deprecated.pl - Check modules and scripts for use of deprecated modules and methods, indicates presence in a file to STDERR. Optionally accepts new modules and adds them to a newly formatted deprecation file.
deprecated.pl [-d|--dir path ] [-v|--verbose] [-a|--depfile] [-n|--new] [-w|--write] [-o|--outfile] [-?|-h|--help]
Overides the default directories to check by one directory 'path' and all its subdirectories.
path from working directory that contains the DEPRECATED file.
New addition to the deprecation list; this should be in the form of 'Module,dep_release,remove_release,notes'. Notes should only be 40 chars long.
BioPerl version. This only appears to work correctly when using numerical versions (1.5.2 instead of 1.005002)
Write out new deprecation file to $outfile. If --new is used this is assumed.
Name of output file to write deprecation table to. DEPRECATED.NEW is the default name
Show the progress through files during the checking.
This help text.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
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Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Email cjfields-at-bioperl-dot-org
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.