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Fix legacy notebook edge cases exposed by MWE sample sheets, compressed FASTQ names, lookup remapping, and Marchenko k=1 #1317

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Merged
gaow merged 1 commit into from
Apr 24, 2026
+38 −14
Merged

Fix legacy notebook edge cases exposed by MWE sample sheets, compressed FASTQ names, lookup remapping, and Marchenko k=1 #1317

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2 changes: 1 addition & 1 deletion code/data_preprocessing/covariate/covariate_hidden_factor.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -741,7 +741,7 @@
" }\n",
" if (MPPCNum == 0) stop(\"Invalid choice of methods to choose K for PCA: ${choose_k_method}\")\n",
"\n",
" MPPCsDF <- as.data.frame(residExpPC$rotated[, 1:MPPCNum])\n",
" MPPCsDF <- as.data.frame(residExpPC$rotated[, 1:MPPCNum, drop = FALSE])\n",
" MPColMatrix <- matrix(c(rep('Hidden_Factor_PC', times=MPPCNum), seq(1, MPPCNum)), ncol=2, nrow=MPPCNum)\n",
" colnames(MPPCsDF) <- apply(MPColMatrix, 1, function(X){return(paste0(X[1], X[2]))})\n",
" # Add #id Column\n",
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26 changes: 18 additions & 8 deletions code/data_preprocessing/genotype/GWAS_QC.ipynb
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Expand Up @@ -1352,13 +1352,21 @@
" phenoFile <- read_delim(${_input[1]:ar}, col_names=TRUE)\n",
" if (${\"TRUE\" if sample_participant_lookup.is_file() else \"FALSE\"}) {\n",
" sample_lookup <- fread(${sample_participant_lookup:ar}, header=TRUE)\n",
" colnames(sample_lookup) <- c(\"sample_id\", \"genotype_id\") # FIXME: This is for the old lookup table with columns c(\"sample_id\", \"participant_id\")\n",
" # rename phenotype file according to lookup file\n",
" colnames(phenoFile)[-c(1:4)] <- phenoFile %>%\n",
" colnames() %>%\n",
" .[-c(1:4)] %>%\n",
" match(sample_lookup$sample_id) %>%\n",
" sample_lookup$genotype_id[.]\n",
" if (all(c(\"sample_id\", \"genotype_id\") %in% colnames(sample_lookup))) {\n",
" sample_lookup <- sample_lookup[, .(sample_id, genotype_id)]\n",
" } else if (all(c(\"sample_id\", \"participant_id\") %in% colnames(sample_lookup))) {\n",
" sample_lookup <- sample_lookup[, .(sample_id, genotype_id = participant_id)]\n",
" } else {\n",
" sample_lookup <- sample_lookup[, 1:2]\n",
" colnames(sample_lookup) <- c(\"sample_id\", \"genotype_id\")\n",
" }\n",
" sample_lookup <- unique(sample_lookup)\n",
" pheno_sample_ids <- colnames(phenoFile)[-c(1:4)]\n",
" renamed_genotype_ids <- sample_lookup$genotype_id[match(pheno_sample_ids, sample_lookup$sample_id)]\n",
" if (any(is.na(renamed_genotype_ids))) {\n",
" stop(\"Some phenotype samples could not be mapped to genotype IDs using sample_participant_lookup\")\n",
" }\n",
" colnames(phenoFile)[-c(1:4)] <- renamed_genotype_ids\n",
" output_file <- paste0(${phenoFile:nnr}, '.rename_sample.bed')\n",
" # rename phenotype file\n",
" phenoFile$start <- as.integer(phenoFile$start) \n",
Expand All @@ -1374,9 +1382,11 @@
" colnames(sample_lookup) <- c(\"genotype_id\", \"sample_id\")\n",
" }\n",
" sample_lookup <- sample_lookup %>%\n",
" transmute(genotype_id = genotype_id, sample_id = sample_id) %>%\n",
" distinct() %>%\n",
" filter(\n",
" genotype_id %in% genoFam$V2,\n",
" sample_id %in% colnames(phenoFile)\n",
" genotype_id %in% colnames(phenoFile)\n",
" )\n",
" \n",
" genoFam %>%\n",
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24 changes: 19 additions & 5 deletions code/molecular_phenotypes/calling/RNA_calling.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -681,6 +681,13 @@
"parameter: uncompressed = False\n",
"import os\n",
"import pandas as pd\n",
"def fastqc_output_base(target):\n",
" target = target[0] if hasattr(target, '__getitem__') and not isinstance(target, (str, bytes, os.PathLike)) else target\n",
" name = os.path.basename(str(target))\n",
" for suffix in (\".fastq.gz\", \".fq.gz\", \".fastq\", \".fq\", \".bam\", \".sam\", \".cram\"):\n",
" if name.endswith(suffix):\n",
" return name[:-len(suffix)]\n",
" return os.path.splitext(name)[0]\n",
"## FIX: The way to get sample needs to be revamped to 1. Accomodate rf/fr as column 2. accomodate single end read (Only 2 fq/samples)\n",
"sample_inv = pd.read_csv(sample_list,sep = \"\\t\")\n",
"\n",
Expand All @@ -704,14 +711,21 @@
" sample_inv = sample_inv.drop(\"read_length\" , axis = 1)\n",
" \n",
"\n",
"## Read columns follow the documented fq1/fq2 contract; fall back only for legacy one/two-read-column sample sheets\n",
"file_columns = [x for x in [\"fq1\", \"fq2\"] if x in sample_inv.columns]\n",
"if len(file_columns) == 0:\n",
" legacy_file_columns = [x for x in sample_inv.columns if x != \"ID\"]\n",
" stop_if(len(legacy_file_columns) == 0 or len(legacy_file_columns) > 2,\n",
" msg = \"Sample list must contain fq1 and optional fq2 columns, or a legacy ID + one/two read-column layout after removing strand/read_length\")\n",
" file_columns = legacy_file_columns\n",
"\n",
"## Extract sample_id\n",
"sample_inv_list = sample_inv.values.tolist()\n",
"sample_inv_list = sample_inv[[\"ID\"] + file_columns].values.tolist()\n",
"sample_id = [x[0] for x in sample_inv_list]\n",
"\n",
" \n",
"## Get the file name for single/paired end data\n",
"file_inv = [x[1:] for x in sample_inv_list]\n",
"file_inv = [item for sublist in file_inv for item in sublist]\n",
"file_inv = [item for sublist in file_inv for item in sublist if pd.notna(item) and str(item).strip() != \"\"]\n",
"\n",
"raw_reads = [f'{data_dir}/{x}' for x in file_inv]\n",
"\n",
Expand Down Expand Up @@ -793,7 +807,7 @@
"source": [
"[fastqc]\n",
"input: raw_reads, group_by = 1\n",
"output: f'{cwd}/{_input:bn}_fastqc.html',f'{cwd}/{_input:bn}_fastqc.zip' \n",
"output: f'{cwd}/{fastqc_output_base(_input)}_fastqc.html',f'{cwd}/{fastqc_output_base(_input)}_fastqc.zip' \n",
"task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, cores = numThreads\n",
"bash: expand= \"${ }\", stderr = f'{_output[0]:n}.stderr', stdout = f'{_output[0]:n}.stdout', container=container\n",
" fastqc ${_input} -o ${_output[0]:d}"
Expand Down Expand Up @@ -2094,4 +2108,4 @@
},
"nbformat": 4,
"nbformat_minor": 5
}
}