ammarcsj
commented
2 weeks ago Hi, thanks for the feedback! It seems that DIA-NN changed some output table columns in the new version. I will adapt to this in the next release. Does setting to "DIA-NN precursor.tsv" still work?
Additionally, you can save the reformatted file you have now with the ending .aq_reformat.tsv directLFQ will then recognise that it is already in the correct format. In the new release I will add an option of setting "directlfq_format" to the GUI (currently only available in the python version).
ht-lau
Hi,
I am using DIA-NN 1.9.1, so I tried to general a generic tsv (attached). With directlfq 0.2.20 GUI with no setting change, I got the errors below. directlfq_in.zip
I also get similar error if I run the diann.tsv in your test_data/unit_tests/input_table_formats folder if I change the setting to DIANN precursor MS1 and MS2.
Thanks HT
below are the error =========================
2024-08-23 15:45:20,642 - directlfq.lfq_manager - INFO - Starting directLFQ analysis. ERROR:bokeh.server.protocol_handler:error handling message message: Message 'PATCH-DOC' content: {'events': [{'kind': 'MessageSent', 'msg_type': 'bokeh_event', 'msg_data': {'type': 'event', 'name': 'button_click', 'values': {'type': 'map', 'entries': [['model', {'id': 'p1149'}]]}}}]} error: TypeError('format not specified in intable_config.yaml!') Traceback (most recent call last): File "bokeh\server\protocol_handler.py", line 97, in handle work = await handler(message, connection) File "bokeh\server\session.py", line 94, in _needs_document_lock_wrapper result = func(self, *args, *kwargs) File "bokeh\server\session.py", line 288, in _handle_patch message.apply_to_document(self.document, self) File "bokeh\protocol\messages\patch_doc.py", line 104, in apply_to_document invoke_with_curdoc(doc, lambda: doc.apply_json_patch(self.payload, setter=setter)) File "bokeh\document\callbacks.py", line 443, in invoke_with_curdoc return f() File "bokeh\protocol\messages\patch_doc.py", line 104, in
invoke_with_curdoc(doc, lambda: doc.apply_json_patch(self.payload, setter=setter))
File "bokeh\document\document.py", line 376, in apply_json_patch
DocumentPatchedEvent.handle_event(self, event, setter)
File "bokeh\document\events.py", line 246, in handle_event
event_cls._handle_event(doc, event)
File "bokeh\document\events.py", line 281, in _handle_event
cb(event.msg_data)
File "bokeh\document\callbacks.py", line 390, in trigger_event
model._trigger_event(event)
File "bokeh\util\callback_manager.py", line 113, in _trigger_event
self.document.callbacks.notify_event(cast(Model, self), event, invoke)
File "bokeh\document\callbacks.py", line 260, in notify_event
invoke_with_curdoc(doc, callback_invoker)
File "bokeh\document\callbacks.py", line 443, in invoke_with_curdoc
return f()
File "bokeh\util\callback_manager.py", line 109, in invoke
cast(EventCallbackWithEvent, callback)(event)
File "panel\reactive.py", line 491, in _server_event
self._comm_event(doc, event)
File "panel\reactive.py", line 478, in _comm_event
state._handle_exception(e)
File "panel\io\state.py", line 436, in _handle_exception
raise exception
File "panel\reactive.py", line 476, in _comm_event
self._process_bokeh_event(doc, event)
File "panel\reactive.py", line 413, in _process_bokeh_event
self._process_event(event)
File "panel\widgets\button.py", line 243, in _process_event
self.clicks += 1
File "param\parameterized.py", line 528, in _f
instance_param.set(obj, val)
File "param\parameterized.py", line 530, in _f
return f(self, obj, val)
File "param\parameters.py", line 543, in set
super().set(obj,val)
File "param\parameterized.py", line 530, in _f
return f(self, obj, val)
File "param\parameterized.py", line 1553, in set
obj.param._call_watcher(watcher, event)
File "param\parameterized.py", line 2526, in _callwatcher
self._execute_watcher(watcher, (event,))
File "param\parameterized.py", line 2506, in _execute_watcher
watcher.fn( args, **kwargs)
File "directlfq\dashboard_parts.py", line 331, in run_pipeline
lfq_manager.run_lfq(input_file = input_file, input_type_to_use = input_type_to_use, maximum_number_of_quadratic_ions_to_use_per_protein = 10,
File "directlfq\lfq_manager.py", line 48, in run_lfq
input_df = lfqutils.import_data(input_file=input_file, input_type_to_use=input_type_to_use, filter_dict=filter_dict)
File "directlfq\utils.py", line 807, in import_data
file_to_read = reformat_and_save_input_file(input_file=input_file, input_type_to_use=input_type_to_use, filter_dict=filter_dict)
File "directlfq\utils.py", line 824, in reformat_and_save_input_file
input_type, config_dict_for_type, sep = get_input_type_and_config_dict(input_file, input_type_to_use)
File "directlfq\utils.py", line 890, in get_input_type_and_config_dict
raise TypeError("format not specified in intable_config.yaml!")
TypeError: format not specified in intable_config.yaml!