I wrote a parser for OpenPyCR which interprets "Naturally Written" programs and converts them to the YAML used by the device. So, programs are a series of key-colon-value-newline headers for data like name, lid temp, etc, followed by iterations-colon blocks, each of which contains one or more statements of time @ temp - description lines.
Or, for a direct example (from memory):
Title: My best program
Lid: 95°C
1x:
600s @ 95°C; Burn-in
35x:
20s @ 95°C; Melt
12s @ 60°C; Anneal
30s @ 72°C; Extend
1x:
1s @ 15°C; Cool it!
...the parser could probably use rewriting, I've learned much of Python since. An *actual* tokenising parser would be superfluous but maybe cleaner: mine used string methods and was line-wise / stateful.
From: Horea Christian <h.chr@mail.ru>
Date: Wed, May 13, 2015 at 6:38 AM
Subject: [Biopython] Thermocycler program file format(ting)
To: biopython@mailman.open-bio.org
I would like to store my Thermocycler (pcr) programs on my server to better keep track of them. Do you know any good format/style to do that in? does biopythonhave any thermocycler program objects?
Right now I was thinking of saving this in a normal .csv file, but the entire iterative aspect of PCR seems difficult for me to convey in a concise matter in a .csv file. Would you have any suggestions?
Best Regards,
Christian
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.
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