-//g' | recs-tofasta > seqs-nogaps.fa