cnic-proteomics / isanxot Goto Github PK

• New interface for the RELS CREATOR module.
• The Program accepts the whole task-table, read one time the input file, and then, execute each row in parallel internally.

Dear Jose,
I find this software very interesting and I'm trying to use it on my TMT proteomics data. I am trying to use MaxQuant output file: msmsScans.txt as described in the documentation. I am not sure what to do at the stage of indicating identifiers (my background is strictly genomic and transcriptomic with some basic downstream proteomics dataviz, however I might be missing something here).

after trying to create adapted input file, I am getting the error below.

`CREATEIDQ - 35636 - 11/04/2023 07:12:14 PM - INFO - executing CREATE_IDQ module ---
CREATEIDQ - 35636 - 11/04/2023 07:12:14 PM - INFO - reading the experiment task-table
CREATEIDQ - 35636 - 11/04/2023 07:12:14 PM - INFO - processing the input file: read, add exp
CREATEIDQ - 35636 - 11/04/2023 07:12:22 PM - INFO - reading the level task-table
CREATEIDQ - 35636 - 11/04/2023 07:12:22 PM - INFO - adding level identifiers
Traceback (most recent call last):
File "D:\Programs\iSanXoT\resources\exec\python-3.9.7-win-x64\lib\site-packages\pandas\core\indexes\base.py", line 3361, in get_loc
return self._engine.get_loc(casted_key)
File "pandas_libs\index.pyx", line 76, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc
File "pandas_libs\hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas_libs\hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'label_name'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "D:\Programs\iSanXoT\resources\src\cmds\createIDq.py", line 375, in
main(sys.argv[1:])
File "D:\Programs\iSanXoT\resources\src\cmds\createIDq.py", line 205, in main
df = add_levelids(df, indata)
File "D:\Programs\iSanXoT\resources\src\cmds\createIDq.py", line 81, in add_levelids
ll = list(indata['label_name'])
File "D:\Programs\iSanXoT\resources\exec\python-3.9.7-win-x64\lib\site-packages\pandas\core\frame.py", line 3458, in getitem
indexer = self.columns.get_loc(key)
File "D:\Programs\iSanXoT\resources\exec\python-3.9.7-win-x64\lib\site-packages\pandas\core\indexes\base.py", line 3363, in get_loc
raise KeyError(key) from err
KeyError: 'label_name'`

• AddQuant adaptor has to accept the TMT16 and TMT18 the reporter ions

• ProteinAssigner adaptor has to accept the FASTA and Regexp parameters.

• The core of workflow must to accepts huge number of samples.

• Reduce the times in the SanXoTSieve program.

Improve the programs to accept the whole task-table, read one time the input file, and then, execute each row in parallel internally.

• PCA
• Limma
• String
• Represent the Sanson graph in iSanXoT.
• With clicks in the image of Sanson, create the Sigmoides of sigmoides.