fasta2bed.py - segment sequences¶
- Tags
Genomics Sequences Intervals FASTA BED Conversion
Purpose¶
This script takes a genomic sequence in fasta format and applies various segmentation algorithms.
The methods implemented (--methods
) are:
- cpg
output all locations of cpg in the genome
- fixed-width-windows-gc
output fixed width windows of a certain size adding their G+C content as score
- gaps
ouput all locations of assembly gaps (blocks of N) in the genomic sequences
- ungapped
output ungapped locations in the genomic sequences
Usage¶
Type:
python fasta2bed.py --method=gap < in.fasta > out.bed
Type:
python fasta2bed.py --help
for command line help.
Command line options¶
usage: fasta2bed [-h] [--version]
[-m {fixed-width-windows-gc,cpg,windows-cpg,gaps,ungapped,windows}]
[-w WINDOW_SIZE] [-s WINDOW_SHIFT] [--min-cpg MIN_CPG]
[--min-interval-length MIN_LENGTH] [--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]
fasta2bed: error: argument -?: expected one argument