Comparison of GO Terms between list

[BioinformaNicks]

Dear authors,

I would like to ask for an example of using compare_gos.py to compare occurences of GO ID's between two different sets/lists.

I have a table like this for example:

Protein \t GO ID \t Function
X \t GO:0005737 \t cytoplasm

And a similar one for another condition. How do I compare whether certain GO ID's are enriched in comparison to the other condition?

[dvklopfenstein]

Thank you for taking the time to contact us and for the great question. Other user's will surely benefit from our answering your question. I will add a link in the README.md to this issue so they can see how to run it.

[dvklopfenstein]

Here is an example that you can run if you clone the goatools repo:

$ scripts/compare_gos.py data/compare_gos/tat_gos_simple1.tsv data/compare_gos/tat_gos_simple2.tsv

XX GO:0008150 BP 29210 D00  biological_process
XX GO:0065007 BP 12884 D01  biological regulation
XX GO:0050789 BP 11559 D02  regulation of biological process
XX GO:0050794 BP  8746 D03  regulation of cellular process
X. GO:0048519 BP  3641 D03  negative regulation of biological process
.X GO:0048518 BP  3519 D03  positive regulation of biological process
X. GO:0048523 BP  2662 D04  negative regulation of cellular process

# Marker keys:
#     X -> GO is present in tat_gos_simple1
#     X -> GO is present in tat_gos_simple2

[dvklopfenstein]

Your file format should work just fine. Here is a sample. GO IDs in i162a.tsv and i162b.tsv will be compared:

Contents of i162a.tsv

Protein \t GO ID \t Function
X \t GO:0005737 \t cytoplasm
X \t GO:0048523 \t cytoplasm

Contents of i162b.tsv

Protein \t GO ID \t Function
X \t GO:0005737 \t cytoplasm
X \t GO:0048518 \t cytoplasm

Run:

$ scripts/compare_gos.py i162a.tsv i162b.tsv
.X GO:0048518 BP  3519 D03  positive regulation of biological process
X. GO:0048523 BP  2662 D04  negative regulation of cellular process
XX GO:0005737 CC  1200 D02  cytoplasm

# Marker keys:
#     X -> GO is present in i162a
#     X -> GO is present in i162b

[dvklopfenstein]

The compare_gos script picks up all GO IDs on a line using regex.

Lines beginning with # are considered comments and are ignored, even if they contain GO IDs.

[Habush]

Thanks for creating this script and the library, it's really helpful. Is there a way to save the output of the comparison into a format that can be imported from another such as tsv, csv..etc?

EDIT: I found the solution by going through the script. I can use the --xlsx option to output as an excel file.

[dvklopfenstein]

Thank you so much for your interest in GOA Tools and for taking your time to write us. I would like to add a tsv format too. I am putting this on our TODO list.

Please let us know any more information that might be relevant to this issue or your thoughts about any specific features or implementations.

[tanghaibao]

Issue appears to be resolved with --xlsx option as reported.