Convert SAM/BAM files with transcript coordinates to SAM files with genomic coordinates
$ transcoord -h
usage: transcoord [-h] [-o OUT] [-t TAG_NAME] [--debug] [--version] gtf bam fasta
positional arguments:
gtf GTF file containing transcripts
bam SAM or BAM files aligned to transcriptome
fasta FASTA format assembly coresponding to GTF
optional arguments:
-h, --help show this help message and exit
-o OUT, --out OUT output file for genomic SAM (default: stdout)
-t TAG_NAME, --tag-name TAG_NAME
SAM tag name for storing transcript identifier. default: ZT
--debug enable debugging
--version display version number
Note: This is an incomplete work in progress script and you shouldn't rely on its output. I made this as a proof of concept, and never had time to finish. It currently runs very slowly and only handles reads that are mapped entirely within an exon.