Re: Extract sequences of CDS regions from Genbank formatted file
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Attached is a script I use for exactly this purpose. It also makes
a gff and some other stuff which might be of interest.
It makes use of Getopt::Long and assumes you will feed it --input or
- -i followed by the genbank file. If you forget (as I often do), it
will ask you for the genbank filename.
If you provide -o or --output, that will be the basename of the
following output files:
1. A gff of all entries
2. A gff of all the gene entries
3. A gff of CDS entries
4. A gff of the inter-cds regions
5. A fasta file of all the coding sequences
6. A fasta file of the coding sequences as peptide sequence.