Creates functional annotation of complete genome based on features on GFF file.

Reports coding-sequence (CDS) and untranslated-regions (UTR) and extracts features such as introns, intergenic space, TSSs and promoters. It also distinguishes between 5' and 3' UTRs.

Promoters and intergenic space are annotated dynamically based on a specified promoter size but rezisable to fit genome boundaries and small intergenic space. This can account for the occurence of operons, annotating intergenic space within operons accordingly.

python annotateFromGFF.py [OPTIONS] file.gff chrmSizes.tsv > annotation.bed

gff - GFF file with annotation.

chrmFile - Tab-delimited file with sizes of each chromossome (chr:size).

-o, --outfile - Specifies the name of the output file. If not specified, will output to stdout.

-p, --promoterSize - Average size of promoter elements. Dynamically resizable.

-op, --operons - Consider operons. In this mode, the promoters and TSSs of consecutive genes in the same orientation separated by less than the distance specified by --operonDistance will not be annotated, and this distance is annotated as intergenic space.

--operonDistance - Distance between genes to classify as belonging to same operon.

-l, --logfile - Specify the name of the log file.

-s - Silent behaviour. Don't make log file.

Promoters are defined as a region upstream of transcription start sites (TSSs) by a fixed length (-p argument) but are resized to less if that distance would overlap a chromossome boundary or other gene.

Intergenic regions are resized accordingly to the complementary space between two genes minus the promoter space.

If considering operons (option --operons), intergenic space within operons will be annotated accordingly, excluding promoter and TSS annotations within operons.