Update OSD-514 proteomics analysis#2
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Pull request overview
This PR updates the OSD-514 proteomics analysis for an “ms3fix” processing path by adding refreshed sample metadata, regenerated differential expression/GSEA result tables, and a reproducible FragPipe TMT runner + export tooling, while removing older local-path R scripts.
Changes:
- Added
ms3fixsample/assay metadata and regenerated model summary tables (condition/batch/sex and sex-stratified). - Added a reproducible FragPipe TMT (MS3) headless runner plus Python helpers to extract a protein matrix and export PD-like
TMT_all-style files. - Removed prior workstation-specific R scripts (
CombineTMT.r,Proteomics_QC.r).
Reviewed changes
Copilot reviewed 108 out of 198 changed files in this pull request and generated 9 comments.
Show a summary per file
| File | Description |
|---|---|
| Mitochondria/OSD-514/Proteomics/sample_metadata_ms3fix.csv | New per-sample metadata (sample/run/condition/sex) for ms3fix workflow |
| Mitochondria/OSD-514/Proteomics/a_OSD-514_protein-expression-profiling_mass-spectrometry_Orbitrap Fusion.txt | Added assay labeling metadata used to build TMT annotations/mappings |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/run_fragpipe_dmel_tmt.sh | End-to-end FragPipe TMT (MS3) runner script |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/README.md | Documentation for running FragPipe TMT pipeline and expected outputs |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/build_tmt_annotation.py | Builds per-plex FragPipe annotation files from assay metadata / TMT_all headers |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/extract_tmt_protein_matrix.py | Extracts protein × sample matrix from FragPipe TMT outputs |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/export_tmt_all_like.py | Legacy exporter to PD-like per-sample files from tmt-report tables |
| Mitochondria/OSD-514/Proteomics/fragpipe_dmel_tmt/export_tmt_all_like_from_psm.py | Recommended PD-like exporter aggregating from psm.tsv |
| Mitochondria/OSD-514/Proteomics/Proteomics_QC.r | Removed old QC script with workstation-specific paths |
| Mitochondria/OSD-514/Proteomics/CombineTMT.r | Removed old combine script with workstation-specific paths |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/sample_metadata_ms3fix.csv | Result-bundled copy of ms3fix sample metadata |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/sex_stratified_significant_counts_summary.csv | Sex-stratified DE significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/sex_stratified_significant_counts_direction_summary.csv | Sex-stratified DE counts with up/down directionality |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/all_model_significant_counts_summary.csv | Combined significant-count summary across models |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_significant_counts_summary.csv | Model output: sex-stratified significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/significant_counts_summary.csv | Model output: sex-stratified condition+batch significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/significant_counts_direction_summary.csv | Model output: sex-stratified condition+batch directional counts |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/model_metadata_SFug_males_vs_Earth_males.csv | Model metadata for SFug males vs Earth males |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/model_metadata_SFug_females_vs_Earth_females.csv | Model metadata for SFug females vs Earth females |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/model_metadata_SF1g_males_vs_Earth_males.csv | Model metadata for SF1g males vs Earth males |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/model_metadata_SF1g_females_vs_Earth_females.csv | Model metadata for SF1g females vs Earth females |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/design_matrix_SFug_males_vs_Earth_males.csv | Design matrix for sex-stratified condition+batch model (SFug males vs Earth males) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/design_matrix_SFug_females_vs_Earth_females.csv | Design matrix for sex-stratified condition+batch model (SFug females vs Earth females) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/design_matrix_SF1g_males_vs_Earth_males.csv | Design matrix for sex-stratified condition+batch model (SF1g males vs Earth males) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/design_matrix_SF1g_females_vs_Earth_females.csv | Design matrix for sex-stratified condition+batch model (SF1g females vs Earth females) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/sex_stratified_condition_batch/Limma_SF1g_males_vs_Earth_males_significant.csv | Significant proteins for SF1g males vs Earth males |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/significant_counts_summary.csv | Condition-only model: significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/model_metadata_SFug_vs_Earth.csv | Condition-only model metadata (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/model_metadata_SF1g_vs_SFug.csv | Condition-only model metadata (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/model_metadata_SF1g_vs_Earth.csv | Condition-only model metadata (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/Limma_SFug_vs_Earth_significant.csv | Condition-only: significant results table (empty header-only export) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/Limma_SF1g_vs_SFug_significant.csv | Condition-only: significant results table (empty header-only export) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/Limma_SF1g_vs_Earth_significant.csv | Condition-only: significant results table (empty header-only export) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/design_matrix_SFug_vs_Earth.csv | Condition-only design matrix (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/design_matrix_SF1g_vs_SFug.csv | Condition-only design matrix (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_only/design_matrix_SF1g_vs_Earth.csv | Condition-only design matrix (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/significant_counts_summary.csv | Condition+batch model: significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/model_metadata_SFug_vs_Earth.csv | Condition+batch model metadata (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/model_metadata_SF1g_vs_SFug.csv | Condition+batch model metadata (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/model_metadata_SF1g_vs_Earth.csv | Condition+batch model metadata (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/Limma_SF1g_vs_SFug_significant.csv | Condition+batch: significant proteins (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/Limma_SF1g_vs_Earth_significant.csv | Condition+batch: significant proteins (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/design_matrix_SFug_vs_Earth.csv | Condition+batch design matrix (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/design_matrix_SF1g_vs_SFug.csv | Condition+batch design matrix (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch/design_matrix_SF1g_vs_Earth.csv | Condition+batch design matrix (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/significant_counts_summary.csv | Condition+batch+sex model: significant-count summary |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/model_metadata_SFug_vs_Earth.csv | Condition+batch+sex model metadata (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/model_metadata_SF1g_vs_SFug.csv | Condition+batch+sex model metadata (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/model_metadata_SF1g_vs_Earth.csv | Condition+batch+sex model metadata (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/Limma_SF1g_vs_SFug_significant.csv | Condition+batch+sex: significant proteins (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/Limma_SF1g_vs_Earth_significant.csv | Condition+batch+sex: significant proteins (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/design_matrix_SFug_vs_Earth.csv | Condition+batch+sex design matrix (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/design_matrix_SF1g_vs_SFug.csv | Condition+batch+sex design matrix (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/model_outputs/condition_batch_sex/design_matrix_SF1g_vs_Earth.csv | Condition+batch+sex design matrix (SF1g vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_significant_counts_summary_ms3fix.csv | Overall limma significant-count summary for ms3fix |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SFug_vs_Earth_significant.csv | Significant proteins table (non-ms3fix naming) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SFug_vs_Earth_significant_ms3fix.csv | Significant proteins table for ms3fix (SFug vs Earth) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SF1g_vs_SFug_significant.csv | Significant proteins table (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SF1g_vs_SFug_significant_ms3fix.csv | Significant proteins table for ms3fix (SF1g vs SFug) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SF1g_vs_Earth_significant.csv | Significant proteins table (empty header-only export) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/Limma_SF1g_vs_Earth_significant_ms3fix.csv | Significant proteins table for ms3fix (empty header-only export) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/tables/design_matrix_condition_batch_sex_ms3fix.csv | Design matrix used for ms3fix condition+batch+sex model |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Molecular_Function_GeneRIF.csv | GSEA enrichment results (SFug vs Earth, MF, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Molecular_Function_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SFug vs Earth, MF, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Molecular_Function_AutoRIF.csv | GSEA enrichment results (SFug vs Earth, MF, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Molecular_Function_AutoRIF_Predicted_zscore.csv | GSEA enrichment results (SFug vs Earth, MF, predicted z-score, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Molecular_Function_2018.csv | GSEA enrichment results (SFug vs Earth, MF, 2018 gene sets) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Cellular_Component_GeneRIF.csv | GSEA enrichment results (SFug vs Earth, CC, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Cellular_Component_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SFug vs Earth, CC, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Cellular_Component_AutoRIF.csv | GSEA enrichment results (SFug vs Earth, CC, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Cellular_Component_AutoRIF_Predicted_zscore.csv | GSEA enrichment results (SFug vs Earth, CC, predicted z-score, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Cellular_Component_2018.csv | GSEA enrichment results (SFug vs Earth, CC, 2018 gene sets) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Biological_Process_GeneRIF.csv | GSEA enrichment results (SFug vs Earth, BP, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Biological_Process_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SFug vs Earth, BP, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Biological_Process_AutoRIF.csv | GSEA enrichment results (SFug vs