compare-graphs.pl
compare-graphs.pl --file_1 go/ontology/old_gene_ontology.obo --file_2 go/ontology/gene_ontology.obo -s goslim_generic -o results.txt
# must supply these arguments... or else! # INPUT -f1 || --file_1 /path/to/<file_name> "old" ontology file -f2 || --file_2 /path/to/<file_2_name> "new" ontology file
# OUTPUT -o || --output /path/to/<file_name> output file for results
# SUBSET -s || --subset <subset_name> subset to use for graph-based comparisons
# optional args
-v || --verbose prints various messages
Compares two OBO files and records the differences between them. These differences include:
* new terms * term merges * term obsoletions * changes to term content, such as addition, removal or editing of features like synonyms, xrefs, comments, def, etc.. * term movements into or out of the subset designated by the subset option
At present, only term differences are recorded in detail, although this could presumably be extended to other stanza types in an ontology file. The comparison is based on creating hashes of term stanza data, mainly because hashes are more tractable than objects.
input: a multi-line block of text (preferably an OBO format stanza!) output: ref to an array with the following removed - empty lines - lines starting with "id: ", "[", and "...]" - trailing whitespace
the array is sorted
input: array ref containing ": " separated tag-value pairs output: lines in the array split up by ": " and put into a hash of the form key-[array of values]
input: two hashes of arrays regex a regular expression for hash keys to ignore
output: hash of differences in the form {hash key}{ f1 => number of values unique to f1, f2 => number of values unique to f2 }
2 POD Errors
The following errors were encountered while parsing the POD:
=cut found outside a pod block. Skipping to next block.
To install GOBO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GOBO
CPAN shell
perl -MCPAN -e shell install GOBO
For more information on module installation, please visit the detailed CPAN module installation guide.