FASTA input and output in place of TPF & AGP format files

sanger-tol / agp-tpf-utils

Code for manipulating AGP and TPF assembly files

MIT License

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FASTA input and output in place of TPF & AGP format files #6

Open jgrg opened 5 days ago

jgrg commented 5 days ago

Use FASTA sequence data input instead of TPF. Current script used: rapid_split.pl

Creation of FASTA output rather than TPF, so that curators don't have to run another script, might be nice to save an AGP alongside the FASTA. Current scripts used: rapid_join.pl or multi_join.py

pretext-to-tpf should take over naming of chromosomes.
Generate an AGP file instead of a TPF.
- Add mapping of PretextView scaffold numbers to chromosome names in AGP header

yumisims commented 4 days ago

Hi James, I'm not sure if this is the same issue that I addressed at the group meeting. I'd like the corrected AGP (based on the pretext AGP) to have the same autosome naming as the FASTA. Ideally, the pretext-to-tpf tool should take the pretext AGP and the correct autosome list and output the corrected AGP.

jgrg commented 4 days ago

No, that's different.

yumisims commented 4 days ago

No, that's different.

OK, thanks, just wondered if that can be achieved? and should I add in an issue?