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mzid file can't be parsed #10

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Kimmiecc19 opened this issue Jul 19, 2023 · 0 comments
Open

mzid file can't be parsed #10

Kimmiecc19 opened this issue Jul 19, 2023 · 0 comments

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@Kimmiecc19
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Hello,

I am trying to run proBAMconvert using Python3 with a mzid file.
I get the following error:

Mapping key not found.
Traceback (most recent call last):
File "/proBAMconvert/python/proBAM_input.py", line 37, in get_PSM_hash
PSM=proBAM_mzid.get_PSM_mzid(psm_file,validated_only)
File "/proBAMconvert/python/proBAM_mzid.py", line 53, in get_PSM_mzid
proteins.append({"protein":accession_hash[protein['peptideEvidence_ref']]})
KeyError: 'peptideEvidence_ref'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/proBAMconvert/python/proBAM.py", line 823, in
psm_hash=proBAM_input.get_PSM_hash(psm_file,decoy_annotation,validated_only)
File "/proBAMconvert/python/proBAM_input.py", line 55, in get_PSM_hash
print (e.message)
AttributeError: 'KeyError' object has no attribute 'message'

My command is:
python proBAM.py --name test --version 89 --species homo_sapiens --file /proBAMconvert/14i-n1_P27_1-10-10_1-1_1-1-AM_150803_SWATH-vw100_iPSC_14i-1_Batch3.msgf.mzid --directory ~/ --rm_duplicates Y --three_frame_translation Y --pre_picked_annotation all --conversion_mode proBAM_peptide

Is there any way I can adjust the script to make it work? I already had to edit all of the scripts to make them compatible with Python3.

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