EXTRACTTRANSCRIPTINFO.PY

NAME

extractTranscriptInfo.py - extracts information about transcripts from reference Fasta file

SYNOPSIS

extractTranscriptInfo.py [options] <inputFile> <outputFile>

DESCRIPTION

This program extracts information about transcripts from reference Fasta file. This is partially replaced by using SAM header, which however does not include information about transcript-gene grouping. Current version of parseAlignment extracts this information from a reference sequence file (making this script obsolete).

OPTIONS

-h, --help

show this help message and exit

-v, --verbose

Verbose output

-t TYPE, --type=TYPE

Type of file to parse: ensembl, cuff, other