Parsing codeml output

[Rodolfo Probst]

Dear PAML community,

I've been conducting ancestral sequence reconstructions using codeml and I was wondering if there is an easy way to parse the rst file. I would like to extract the ancestral sequences from the rst file and save them in another file in FASTA format. I've been struggling to parse the rst file, and any feedback or script would be highly appreciated!

Thank you,

Rodolfo

[Ziheng]

haha, i am of no use for this.  

can you write some python code to do it, or perhaps shell scripts are good enough.  

i think it takes about a day to learn basic commands, and another day or two to start programming.

best, ziheng

[Rodolfo Probst]

Hi Ziheng,

Thank you for your feedback! I solved the issue a while back with a quick python parser.

Best,

Rodolfo