extract-transcript-regions

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. 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).

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

Usage

./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)