AlgoLab/PIntron — Issue #12: Execution aborted with "KeyError: 'delimiter'"
Author: yp
Created: 2012-01-31 15:04:27+00:00
State: open
Labels: bug

The execution of PIntron aborts with the following error message while processing gene AAMP:

[INFO ] 2012-01-31 15:53:03,418 - STEP 9: Saving outputs...
Traceback (most recent call last):
File "./bin/pintron", line 980, in
pintron_pipeline(options)
File "./bin/pintron", line 918, in pintron_pipeline
json2gtf(options.output_filename, options.gtf_filename, options.genome_filename, options.gene, False)
File "./bin/pintron", line 383, in json2gtf
". Found " + data_strand[p]['codon'] + " instead of " +
KeyError: 'delimiter'

PIntron version: `v1.2.25-4-g27957e6`
Input files: https://gist.github.com/1eca1c27866a95d754c6
Command-line:

./bin/pintron --bin-dir=./bin/ -k --genomic=genomic.txt --EST=ests.txt --organism=human --gene=AAMP --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