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).