Updating categorize_ncRNAs.pl to run in parts
c_time() returns elapsed time in seconds, minutes, hours and days
Updating categorize_lncRNAs.pl to run in parts
Progress with categorize_lncRNAs.pl
Changing name of the script
Adding Cufflinks class code information to putative ncRNAs list
Antisense lncRNAs now are sure of having strand information
Committing today's progress
Committing today's progress
The code in current status seems to classify Cufflinks transcripts into LincRNAs, incs and concs, but need to work on including code to classify poncs. Ref: http://genome.cshlp.org/content/22/3/577.full
Adding stats to the output
Error messages spit more details
Seems like all categorizing functions of categorize_ncRNAs.pl are working properly. Need to verify it from UCSC...
Adding Set::IntervalTree by Benjamin Booth as it is needed by categorize_ncRNAs.pl
Removing debug code blocks from categorize_ncRNAs.pl
Adjusing code for Conc... Seems to be only piece in the puzzle remaining...
get_unique_features.pl now categorizes features as either intronic (i) or as intergenic (u)
Interval tree now only stores per chromosome
Interval tree does not like interpolated strings as id names. Fixing it
Fixing IO::Routine