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

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

For help enter extract_transcript_regions.py -h

UCSC knownGene.txt or Ensembl GTF. For this to work properly the knownGenes or input GTF must define the CDS either using thickStart/thickEnd (knownGenes) or with CDS/start_codon/stop_codon directives (GTF).

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.

• 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

./extract_transcript_regions.py -h 

usage: extract_transcript_regions.py [-h] -i INPUT -o OUTPUT [--ucsc] [--gtf]

Create transcript regions (5' UTR/CDS/3'UTR etc) from knownGenes or a GTF

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input filename
  -o OUTPUT, --output OUTPUT
                        output basename
  --ucsc                Read from a UCSC knownGenes formatted file (BED)
  --gtf                 Read from a GTF (only tested with Ensembl GTFs)