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Fix .bed input path handling and reference_data paths #1373

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Merged
gaow merged 3 commits into from
Jun 23, 2026
Merged

Fix .bed input path handling and reference_data paths #1373

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fb937fb
Fix output filename for .bed TPM input in bulk_expression_QC.R
Jun 23, 2026
c1162c3
Fix reference_data paths to use input/reference_data prefix in gene_a…
Jun 23, 2026
ede57c1
Remove spurious input/ prefix from descriptive text in gene_annotatio…
Jun 23, 2026
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18 changes: 8 additions & 10 deletions code/SoS/data_preprocessing/phenotype/gene_annotation.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -63,8 +63,8 @@
"| `input/rnaseq/protocol_example.leafcutter.intron_count.tsv` | Toy leafcutter intron-count table (IDs `chr:start:end:clu_N_strand`). |\n",
"| `input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz` | Toy leafcutter intron-excision phenotype matrix. |\n",
"| `input/rnaseq/protocol_example.psichomics.phenotype.tsv` | Toy psichomics phenotype matrix (IDs end in `_<gene_id>`). |\n",
"| `reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf` | Collapsed gene-model GTF (gene/protein annotation). |\n",
"| `reference_data/Homo_sapiens.GRCh38.103.chr.gtf` | Full gene-model GTF with exons (leafcutter/psichomics). |\n"
"| `input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf` | Collapsed gene-model GTF (gene/protein annotation). |\n",
"| `input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf` | Full gene-model GTF with exons (leafcutter/psichomics). |\n"
]
},
{
Expand Down Expand Up @@ -132,7 +132,7 @@
"sos run pipeline/gene_annotation.ipynb annotate_coord \\\n",
" --cwd output/gene_annotation \\\n",
" --phenoFile input/rnaseq/protocol_example.rnaseq.bed.gz \\\n",
" --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
" --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
" --phenotype-id-column gene_id\n"
]
},
Expand Down Expand Up @@ -183,7 +183,7 @@
"sos run pipeline/gene_annotation.ipynb annotate_coord \\\n",
" --cwd output/gene_annotation \\\n",
" --phenoFile input/proteomics/protocol_example.protein.no_coord.tsv \\\n",
" --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
" --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
" --phenotype-id-column gene_id \\\n",
" --molecular-trait-type protein\n"
]
Expand Down Expand Up @@ -227,7 +227,7 @@
" --cwd output/gene_annotation \\\n",
" --phenoFile input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz \\\n",
" --intron-count input/rnaseq/protocol_example.leafcutter.intron_count.tsv \\\n",
" --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
" --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
" --map-stra site\n"
]
},
Expand Down Expand Up @@ -293,7 +293,7 @@
" --cwd output/gene_annotation \\\n",
" --phenoFile input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz \\\n",
" --intron-count input/rnaseq/protocol_example.leafcutter.intron_count.tsv \\\n",
" --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
" --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
" --map-stra site\n"
]
},
Expand Down Expand Up @@ -335,7 +335,7 @@
"sos run pipeline/gene_annotation.ipynb annotate_psichomics_isoforms \\\n",
" --cwd output/gene_annotation \\\n",
" --phenoFile input/rnaseq/protocol_example.psichomics.phenotype.tsv \\\n",
" --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf\n"
" --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf\n"
]
},
{
Expand Down Expand Up @@ -622,9 +622,7 @@
"metadata": {
"kernel": "SoS"
},
"source": [
"The gtf used here should be the collapsed gtf, i.e. the final output of reference_data gtf processing and the one used to called rnaseq."
]
"source": "The gtf used here should be the collapsed gtf, i.e. the final output of reference_data gtf processing and the one used to called rnaseq."
},
{
"cell_type": "code",
Expand Down
7 changes: 3 additions & 4 deletions code/script/molecular_phenotypes/QC/bulk_expression_QC.R
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Original file line number Diff line number Diff line change
Expand Up @@ -52,10 +52,9 @@ if (is.null(opt[["tpm-gct"]])) stop("--tpm-gct is required")

dir.create(opt$cwd, showWarnings = FALSE, recursive = TRUE)

normalize_output_prefix <- function(path) {
stem <- sub("\\.(gct|GCT)(\\.gz)?$", "", basename(path))
stem <- sub("\\.gene_tpm$", "", stem)
stem <- sub("\\.tpm$", "", stem)
normalize_output_prefix <- function(path, n_ext = 3) {
stem <- basename(path)
for (i in seq_len(n_ext)) stem <- sub("\\.[^.]+$", "", stem)
stem
}

Expand Down
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