Quickstart¶
This short HowTo guides you from downloading obogaf::parser
to make your first parsing with obogaf::parser
.
Installation¶
Please goto the Installation section and chose one of the shown ways to install obogaf::parser
(we suggest to use the Installation via Conda option).
Load obogaf::parser library¶
To load obogaf::parser
module, just type inside a Perl script use obogaf::parser
. More precisely, the header of your Perl script should be:
#!/usr/bin/perl
use strict;
use warnings;
use obogaf::parser;
... beginning of your perl code ...
To run the Perl script you can make it executable by typing chmod +x perl-script.pl
or by prefacing the script with the Perl interpreter (perl perl-script.pl
).
Your first parsing¶
Let us use obogaf::parser
to extract edges (in the form source-destination
) from the Gene Ontology (GO) obo file. Firstly we must download the GO obo file from the Gene Ontoloy website. Then we use obogaf::parser
to extract edges.
## perl shebang (unix)
#!/usr/bin/perl
## load the module
use obogaf::parser;
## download GO obo file
my $obofile= "gobasic.obo";
my $gobo= qx{wget --output-document=$obofile http://purl.obolibrary.org/obo/go/go-basic.obo};
print "GO obo file downloaded: done\n\n";
## extract and print GO edges
my $gores= obogaf::parser::build_edges($obofile);
print "${$gores}";
obogaf::parser
can do much more than that! Go to the Tutorial section to discover what this module can do! But first get a look to Installation section …