{"issue":{"state":"open","created_at":"2011-11-15T12:09:20Z","updated_at":"2011-11-23T10:52:48Z","user":{"gravatar_id":"ceeee22eff014a93ef44a53f7adb1556","id":275483,"url":"https://api.github.com/users/yp","login":"yp","avatar_url":"https://secure.gravatar.com/avatar/ceeee22eff014a93ef44a53f7adb1556?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"comments":2,"body":"During the creation of the GTF file with all the isoforms (--extended-gtf), it reports:\r\n\r\n    Traceback (most recent call last):\r\n      File \"./bin/pintron\", line 935, in <module>\r\n        pintron_pipeline(options)\r\n      File \"./bin/pintron\", line 877, in pintron_pipeline\r\n        json2gtf(options.output_filename, options.extended_gtf_filename, options.genome_filename, options.gene, True)\r\n      File \"./bin/pintron\", line 280, in json2gtf\r\n        total_cds_length = isoform['CDS length'] -3 # Because the stop codon is outside the CDS\r\n    KeyError: 'CDS length'\r\n\r\nPIntron version: `v1.2.16`\r\nInput files: https://gist.github.com/d899905f5df10d1e9d30\r\nCommand-line: \r\n\r\n    ./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\r\n","assignee":{"gravatar_id":"eb20f809d9807c9685e13c31fa27f763","id":147768,"url":"https://api.github.com/users/gdv","login":"gdv","avatar_url":"https://secure.gravatar.com/avatar/eb20f809d9807c9685e13c31fa27f763?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"number":2,"id":2242632,"labels":[],"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"title":"Problem in GTF creation","closed_at":null,"html_url":"https://github.com/AlgoLab/PIntron/issues/2","milestone":null,"url":"https://api.github.com/repos/AlgoLab/PIntron/issues/2"},"action":"created","comment":{"created_at":"2011-11-23T10:52:48Z","updated_at":"2011-11-23T10:52:48Z","user":{"gravatar_id":"ceeee22eff014a93ef44a53f7adb1556","id":275483,"url":"https://api.github.com/users/yp","login":"yp","avatar_url":"https://secure.gravatar.com/avatar/ceeee22eff014a93ef44a53f7adb1556?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"body":"I think that the \"extended GTF\" file should include only the `exon` feature for the _not_ CDS-annotated isoforms and \"all\" the available features for the CDS-annotated isoforms (namely `exon`, `5UTR`, `start_codon`, `CDS`, `stop_codon`, and `3UTR`).","id":2847297,"url":"https://api.github.com/repos/AlgoLab/PIntron/issues/comments/2847297"}}