BrendelGroup/AEGeAn — pull request #18 by standage (2014-01-27 21:20:34+00:00)
Title: Update check-gff3 to report counts

Updated the script to report counts, both for feature types and for relationships. Here is the updated output.

```
$ cat /DATA/GROUP/standage/Hym-iLoci-2014-01-25/*.toplevel.gff3 \
/DATA/GROUP/jfdenton/ILOCI/gff3/annotwritten/solenopsis.gff3 \
/DATA/GROUP/jfdenton/ILOCI/gff3/annotwritten/harpegnathos.gff3 | \
~/Software/AEGeAn/data/scripts/check-gff3 2> ~/Software/AEGeAn/warnings

===== Types =====
CDS (743493 total, 11 top-level)
exon (843206 total, 0 top-level)
gene (95667 total, 95667 top-level)
mRNA (108186 total, 14 top-level)
match (128877 total, 128877 top-level)
ncRNA (5978 total, 0 top-level)
primary_transcript (172 total, 0 top-level)
rRNA (353 total, 353 top-level)
region (47343 total, 47343 top-level)
tRNA (1118 total, 748 top-level)
transcript (4242 total, 0 top-level)

===== Relationships (child --> parent) =====
CDS --> gene (161 occurrences)
CDS --> mRNA (743321 occurrences)
exon --> gene (6815 occurrences)
exon --> mRNA (780241 occurrences)
exon --> ncRNA (20341 occurrences)
exon --> primary_transcript (172 occurrences)
exon --> rRNA (353 occurrences)
exon --> tRNA (1118 occurrences)
exon --> transcript (34166 occurrences)
mRNA --> gene (108172 occurrences)
ncRNA --> gene (5978 occurrences)
primary_transcript --> gene (172 occurrences)
tRNA --> gene (370 occurrences)
transcript --> gene (4242 occurrences)
```