Feature/non cleavable xl #85

mostafakalhor · 2024-04-02T12:11:10Z

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Description of changes

-added functionalites for non-cleavable and cleavable XL
Technical details

Additional context

…f initialize_peaks

…for xl peptides

…m-lab/spectrum_fundamentals into feature/ptm_model_support

…d then push my branch to development

…eed to be fixed

spectrum_fundamentals/metrics/percolator.py

spectrum_fundamentals/constants.py

spectrum_fundamentals/metrics/similarity.py

- major cleanup to fix too complex function issue - correctly call generate_annotation_matrix with charge instead of xl_pos - added type annotations and fixed typeguard / mypy issues

mostafakalhor and others added 30 commits May 29, 2023 21:24

added crosslinking mods

29dc722

adding initialize_peaks_xl function for CMS2

bbbf16e

changing peptide_length-1 to peptide_length as previous version in de…

7108a8d

…f initialize_peaks

add some functions for annotation cms2

adb97c4

remove unnecessary functions

4c51145

change CROSSLINKER_POSITION to CROSSLINKER_POSITION_A in annotation.py

83540ac

changed annotation

87fc364

extend parallel_annotate for pep a and b

e8c0ea5

Added molecular mass of ptms to constants

5471198

fix scripts directory

b3c1572

rescoring is working but xl_fdr should be added

d8ca8a5

cover xisearch and fix issue of mach_peaks are zero

125adee

Merge branch 'development' into feature/ptm_model_support

d9afb19

commented out removal of dash in mod seq

74a9a04

check length < 30 prior to executing function

8fc877a

cleanup and simplify mass calculation

7859893

updated and corrected tests

33e6a7c

Merge branch 'development' into feature/crosslinked_peptides

b29a081

removed config dependency from fragment_ratio

3a4d8fe

fixed unit tests

84acdf9

added non_cleavable 1898 mod (DSS/BS3)

d07469d

intermediate commit fixing the tests

fa0a8d7

Added tests for initialize_peaks, initialize_peaks_xl and annotation …

7b2c126

…for xl peptides

Added test for cleavable crosslinked peptide fragmentation

db1f9f9

Merge branch 'development' into feature/ptm_model_support

544150d

Merge branch 'feature/ptm_model_support' of https://github.com/wilhel…

5ccbbfa

…m-lab/spectrum_fundamentals into feature/ptm_model_support

Add permutation to mods for localization

25a3d84

this branch is working - time to pull development to noncl branch an…

9333b15

…d then push my branch to development

Merge branch 'development' into feature/non_cleavable_XL

c513695

fixed issues found by nox

9b8573c

picciama assigned arne-vdb and mostafakalhor Apr 10, 2024

picciama removed the request for review from arne-vdb April 10, 2024 13:09

picciama marked this pull request as draft April 10, 2024 13:09

mostafakalhor and others added 9 commits April 11, 2024 13:33

added xisearch to internal function

5db3d52

removed unnecessary comments

f6ee978

intermediate commite

8b5cc72

Merge branch 'development' into feature/non_cleavable_XL

7452578

fixed count_with_ion_mask

d81af62

added test code for cl xl

44ec5ba

added tests for cl xl anotation

c9bf404

added test code in fragmnet_ratio for cross-linked peptides - still n…

af645d8

…eed to be fixed

fixed all errors except initialise_peak is complex

3e7fffd

picciama requested changes Apr 16, 2024

View reviewed changes

picciama and others added 12 commits April 16, 2024 15:02

Merge branch 'development' into feature/ptm_model_support

67fdc4c

Merge branch 'feature/ptm_model_support' into feature/non_cleavable_XL

8fe8676

fixed tests and non_cleavable_xl bugs:

0edeb1a

- major cleanup to fix too complex function issue - correctly call generate_annotation_matrix with charge instead of xl_pos - added type annotations and fixed typeguard / mypy issues

fixed MASK_DICT and MASK_DIC_XL

60ca691

fixed def cal()

7ac62af

fixed def _cal_additional_metric for xl

2615de0

fixed precommit error

46e92ae

removed writing output file

f545fd3

removed indices_to_onehot function

7b7b6a1

fixed darglint

7c9da6d

readded missing test

388b6f3

fix typeguard

5358f58

picciama marked this pull request as ready for review April 17, 2024 11:03

picciama approved these changes Apr 17, 2024

View reviewed changes

mostafakalhor merged commit 434f41e into development Apr 17, 2024
26 checks passed

picciama deleted the feature/non_cleavable_XL branch July 8, 2024 14:18

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Feature/non cleavable xl #85

Feature/non cleavable xl #85

mostafakalhor commented Apr 2, 2024 •

edited by picciama

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Feature/non cleavable xl #85

Feature/non cleavable xl #85

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mostafakalhor commented Apr 2, 2024 • edited by picciama Loading

mostafakalhor commented Apr 2, 2024 •

edited by picciama

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