split_otu_table.py fail, option-c

[alcedo76]

Option –c (COLUMN_RENAME_IDS) in this script fails to assign a new #SampleID in the output files. This new #SampleID comes from a column in the mapping file, however if you use a non-existent column you will get no errors or warnings, which indicates there is no usage of this field.

I’m using the development version of QIIME at commit b8685383ac3a2d863bb8494110dd1c657e1a44b8.

split_otu_table.py -i table.biom -m mapping_file.txt -f Diet -o split_table.biom -c Replacement

[gregcaporaso]

@antgonza or @josenavas, can one of you take a look into this? It looks like you added this feature.

[antgonza]

I added this functionality in this commit: https://github.com/qiime/qiime/commit/bdbbd0411c3f3379c48218bb2e31d6dd91cadcff#scripts/split_otu_table.py but it was erased by @gregcaporaso in this other commit: https://github.com/qiime/qiime/commit/19f0fe80526ea20861c838dc04c8ecb3b343b599#scripts/split_otu_table.py

Should we erase it from the script or add it? I believe this could still be useful.

[gregcaporaso]

@antgonza, can you comment on the usecase for this? I'm not sure why I removed it but I may have been confused about what it did and thought it wasn't relevant any more when I was cleaning up some documentation while creating qiime_test_data. Sorry!

[antgonza]

Sometimes when we do procrustes, this is one case but I can imagine others, we have one biom table that we split and then run procrustes on the splited tables; one specific case is body sites to see is their shifts within individuals is similar. In this case after split, we do not have a two column mapping file to relate the new split files and use with procrustes so we have to create it by hand. The solution was to pass -c column to replace the #SampleID column by the column of choice, in my example HOST_SUBJECT_ID to make it easier to relate. Additionally, as far as I can remember I also validated that the column was unique in the new split files.

[ElDeveloper]

Will we do anything with this issue for this release? Either remove the option from the script interface now or fix it? These issues are usually frustrating for some users.

[gregcaporaso]

Anyone have bandwidth to do it? I agree that it would be great, but not sure I can get to it myself.

[ElDeveloper]

If I'm understanding @antgonza's comment this functionality was already in place but was basically deleted right?. I'll try bringing that commit back to life ;)

[gregcaporaso]

It may be pretty different as I think the functionality was dropped in the transition to biom.

[ElDeveloper]

Ok, since that's the case and I don't think I can get that done today, would you be ok if I removed the option from the script interface as it is no longer used and then I open a new issue to bring back that feature?

[gregcaporaso]

Sounds good - want to just comment it out for now?

[ElDeveloper]

Sure.

El 10/05/2013, a las 16:05, Greg Caporaso notifications@github.com escribió:

Sounds good - want to just comment it out for now?

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