plastid.bin.findjuncs module

This script identify all the unique splice junctions in one or more transcript annotations, and exports these as a BED file with one splice junction per line Optionally, this script can also export junctions as a Tophat .juncs file.

If a splice junction appears multiple times (e.g. used by more than one transcript), only the first occurrence of the junction will be reported. Scores, if present, are exported unaltered in BED output.

Examples:

# identify splice junctions from a transcript annotation supplied in GTF2
# creates output file 'annotation.bed'
$ findjuncs my_annotation --annotation_format GTF2 \
            --annotation_files transcripts.gtf

# merge unique annotations from annotation.bed and newly_discovered.bed,
# export only unique junctions to 'merged_unique.bed'
$ findjuncs merged_unique --annotation_format BED \
            --annotation_files annotation.bed newly_discovered.bed

See also

plastid.bin.slidejuncs

Script that makes richer comparisons between discovered and annotated junctions, using genomic sequence and plastid.bin.crossmap results to classify junctions

plastid.bin.findjuncs.main(argv=['-T', '-E', '-b', 'html', '-d', '_build/doctrees', '-D', 'language=en', '.', '_build/html'])[source]

Command-line program

Parameters
argvlist, optional

A list of command-line arguments, which will be processed as if the script were called from the command line if main() is called directly.

Default: sys.argv[1:] (actually command-line arguments)