From a7249f39534a8b897779f67cd0b2f49998ad09e4 Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 14:11:40 +0000 Subject: [PATCH 01/13] Add configurable attribute_type parameter for featureCounts MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This enhancement makes the featureCounts `-g` parameter configurable instead of being hardcoded to "gene_id". Users can now specify different attribute types (e.g., transcript_id, ID) in their config.yaml file, providing greater flexibility for different annotation formats including GFF files. Changes: - Add attribute_type parameter to config.yaml and test_config.yaml (defaults to "gene_id" for backward compatibility) - Update paired_counts.smk to use configurable attribute_type in both all and unique read counting rules - Update single_counts.smk to use configurable attribute_type in both all and unique read counting rules 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude --- config.yaml | 1 + rules/counting/paired_counts.smk | 8 +++++--- rules/counting/single_counts.smk | 8 +++++--- test_config.yaml | 1 + 4 files changed, 12 insertions(+), 6 deletions(-) diff --git a/config.yaml b/config.yaml index 009e03f..0b1e09e 100644 --- a/config.yaml +++ b/config.yaml @@ -23,6 +23,7 @@ cores_fastp: 8 cores_default: 1 max_cores: 8 feature_type: "CDS" +attribute_type: "gene_id" # Attribute used for grouping features (e.g., gene_id, transcript_id, ID) # Nanopore-specific settings nanopore_preset: "map-ont" # Minimap2 preset for nanopore diff --git a/rules/counting/paired_counts.smk b/rules/counting/paired_counts.smk index 1d4ac0f..b337f68 100644 --- a/rules/counting/paired_counts.smk +++ b/rules/counting/paired_counts.smk @@ -39,6 +39,7 @@ rule featurecounts_paired_all: params: gtf = config["processing_gtf_file"], feature_type = config["feature_type"], + attribute_type = config["attribute_type"], extra = "-p -B -C -M -O --countReadPairs" # Paired-end specific options # -B requireBothEndsMapped # -p isPairedEnd @@ -81,7 +82,7 @@ rule featurecounts_paired_all: featureCounts {params.extra} \\ -T {threads} \\ -t {params.feature_type} \\ - -g gene_id \\ + -g {params.attribute_type} \\ -a {params.gtf} \\ -o {output.counts} \\ {input.bam} \\ @@ -121,7 +122,8 @@ rule featurecounts_paired_unique: flag = get_processing_path("{run_tag}/featurecounts_paired_complete.flag") params: gtf = config["processing_gtf_file"], - feature_type = config["feature_type"], + feature_type = config["feature_type"], + attribute_type = config["attribute_type"], extra = "-p -B -C -O --countReadPairs", # Paired-end specific options min_mapping_quality = config.get("min_mapping_quality", 2) log: @@ -161,7 +163,7 @@ rule featurecounts_paired_unique: featureCounts {params.extra} \\ -T {threads} \\ -t {params.feature_type} \\ - -g gene_id \\ + -g {params.attribute_type} \\ -Q {params.min_mapping_quality} \\ -a {params.gtf} \\ -o {output.counts} \\ diff --git a/rules/counting/single_counts.smk b/rules/counting/single_counts.smk index fe9b040..2aeefe7 100644 --- a/rules/counting/single_counts.smk +++ b/rules/counting/single_counts.smk @@ -38,7 +38,8 @@ rule featurecounts_single_all: summary = get_processing_path("{run_tag}/qc/feature_counts/{run_tag}_counts_single_all.txt.summary") params: gtf = config["processing_gtf_file"], - feature_type = config["feature_type"], + feature_type = config["feature_type"], + attribute_type = config["attribute_type"], extra = "-C -O -M" # Single-end specific options (no -p, -B) log: get_processing_path("{run_tag}/logs/featurecounts_single_all.log") @@ -76,7 +77,7 @@ rule featurecounts_single_all: featureCounts {params.extra} \\ -T {threads} \\ -t {params.feature_type} \\ - -g gene_id \\ + -g {params.attribute_type} \\ -a {params.gtf} \\ -o {output.counts} \\ {input.bam} \\ @@ -117,6 +118,7 @@ rule featurecounts_single_unique: params: gtf = config["processing_gtf_file"], feature_type = config["feature_type"], + attribute_type = config["attribute_type"], extra = "-C -O", # Single-end specific options (no -p, -B) min_mapping_quality = config.get("min_mapping_quality", 2) log: @@ -156,7 +158,7 @@ rule featurecounts_single_unique: featureCounts {params.extra} \\ -T {threads} \\ -t {params.feature_type} \\ - -g gene_id \\ + -g {params.attribute_type} \\ -Q {params.min_mapping_quality} \\ -a {params.gtf} \\ -o {output.counts} \\ diff --git a/test_config.yaml b/test_config.yaml index a206ac6..c15bcbc 100644 --- a/test_config.yaml +++ b/test_config.yaml @@ -23,6 +23,7 @@ cores_fastp: 8 cores_default: 1 max_cores: 8 feature_type: "CDS" +attribute_type: "gene_id" # Attribute used for grouping features (e.g., gene_id, transcript_id, ID) # Mark Duplicates parameters remove_duplicates: False # Set to true to remove duplicates, false to only mark them From 8ef014399316875e94256aec0a46a37227af73eb Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 14:41:30 +0000 Subject: [PATCH 02/13] Reduce CI Snakemake resource usage --- .github/workflows/test-PR.yml | 24 ++++++++++++++---------- .github/workflows/test_push.yml | 18 ++++++++++-------- 2 files changed, 24 insertions(+), 18 deletions(-) diff --git a/.github/workflows/test-PR.yml b/.github/workflows/test-PR.yml index 339cd4d..cfc9050 100644 --- a/.github/workflows/test-PR.yml +++ b/.github/workflows/test-PR.yml @@ -8,12 +8,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - + - name: Setup Python for FTP server uses: actions/setup-python@v4 with: python-version: '3.x' - + - name: Install pyftpdlib and start FTP server run: | pip install pyftpdlib @@ -21,9 +21,9 @@ jobs: python ftp_server.py & echo $! > $GITHUB_WORKSPACE/ftp_server.pid sleep 3 - curl ftp://localhost:21/ || echo "FTP server connection test failed" + curl ftp://localhost:2121/ || echo "FTP server connection test failed" echo "FTP server started with PID: $(cat $GITHUB_WORKSPACE/ftp_server.pid)" - + - name: Install Miniforge and Snakemake shell: bash -l {0} run: | @@ -40,27 +40,31 @@ jobs: run: | source "${HOME}/conda/etc/profile.d/conda.sh" conda activate snakemake - + echo "Running dry-run test..." - snakemake --cores 10 --use-conda --dry-run --config \ + snakemake --cores 4 --use-conda --dry-run --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ samples_csv="test_samples_long.csv" \ - cleanup_processing='True' + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 echo "Running full test with FTP..." - snakemake --cores 10 --use-conda --config \ + snakemake --cores 4 --use-conda --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ samples_csv="test_samples_long.csv" \ - cleanup_processing='True' - + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 + ls tests/test_counts/test_out/results -l head tests/test_counts/test_out/results/SAMPLE_02/SAMPLE_02_counts_single_all.txt diff --git a/.github/workflows/test_push.yml b/.github/workflows/test_push.yml index 784efc6..747667a 100644 --- a/.github/workflows/test_push.yml +++ b/.github/workflows/test_push.yml @@ -11,12 +11,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - + - name: Setup Python for FTP server uses: actions/setup-python@v4 with: python-version: '3.x' - + - name: Install pyftpdlib and start FTP server run: | pip install pyftpdlib @@ -24,9 +24,9 @@ jobs: python ftp_server.py & echo $! > $GITHUB_WORKSPACE/ftp_server.pid