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compomics / moFF

A modest Feature Finder (moFF) to extract MS1 intensities from Thermo raw file
Apache License 2.0
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moFF mzML #32

Closed wenbostar closed 5 years ago

wenbostar commented 6 years ago

Hi,

I just tried the latest version of moFF. I got the following error using the example dataset.

~/anaconda2/bin/python moff_all.py --mbr off --tsv_list sample_data/20080311_CPTAC6_07_6A005.txt --raw_list sample_data/20080311_CPTAC6_07_6A005.mzML --tol 10 --loc_out output_moff
Starting Apex for sample_data/20080311_CPTAC6_07_6A005.txt ...
moff Input file: sample_data/20080311_CPTAC6_07_6A005.txt  XIC_tol 10.0 XIC_win 3.0000 moff_rtWin_peak 1.0000
RAW file  :  ['sample_data/20080311_CPTAC6_07_6A005.mzML']
Output file in :  output_moff
starting  peptide quantification (ms2 / matched ) ..
Traceback (most recent call last):
  File "/home/test/moFF/moff.py", line 612, in apex_multithr
    xic_data= get_xic_data (  flag_mzml, flag_windows, temp, loc_output, name_file, txic_path, loc,  0   )
  File "/home/test/moFF/moff.py", line 734, in get_xic_data
    run_temp = pymzml.run.Reader(raw_name)
NameError: global name 'raw_name' is not defined

Bo

Maux82 commented 6 years ago

Hi,

the new version it has not tested on mzML file. I let know when it will be fixed. thanks for using moFF. Andrea

wenbostar commented 6 years ago

Hi @Maux82, did you get a chance to take a look at this issue? Thanks a lot. Bo

antortjim commented 5 years ago

Hi @wenbostar could you please share your txt file? I can look at the issue.

Thanks beforehand!

Antonio

antortjim commented 5 years ago

Forgot it's on sample_data of course :angel: Thanks anyway Antonio