NAME
recs-tofasta
USAGE
Help from: --help-basic:
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
Help from: --help-keyspecs:
KEY SPECS
A key spec is short way of specifying a field with prefixes or regular
expressions, it may also be nested into hashes and arrays. Use a '/' to nest
into a hash and a '#NUM' to index into an array (i.e. #2)
An example is in order, take a record like this:
{"biz":["a","b","c"],"foo":{"bar 1":1},"zap":"blah1"}
{"biz":["a","b","c"],"foo":{"bar 1":2},"zap":"blah2"}
{"biz":["a","b","c"],"foo":{"bar 1":3},"zap":"blah3"}
In this case a key spec of 'foo/bar 1' would have the values 1,2, and 3 in
the respective records.
Similarly, 'biz/#0' would have the value of 'a' for all 3 records
You can also prefix key specs with '@' to engage the fuzzy matching logic
Fuzzy matching works like this in order, first key to match wins
1. Exact match ( eq )
2. Prefix match ( m/^/ )
3. Match anywehre in the key (m//)
So, in the above example '@b/#2', the 'b' portion would expand to 'biz' and 2
would be the index into the array, so all records would have the value of 'c'
Simiarly, @f/b would have values 1, 2, and 3
You can escape / with a \. For example, if you have a record:
{"foo/bar":2}
You can address that key with foo\/bar