Only one category under -c

[mnhuda]

Hello,

Most of the time I do not use subclass for LEfSe analysis. However, in your tool you have both class and subclass under “-c category1,category2”. I was wondering if there is any way I can put only one category. I do agree that a subcategory option is also useful sometimes.

Regards, Nazmul

[gblanchard4]

That's a great idea! I wrote this script for one of collaborators that needed two categories, but in reality you should be able to set as many as you need. I am out of the office and AFK (away from keyboard) until the 21st. I should totally be able to get that done for you then.

I don't really even remember what the output of the script is supposed to look like without being near my computer.

You can try putting the same category in twice. Let me know if that works for now.

[mnhuda]

Thank you so much. That will be awesome. I appreciate your kind help.

I had tried putting the same category twice as you suggested and it put the same category twice in the output file. I can delete one after opening the file in excel. However, it would be great if your software has the optional subclass option and thus allow us to put one or two category according to our need. Thank you again.

Regards, Nazmul

[gblanchard4]

@mnhuda I have updated the code to allow any number of categories (well 1 or more)! I cleaned things up a bit and made more comments. Thanks for the suggestion and let me know if you run into any more issues.

[mnhuda]

Hey, This version is not adding any variable/category from map file. I have tried both with one and two categories, but got the same result.

Additionally, your previous version of the software could clean the taxa file by removing “unassigned” and “Other”. Would you please put it back?

Additionally, please make the “space seperated list of categories” to “coma seperated list of categories” under “-c” like was in previous version. It will make the command format consistent with other QIIME command.

Thank you so much for your kind help.

Regards, Nazmul

[gblanchard4]

@mnhuda

This version is not adding any variable/category from map file. I have tried both with one and two categories, but got the same result.

That doesn't sound right, I have tested it on my end without any issues. Can you maybe post a subset of your data (or email me directly me@geneblanchard.com with it if you don't feel comfortable sharing on the web)

your previous version of the software could clean the taxa file by removing “unassigned” and “Other”. Would you please put it back?

Hmmmm... I don't see that anywhere in my old code, but I would be willing to put it in for you. It will probably cause issues though. Take this for instance:

Bacteria|Firmicutes|Bacilli|Bacillales
Bacteria|Firmicutes|Bacilli|Bacillales|Bacillaceae
Bacteria|Firmicutes|Bacilli|Bacillales|Other|Other

If I trim the Other|Other from the last entry how will you differentiate the first and last item from each other?

please make the “space seperated list of categories” to “coma seperated list of categories” under “-c” like was in previous version. It will make the command format consistent with other QIIME command.

I changed it back over to commas for you

[gblanchard4]

I have added the --clean method to the script that will remove anything with the "Other" classification and add its abundances to the lowest taxa level match. i.e.

Bacteria|Firmicutes|Bacilli|Bacillales    0.0    0.5    0.0    0.5
Bacteria|Firmicutes|Bacilli|Bacillales|Other|Other    0.0    0.0    0.5    0.5

would become

Bacteria|Firmicutes|Bacilli|Bacillales    0.0    0.5    0.5    1.0

As far as unclassified reads, I don't have any test data with that in there. Can you show me an example of how it is represented in your data?

[mnhuda]

It is working perfectly on my laptop. Probably I have done something wrong on my Lab pc. Sorry about this.

Thank you for the cleaning option.

Please see your inbox for a portion of my data.

Regards, Nazmul