bed2gff.py - convert bed to gff/gtf¶
- Tags
Genomics Intervals BED GFF Conversion
Purpose¶
This script converts a bed-formatted file to a gff or gtf-formatted file.
It aims to populate the appropriate fields in the gff file with columns in the bed file.
If --as-gtf
is set and a name column in the bed file is
present, its contents will be set as gene_id
and
transcript_id
. Otherwise, a numeric gene_id
or
transcript_id
will be set according to --id-format
.
Usage¶
Example:
# Preview input bed file
zcat tests/bed2gff.py/bed3/bed.gz | head
# Convert BED to GFF format
cgat bed2gff.py < tests/bed2gff.py/bed3/bed.gz > test1.gff
# View converted file (excluding logging information)
cat test1.gtf | grep -v "#" | head
chr1 |
bed |
exon |
501 |
1000 |
. |
. |
. |
gene_id “None”; transcript_id “None”; |
chr1 |
bed |
exon |
15001 |
16000 |
. |
. |
. |
gene_id “None”; transcript_id “None”; |
Example:
# Convert BED to GTF format
cgat bed2gff.py --as-gtf < tests/bed2gff.py/bed3/bed.gz > test2.gtf
# View converted file (excluding logging information)
cat test2.gtf | grep -v "#" | head
chr1 |
bed |
exon |
501 |
1000 |
. |
. |
. |
gene_id “00000001”; transcript_id “00000001”; |
chr1 |
bed |
exon |
15001 |
16000 |
. |
. |
. |
gene_id “00000002”; transcript_id “00000002”; |
Type:
cgat bed2gff.py --help
for command line help.
Command line options¶
usage: bed2gff [-h] [-a] [-f ID_FORMAT] [--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]
bed2gff: error: argument -?: expected one argument