check_URLs.pl - validate URLs located in module code and POD
check_URLs.pl [-d|--dir path] [-v|--verbose] [-?|-h|--help]
Checks code and POD of all bioperl-live modules for URLs, and validates them.
Output is a series of lines containing two fields, tab separated. The first field is the file with the bad URL, the second is the URL itself.
The whole URL is not retrieved, only a HTTP "HEAD" request is done to see if the URL exists on the server. The request is done using LWP::Simple so the http_proxy environmental variable will be honoured.
The URL parsing may not be perfect - although I use the Regexp::Common::URI module, I have to manually clean up some URLs which are embedded in Perl strings to convert the matched URL to a more probable real world URL, e.g. most URLs don\'t end in "'," or ")" :-)
Overides the default directory to recursively look for .pm file (Default is '../Bio')
Show the progress through files during the POD 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.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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: torsten-dot-seemann-at-infotech-dot-monash-dot-edu-dot-au
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.