Enveomics collection

Table.filter.pl

Extracts (and re-orders) a subset of rows from a raw table.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Perl.

§ Usage

Table.filter.pl [opts] in_file in_file > out_file

§ Arguments

Key

 -k integer  Column of the table to use as key to filter.

Sep

 -s string  String to use as separation between rows. By default, tabulation.

Inverse

 -i   If set, reports the inverse of the list (i.e., reports only rows absent in the list). Implies 'No re-order'.

Header

 -h   Keep first row of the table (header) untouched.

No re-order

 -n   The output has the same order of the table. By default, it prints in the order of the list.

List*

 in_file  List of IDs to extract.

Table*

 in_file  Table file containing the superset.

Subset*

 out_file  Table file to be created.

* Mandatory.