Earth, BP, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SFug_vs_Earth_GO_Biological_Process_2018.csv | GSEA enrichment results (SFug vs Earth, BP, 2018 gene sets) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Molecular_Function_GeneRIF.csv | GSEA enrichment results (SF1g vs SFug, MF, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Molecular_Function_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, MF, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Molecular_Function_AutoRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, MF, predicted z-score, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Molecular_Function_2018.csv | GSEA enrichment results (SF1g vs SFug, MF, 2018 gene sets) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Cellular_Component_GeneRIF.csv | GSEA enrichment results (SF1g vs SFug, CC, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Cellular_Component_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, CC, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Cellular_Component_AutoRIF.csv | GSEA enrichment results (SF1g vs SFug, CC, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Cellular_Component_AutoRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, CC, predicted z-score, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Cellular_Component_2018.csv | GSEA enrichment results (SF1g vs SFug, CC, 2018 gene sets) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Biological_Process_GeneRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, BP, predicted z-score, GeneRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Biological_Process_AutoRIF_Predicted_zscore.csv | GSEA enrichment results (SF1g vs SFug, BP, predicted z-score, AutoRIF) |
| Mitochondria/OSD-514/Proteomics/RESULTS_OSD514_ms3fix/GSEA/tables/SF1g_vs_SFug_GO_Biological_Process_2018.csv | GSEA enrichment results (SF1g vs SFug, BP, 2018 gene sets) |
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| if [[ -s "${TARGET_DECOY_FASTA}" ]]; then | ||
| echo "[1/6] Using existing FASTA: ${TARGET_DECOY_FASTA}" | ||
| elif [[ -s "${FALLBACK_DB}" ]]; then | ||
| echo "[1/6] Copying FASTA from LFQ setup" | ||
| cp -f "${FALLBACK_DB}" "${TARGET_DECOY_FASTA}" |
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| echo "[2/6] Generating TMT manifest..." | ||
| python3 - << 'PY' | ||
| from pathlib import Path | ||
| import re | ||
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| mzml_dir = Path('/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/mzML') | ||
| out = Path('/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/manifests/brain_awg_tmt.fp-manifest') |
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| echo "[3/6] Generating TMT annotation file..." | ||
| # Clear old annotation files to avoid parser ambiguity | ||
| find "${MZML_DIR}" -maxdepth 1 -type f -name '*annotation.txt' -delete | ||
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| python3 "/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/build_tmt_annotation.py" \ | ||
| --tmt-all-dir "${TMT_ALL_DIR}" \ | ||
| --assay-file "${ASSAY_LABEL_FILE}" \ | ||
| --mzml-dir "${MZML_DIR}" |
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| python3 - << 'PY' | ||
| from pathlib import Path | ||
| wf = Path('/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/manifests/brain_awg_dmel_tmt10.workflow') | ||
| db = '/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/db/dmel_UP000000803_uniprot_target_decoy.fasta' | ||
| lines = wf.read_text().splitlines() |
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| echo "[6/7] Extracting protein matrix from TMT output..." | ||
| python3 "/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/extract_tmt_protein_matrix.py" \ | ||
| --workdir "${OUT_DIR}" \ | ||
| --out "${WORK_DIR}/protein_abundance_tmt_matrix.tsv" |
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| echo "[7/7] Exporting TMT_all-like per-sample txt files..." | ||
| TMT_ALL_EXPORT_DIR="/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/TMT_all_from_psm_pdlike_${RUN_SUBDIR}" | ||
| python3 "/home/AD.UNLV.EDU/Shared_Data/AlternativeSplicing/brain_awg/proteomics/fragpipe_dmel_tmt/export_tmt_all_like_from_psm.py" \ | ||
| --results-dir "${OUT_DIR}" \ | ||
| --assay-file "${ASSAY_LABEL_FILE}" \ | ||
| --out-dir "${TMT_ALL_EXPORT_DIR}" |
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| if any(k in cl for k in ["abundance", "intensity", "reporter", "ratio"]): | ||
| sample_cols.append(c) | ||
| continue |
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| reporter_cols = [f"Intensity {plex}_{c}" for c in ["126", "127N", "127C", "128N", "128C", "129N", "129C", "130N", "130C", "131N"]] | ||
| existing_reporters = [c for c in reporter_cols if c in psm.columns] | ||
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| keep_cols = ["Protein", "Qvalue", "Probability"] + existing_reporters | ||
| psm = psm[keep_cols].copy() | ||
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| # Sum reporter intensities per protein. | ||
| agg_sum = psm.groupby("Protein", as_index=False)[existing_reporters].sum(min_count=1) | ||
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| 1. Reuses your D. melanogaster target-decoy FASTA. | ||
| 2. Builds a TMT manifest grouping files by plex (`TMTA`, `TMTB`, `TMTC`). | ||
| 3. Auto-generates TMT experiment annotation from assay metadata (`a_OSD-514_protein-expression-profiling_mass-spectrometry_Orbitrap Fusion.txt`). | ||
| 4. Runs FragPipe headless using built-in `TMT10` workflow template. | ||
| 5. Extracts a clean protein abundance matrix from the TMT output. |
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