bed2fasta.py - get sequences from bed file¶
- Tags
Genomics Intervals Sequences Conversion BED FASTA
Purpose¶
This script outputs nucleotide sequences for intervals within a bed formatted file using a corresponding genome file.
Usage¶
A required input to bed2fasta.py is a cgat indexed genome. To obtain an idexed human reference genome we would type
- Example::
cat hg19.fasta | index_fasta.py hg19 > hg19.log
This file would then serve as the –genome-file when we wish to extract sequences from a bed formatted file.
For example we could now type:
cat in.bed | python bed2fasta.py --genome-file hg19 > out.fasta
Where we take a set of genomic intervals (e.g. from a human ChIP-seq experiment) and output their respective nucleotide sequences.
Type:
python bed2fasta.py --help
for command line help.
Command line options¶
usage: bed2fasta [-h] [-g GENOME_FILE] [-m {dust,dustmasker,softmask,none}]
[--output-mode {intervals,leftright,segments}]
[--min-sequence-length MIN_LENGTH]
[--max-sequence-length MAX_LENGTH]
[--extend-at {none,3,5,both,3only,5only}]
[--extend-by EXTEND_BY] [--use-strand] [--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]
bed2fasta: error: argument -?: expected one argument