Fasta manipulation

Extract chromosome sequences from FASTA file

The split_fasta.py utility extracts the sequences associated with individual chromosomes from one or more FASTA files.

Specifically, for each chromosome CHROM found in the input FASTA file, outputs a file called CHROM.fa containing just the sequence for that chromosome.

Sequences are identified as belonging to a specific chromosome by a line >CHROM.

Reorder FASTA file into karyotypic order

The reorder_fasta.py utility will reorder the chromosome records in a FASTA file into ‘karyotypic’ order, for example:

chr1
chr2
...
chr10
chr11

in contrast to standard alphanumeric sorting (e.g. chr1, chr10, chr11, chr2 etc).