AlgoLab/PIntron — Issue #2: Problem in GTF creation
Author: yp
Created: 2011-11-15 12:09:20+00:00
State: open

During the creation of the GTF file with all the isoforms (--extended-gtf), it reports:

Traceback (most recent call last):
File "./bin/pintron", line 935, in
pintron_pipeline(options)
File "./bin/pintron", line 877, in pintron_pipeline
json2gtf(options.output_filename, options.extended_gtf_filename, options.genome_filename, options.gene, True)
File "./bin/pintron", line 280, in json2gtf
total_cds_length = isoform['CDS length'] -3 # Because the stop codon is outside the CDS
KeyError: 'CDS length'

PIntron version: `v1.2.16`
Input files: https://gist.github.com/d899905f5df10d1e9d30
Command-line:

./bin/pintron --bin-dir=./bin -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=ABO --output=pintron-full-output.json --gtf=pintron-cds-annotated-isoforms.gtf --extended-gtf=pintron-all-isoforms.gtf --logfile=pintron-pipeline-log.txt --general-logfile=pintron-log.txt