GitHub - pgarrett-scripps/senpy

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
APIO		APIO
sample_files		sample_files
src/senpy		src/senpy
testing		testing
.gitignore		.gitignore
MANIFEST.in		MANIFEST.in
README		README
averge_mass_offset.py		averge_mass_offset.py
combine_rtscore_timscore.py		combine_rtscore_timscore.py
dfolder_to_hdf5.py		dfolder_to_hdf5.py
fragment_ion_extractor.py		fragment_ion_extractor.py
fragmer.py		fragmer.py
generate_output.py		generate_output.py
gui_ms2_extractor.py		gui_ms2_extractor.py
ip2_project_extractor.py		ip2_project_extractor.py
ip2_project_remove_DTA_files.py		ip2_project_remove_DTA_files.py
ip2_project_set_timscore_zero.py		ip2_project_set_timscore_zero.py
map_scan_number_to_precursor_id.py		map_scan_number_to_precursor_id.py
mass_aligner_ppm_estimator.py		mass_aligner_ppm_estimator.py
merge_index_ms2.py		merge_index_ms2.py
ms2_extractor.py		ms2_extractor.py
multiprocess_ms2.py		multiprocess_ms2.py
requirements.txt		requirements.txt
rtScore.py		rtScore.py
saby_convertor.py		saby_convertor.py
setup.py		setup.py
sqt_to_percolator.py		sqt_to_percolator.py
typression.py		typression.py

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Serializer/Encoder for various proteomics files

Update timsdata.py with new version from pe-py-timscore (Dia) package

ms2 vs ms2_fast
    ms2_fast parses ~10x faster
    doesnt store spectra
    deserializes elements upon request

DTASelect-Filter.txt (refactored)
    supported versions:
        v2.1.12
        v2.1.13
        v2.1.12_paser

DTASelect.txt (in progress)
    supported versions:
        ?

*.feature (need refactor)
    supported versions:
        biosaur
        dinosuar

*.ms2 (refactored)
    supported instruments:
        timstof


*.fasta (done)
    supported versions:
        check biopython

*.idx (done)
    supported versions:
        ???

*.out (need refactor)
    supported versions:
        ???

*.sqt (refactored)
    supported versions:
        v1.4
        v2.1.0      <-- timsscore
        v2.1.0_ext  <-- timsscore_ext