Export a file with transmembrane regions
Closed this issue · 12 comments
For Snezhka. See helpdesk ticket #6851
On Wednesday 10 April 2019 at 00:14:46, Oliferenko, Snezhana via RT wrote:
Ideally, I would love to have a tab-delimited text file, with ORF names, full
ORF sequences, transmembrane region coordinates and the actual sequences of
the transmembrane regions. In case of multi-spanning membrane proteins, I
figure the coordinates/TM sequences could be separated by a comma or a
semicolon.
maybe
ID_tm_1_coordinate_coordinate
HHHHLLLLL
ID_tm_2_coordinate_coordinate
LLLHHHHH
so it would end up as standard fasta, with info about position and we could make it available
A tab delimited, one line per gene file would probably be easier to parse. But we could have more than one file in different formats if we wanted to.
OK let's make 2 files, fasta might be useful is people actually want to use the sequence in tools.
Will point Snezhka to this ticket to see if either or both are what she wants
housekeeping note: I have merged helpdesk ticket 6851 into 6850
Dear Val,
Both files would be great, thank you!!
Snezhka
I've had a go at this. For now it's in the nightly_update directory. We need to decide where in the FTP site it should live long term.
ftp://ftp.pombase.org/nightly_update/misc/transmembrane_domain_coords_and_seqs.tsv
Add to protein datasets
https://www.pombase.org/downloads/protein-datasets
and copy to
ftp://ftp.pombase.org/pombe/Protein_data/
?
The file will be in ftp://ftp.pombase.org/pombe/Protein_data/ after the next load.
The file will be in ftp://ftp.pombase.org/pombe/Protein_data/ after the next load.
I just looked there, and I don't see the new file. I'll add a link to https://www.pombase.org/downloads/protein-datasets once it's in its new ftp home.
I can see it: ftp://ftp.pombase.org/pombe/Protein_data/transmembrane_domain_coords_and_seqs.tsv
and now I can see it too .... coulda sworn it wasn't there yesterday (but I may be losing it)