The usage and help documentation of
cut_up_fasta.py can be seen by
usage: - [-h] [-c CHUNK_SIZE] [-o OVERLAP_SIZE] [-m] [-b BEDFILE] contigs [contigs ...] Cut up fasta file in non-overlapping or overlapping parts of equal length. Optionally creates a BED-file where the cutup contigs are specified in terms of the original contigs. This can be used as input to concoct_coverage_table.py. positional arguments: contigs Fasta files with contigs optional arguments: -h, --help show this help message and exit -c CHUNK_SIZE, --chunk_size CHUNK_SIZE Chunk size -o OVERLAP_SIZE, --overlap_size OVERLAP_SIZE Overlap size -m, --merge_last Concatenate final part to last contig -b BEDFILE, --bedfile BEDFILE BEDfile to be created with exact regions of the original contigs corresponding to the newly created contigs
An example of how to run
cut_up_fasta.py original_contigs.fa -c 10000 -o 0 --merge_last -b contigs_10K.bed > contigs_10K.fa
This creates a fasta file and a BED file.
The fasta file
contigs_10K.fa contains the original contigs cut up into parts of length exactly 10K, except for the last contig part which is between 10K and 20K long.
The BED file
contigs_10K.bed contains a list of the contig parts created with coordinates in the original contigs.