recs-tofasta
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. 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
App::RecordStream::Bio
To install App::RecordStream::Bio, copy and paste the appropriate command in to your terminal.
cpanm
cpanm App::RecordStream::Bio
CPAN shell
perl -MCPAN -e shell install App::RecordStream::Bio
For more information on module installation, please visit the detailed CPAN module installation guide.