link broken: inparanoid

[sinanshi]

broken link: http://inparanoid.cgb.ki.se/download/current/sqltables/
https://github.com/Bahler-Lab/yogy/blob/master/YogiUp/run_db.csh#L40

[dbitton]

what the old file looks like?

[sinanshi]

They have a list of files called inparanoid_files.txt. You get something like this,

sqltable.M.musculus.fa-P.trichocarpa.fa
sqltable.M.mulatta.fa-P.troglodytes.fa
sqltable.A.thaliana.fa-M.musculus.fa
sqltable.A.thaliana.fa-T.nigroviridis.fa
sqltable.D.melanogaster.fa-D.rerio.fa
sqltable.S.purpuratus.fa-T.nigroviridis.fa

files are like this,

1       2740    C.hominis.fa    1.000   Chro.30328      100%
1       2740    Y.lipolytica.fa 1.000   YALI0C10648g    100%
2       1617    C.hominis.fa    1.000   Chro.30301      100%
2       1617    Y.lipolytica.fa 1.000   YALI0C16566g    100%
3       1239    C.hominis.fa    1.000   Chro.80425      100%
3       1239    Y.lipolytica.fa 1.000   YALI0C11407g    100%
4       1116    C.hominis.fa    1.000   Chro.60382      100%
4       1116    Y.lipolytica.fa 1.000   YALI0C22550g    100%
5       1049    C.hominis.fa    1.000   Chro.80341      100%
5       1049    Y.lipolytica.fa 1.000   YALI0A00352g    100%
5       1049    Y.lipolytica.fa 0.588   YALI0A20152g
6       1025    C.hominis.fa    1.000   Chro.10043      100%
6       1025    Y.lipolytica.fa 1.000   YALI0F12155g    100%
7       923     C.hominis.fa    1.000   Chro.80150      100%
7       923     Y.lipolytica.fa 1.000   YALI0A17127g    100%
8       913     C.hominis.fa    1.000   Chro.20010      100%
8       913     Y.lipolytica.fa 1.000   YALI0D08184g    99%
8       913     Y.lipolytica.fa 0.846   YALI0F25289g
8       913     Y.lipolytica.fa 0.817   YALI0E35046g
8       913     Y.lipolytica.fa 0.739   YALI0D22352g
9       891     C.hominis.fa    1.000   Chro.60546      100%
9       891     Y.lipolytica.fa 1.000   YALI0B20724g    100%
10      854     C.hominis.fa    1.000   Chro.20293      100%
10      854     Y.lipolytica.fa 1.000   YALI0B13904g    100%
11      852     C.hominis.fa    1.000   Chro.30427      100%
11      852     Y.lipolytica.fa 1.000   YALI0C07953g    100%
12      846     C.hominis.fa    1.000   Chro.60284      100%
12      846     Y.lipolytica.fa 1.000   YALI0F04169g    100%
13      842     C.hominis.fa    1.000   Chro.30434      100%
13      842     Y.lipolytica.fa 1.000   YALI0A00264g    100%
14      767     C.hominis.fa    1.000   Chro.10119      100%
14      767     Y.lipolytica.fa 1.000   YALI0A17941g    100%
15      755     C.hominis.fa    1.000   Chro.30389      100%
15      755     Y.lipolytica.fa 1.000   YALI0C17347g    99%
16      753     C.hominis.fa    1.000   Chro.80361      100%
16      753     Y.lipolytica.fa 1.000   YALI0F20218g    100%
17      753     C.hominis.fa    1.000   Chro.80294      100%
17      753     Y.lipolytica.fa 1.000   YALI0D12210g    99%
18      735     C.hominis.fa    1.000   Chro.80471      100%
18      735     Y.lipolytica.fa 1.000   YALI0B15642g    99%
19      725     C.hominis.fa    1.000   Chro.30216      100%

Files can be found on the old server /home/sk11/load2/inptables/inparanoid.sbc.su.se/download/7.0_current/

[dbitton]

could you trace it here?
http://inparanoid.sbc.su.se/download/current/

[sinanshi]

I found them.
http://inparanoid.sbc.su.se/download/current/Orthologs_other_formats/A.aegypti/
You have to download the .tar.gz file first, extract them and you can find the table in it. I guess we have make this by ourself.

[sinanshi]

I'm still downloading the files. But they are too many. I don't know if it is due to the recent update. There are 4959 files in the old folder, while in for the new data, only counting for entries starting with A, we have already 5409 files. It means that we can expect the number of files will be around 25 time more than the original one. Does that make sence?

[dbitton]

mmmm not sure, maybe not all files are needed.....

[sinanshi]

It has been already one hour since I started downloading, and now it's still at B. We can expect a 10 hours downloading time and around 20-30 Gb storage.

[sinanshi]

Or..., we can use the old data, which can be found here,
http://inparanoid.sbc.su.se/download/old_versions/data_7.0/

This is exactely the same data as the old one.

[dbitton]

no, the whole point is to update...