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