Swath2stat analysis

[mchiapello]

Is ti pyprophet able to export datasets compatible with R package Swath2Stat?

I exported a tsv using the following command:

pyprophet export --in=data/merged.osw --out=data/legacy.tsv

The file does not look like the one I can see in the R package. Do I need to use TRIC? Is it possible to use TRIC with one single file?

[grosenberger]

Usually SWATH2stats expects the output to be processed by TRIC. You can also apply TRIC to a single file, it will just filter the results to the selected cutoffs and append the additional columns.

[mchiapello]

I run the following pipeline:

pyprophet score --in data/osw_output.osw --protein

pyprophet protein --in data/osw_output.osw --context run-specific

pyprophet export --in data/osw_output.osw --out data/protein_inference_FDR001.tsv --protein

feature_alignment.py --in data/protein_inference_FDR001.tsv --out data/TRIC_protein_inference_FDR001.tsv --method LocalMST --realign_method lowess_cython --max_rt_diff 60 --mst:useRTCorrection True --mst:Stdev_multiplier 3.0 --target_fdr 0.01 --max_fdr_quality 0.05

I Got the following error running TRIC:

Parsing input files
Traceback (most recent call last):
File "/usr/local/bin/feature_alignment.py", line 4, in
import('pkg_resources').run_script('msproteomicstools==0.8.0', 'feature_alignment.py')
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 719, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/usr/lib/python2.7/dist-packages/pkg_resources/init.py", line 1511, in run_script
exec(script_code, namespace, namespace)
File "/usr/local/lib/python2.7/dist-packages/msproteomicstools-0.8.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/feature_alignment.py", line 799, in
File "/usr/local/lib/python2.7/dist-packages/msproteomicstools-0.8.0-py2.7-linux-x86_64.egg/EGG-INFO/scripts/feature_alignment.py", line 741, in main
File "build/bdist.linux-x86_64/egg/msproteomicstoolslib/format/SWATHScoringReader.py", line 169, in parse_files
KeyError: 'run_id'

Any clue about what I am doing wrong?

[summerghw]

@mchiapello Hi，I have got the same error, did you figure out what is wrong ? could you tell me how to fix this