For bioinformatics on genome annotation sets. Decompose a UCSC knownGenes file or Ensembl-derived GTF into transcript regions (i.e. exons, introns, UTRs and CDS).

This program takes either a knownGene.txt file for some genome from the UCSC genome browser or a GTF for transcripts from Ensembl and decomposes it into the following transcript regions:

• exons
• introns
• exons from coding transcripts
• introns from coding transcripts
• exons from noncoding transcripts
• introns from noncoding transcripts
• 5' UTRs for coding transcripts
• 5' UTRs plus start codon plus 27 nucleotides for coding transcripts (to calculate Kozak context & uORF overlap with start codon)
• CDS for coding transcripts
• 3' UTRs for coding transcripts

Invocation:

python extract_transcript_regions.py -i knownGenes.txt -o output_basename (--gtf || --ucsc)

For help enter extract_transcript_regions.py -h

Input:

UCSC knownGene.txt or Ensembl GTF

Output:

ten region files in .bed format

This is built on the Transcript class, which constructs transcript objects from the input file and computes metadata about the transcripts.

Notes:

• output is now in blockBedFormat by default (i.e. all exons dumped onto one line using block columns at the end)
• to change output format, change the value of useBlocks in extract_transcript_regions.py