gff2psl.py - convert from gff to psl¶
- Tags
Genomics Intervals GFF PSL Conversion
Purpose¶
This scripts converts from a gff formatted file to a psl formatted file. The output can be modified by the following command line options:
- --allow-duplicates
keep duplicate entries from gff/gtf input file
- --genome-file
restrict output to gff/gtf entries with contigs in fasta file
- --queries-tsv-file
restrict output to queries in fasta file
Usage¶
Example:
python gff2psl.py < in.gff > out.psl
Type:
python gff2psl.py --help
for command line help. genome-file
Command line options¶
usage: gff2psl [-h] [--is-gtf] [--no-header] [-g GENOME_FILE]
[--queries-tsv-file INPUT_FILENAME_QUERIES]
[--allow-duplicates] [--timeit TIMEIT_FILE]
[--timeit-name TIMEIT_NAME] [--timeit-header]
[--random-seed RANDOM_SEED] [-v LOGLEVEL]
[--log-config-filename LOG_CONFIG_FILENAME]
[--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
[-E STDERR] [-S STDOUT]
gff2psl: error: argument -?: expected one argument