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I get the following error after optimization. Windows 10 and Python 3.7.3. Installed with pip. Sorry for the bad formatting.

Optimization terminated normally: Convergence detected: absolute parameter change was below tolerance Traceback (most recent call last): File "c:\users\me\appdata\local\continuum\miniconda3\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\users\me\appdata\local\continuum\miniconda3\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Users\me\AppData\Local\Continuum\miniconda3\Scripts\dart_id.exe\__main__.py", line 9, in <module> File "c:\users\me\appdata\local\continuum\miniconda3\lib\site-packages\dart_id\update.py", line 484, in main df_adjusted = run_internal(df_adjusted, parameter_map) File "c:\users\me\appdata\local\continuum\miniconda3\lib\site-packages\dart_id\fido\BayesianNetwork.py", line 1007, in run_internal fn.load_from_dataframes([df], **parameter_map) File "c:\users\me\appdata\local\continuum\miniconda3\lib\site-packages\dart_id\fido\BayesianNetwork.py", line 761, in load_from_dataframes self = bayesian_network_union(self, sub_fn) File "c:\users\me\appdata\local\continuum\miniconda3\lib\site-packages\dart_id\fido\BayesianNetwork.py", line 176, in bayesian_network_union bn1.add_node(bn2.get_node_from_id(i), **bn2.node[i]) AttributeError: 'fido_network' object has no attribute 'node'

Followin up from issue #2 and after installing the Tkinter module, I have the following missing module

$ dart_id                    
Traceback (most recent call last):
  File "/home/lgatto/.local/bin/dart_id", line 7, in <module>
    from dart_id.update import main
  File "/home/lgatto/.local/lib/python3.7/site-packages/dart_id/update.py", line 15, in <module>
    from dart_id.figures import figures
  File "/home/lgatto/.local/lib/python3.7/site-packages/dart_id/figures.py", line 16, in <module>
    from dart_id.figure_gen import *
  File "/home/lgatto/.local/lib/python3.7/site-packages/dart_id/figure_gen/exp_alignment.py", line 9, in <module>
    from rtlib.helper import *
ModuleNotFoundError: No module named 'rtlib'

Will update this as things are changed

• test separate variance modeling in a structured way
• fix experiment alignment figures image path - needs to be relative to the HTML.
• iteratively run the filters, and check if there are experiments where all observations are filtered out, and then remove them and run the filters again
• fix "sort" issue with pd.concat

q:\anaconda\lib\site-packages\pandas\core\frame.py:6201: FutureWarning: Sorting because non-concatenation axis is not aligned. A future version
of pandas will change to not sort by default.

To accept the future behavior, pass 'sort=True'.

To retain the current behavior and silence the warning, pass sort=False

  sort=sort)

• fix RI columns being wiped when concatenating
• quick and dirty pairwise correlation b/n experiments - to see outliers and warn the user that they should be filtered out
• check the max(PEP) of each raw file, and warn the user if they input a raw file with PEPs that are too low (nothing to boost)
• retention length filtering - raw file specific
• rename output columns
• migrate to config file instead of command-line options
• improve input file-type converting
  • file-type determines column names
  • move filtering blocks into separate functions. file-type determines which functions are run
• pip installable
• violin plot of residual density by RT (RT on x-axis)
• pairwise correlation of RTs - heatmap
• diagnostic figures for the update portion
  • PEP vs PEP.new scatterplot
  • fold change increase in IDs as function of PEP threshold
• validation figures
  • multiple peptides of the same protein - should have the same intensity (measure the CV)
• generate HTML file to view figures
• add and start throwing exceptions
• create entire output directory including all subfolders
• parameter for defining column headers - additional option instead of specifying the file type
• fix experiment exclusion
• optional save alignment parameters
• split up outputs in same way the inputs are split up
  • then remove input_id column
• remove id column as well?
• verbose levels and actually enforce them in code
• additional parameters to select which columns to have
  • default should just be pep_new. maybe have a "diagnostic" flag that includes the other columns?
• logging -> logger
• default retention length filter - (max_retention_time) / 60
• optimize experiment updating
• filter_decoys/contaminants -> include_decoys/contaminants
• add PEP_updated column

FUTURE VERSION

• move off of STAN
• optimize data selection by RT bin, experiment, and peptide. remove as much as possible but retain the same amount of coverage.

Hi there,

First, please let me thanks for your kindness of open the repo for the whole community!
I'm adapting DART-ID for Sequest and Byonic output. When I run the modified code with all required columns (i.e. sequence: Modified sequence; raw_file: Raw file; retention_time: Retention time; pep: PEP).
I bumped into the error below:

dart_id -c input_wrappers/config-no-rt-length.yaml

2019-05-24 15:48:17 [ERROR]  Filter retention_length required a data column retention_length, but this was not found in the input dataframe.
Traceback (most recent call last):
  File "/Users/mofrankhu/.pyenv/versions/3.7.2/bin/dart_id", line 11, in <module>
    load_entry_point('dart-id', 'console_scripts', 'dart_id')()
  File "/DART-ID/dart_id/update.py", line 355, in main
    df, df_original = process_files(config)
  File "/DART-ID/dart_id/converter.py", line 372, in process_files
    df = filter_psms(df, config)
  File "/DART-ID/dart_id/converter.py", line 281, in filter_psms
    raise ConfigFileError('Filter {} required a data column {}, but this was not found in the input dataframe.'.format(f['name'], j))
dart_id.exceptions.ConfigFileError: Filter retention_length required a data column retention_length, but this was not found in the input dataframe.

I added a column with fixed rt length (e.g. 0.1) to avoid this error, and the program seems worked.

I guess there might be some confusion in the comment of the config.yaml sample file. Could you please help me make sure which columns should I contained in the input file in the current version of DART-ID?

However, as standard PD output at PSM level do not contain RT length, ** could you please also comment on what does this (Retention length in MaxQuant evidence.txt) mean? so I could find equivalent in PD output. **

BTW, the wrapper I used is committed to my fork of this repo https://github.com/mofhu/DART-ID. please feel free to use it if you would like to.

Many thanks!
Mo

Hi developer,
I want to install the dart-id in linux and I run the command "pip install dart-id" in linux on install node, however, it doesn't work.
how do I deal with it?

best

Hi,

An error is returned when running the program:

ImportError: cannot import name 'gcd' from 'fractions' (/home/lukas/anaconda3/lib/python3.9/fractions.py)

As per stack overflow the problem is caused by the networkx module which import statements changed upon python updates (I am using python 3.9.7).

BR
Lukas

Hi,

I wes testing the software with example files:

configuration: example_sqc_67_95_varied.yaml
input: SQC_67_95_Varied/evidence.txt

Erros arise as: dart_id.exceptions.ConfigFileError: Params file /Users/chena/dart_id/sqc_varied_test\exp_params.txt does not exist

How to generate an exp_params.txt file together with other parameter file?
dart.log

I would like to try dart_id out. I started by installing it with

$ pip install git+https://github.com/SlavovLab/DART-ID --user 

but hit the following error

$ dart_id -h                                                         
Traceback (most recent call last):
  File "/home/lgatto/.local/bin/dart_id", line 7, in <module>
    from dart_id.update import main
  File "/home/lgatto/.local/lib/python3.7/site-packages/dart_id/update.py", line 14, in <module>
    from dart_id.fido.BayesianNetwork import run_internal
ModuleNotFoundError: No module named 'dart_id.fido'

Any help appreciated.