sleep 3 - curl ftp://localhost:21/ || echo "FTP server connection test failed" + curl ftp://localhost:2121/ || echo "FTP server connection test failed" echo "FTP server started with PID: $(cat $GITHUB_WORKSPACE/ftp_server.pid)" - + - name: Install Miniforge and Snakemake shell: bash -l {0} run: | @@ -43,17 +43,19 @@ jobs: run: | source "${HOME}/conda/etc/profile.d/conda.sh" conda activate snakemake - + echo "Running dry-run test..." - snakemake --cores 10 --use-conda --dry-run --config \ + snakemake --cores 4 --use-conda --dry-run --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ samples_csv="test_samples_long.csv" \ - cleanup_processing='True' - + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 + - name: Stop FTP server if: always() From 3b6fcb592aab573ea8a48e17eee7831c7d249e76 Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 15:12:13 +0000 Subject: [PATCH 03/13] Use smaller CI sample set for Snakemake --- .github/workflows/test-PR.yml | 4 ++-- .github/workflows/test_push.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test-PR.yml b/.github/workflows/test-PR.yml index cfc9050..04a4ca0 100644 --- a/.github/workflows/test-PR.yml +++ b/.github/workflows/test-PR.yml @@ -48,7 +48,7 @@ jobs: benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ - samples_csv="test_samples_long.csv" \ + samples_csv="test_samples_ftp_and_local.csv" \ cleanup_processing='True' \ cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ cores_flagstat=2 cores_nanopore_align=2 max_cores=2 @@ -60,7 +60,7 @@ jobs: benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ - samples_csv="test_samples_long.csv" \ + samples_csv="test_samples_ftp_and_local.csv" \ cleanup_processing='True' \ cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ cores_flagstat=2 cores_nanopore_align=2 max_cores=2 diff --git a/.github/workflows/test_push.yml b/.github/workflows/test_push.yml index 747667a..6b1fcd9 100644 --- a/.github/workflows/test_push.yml +++ b/.github/workflows/test_push.yml @@ -51,7 +51,7 @@ jobs: benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ - samples_csv="test_samples_long.csv" \ + samples_csv="test_samples_ftp_and_local.csv" \ cleanup_processing='True' \ cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ cores_flagstat=2 cores_nanopore_align=2 max_cores=2 From 264443b1b9d0b14dfc196d085ab64117d9e9500f Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 16:18:24 +0000 Subject: [PATCH 04/13] Restore long sample set for PR workflow runs --- .github/workflows/test-PR.yml | 24 ++++++++++++++---------- .github/workflows/test_push.yml | 20 +++++++++++--------- 2 files changed, 25 insertions(+), 19 deletions(-) diff --git a/.github/workflows/test-PR.yml b/.github/workflows/test-PR.yml index 339cd4d..cfc9050 100644 --- a/.github/workflows/test-PR.yml +++ b/.github/workflows/test-PR.yml @@ -8,12 +8,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - + - name: Setup Python for FTP server uses: actions/setup-python@v4 with: python-version: '3.x' - + - name: Install pyftpdlib and start FTP server run: | pip install pyftpdlib @@ -21,9 +21,9 @@ jobs: python ftp_server.py & echo $! > $GITHUB_WORKSPACE/ftp_server.pid sleep 3 - curl ftp://localhost:21/ || echo "FTP server connection test failed" + curl ftp://localhost:2121/ || echo "FTP server connection test failed" echo "FTP server started with PID: $(cat $GITHUB_WORKSPACE/ftp_server.pid)" - + - name: Install Miniforge and Snakemake shell: bash -l {0} run: | @@ -40,27 +40,31 @@ jobs: run: | source "${HOME}/conda/etc/profile.d/conda.sh" conda activate snakemake - + echo "Running dry-run test..." - snakemake --cores 10 --use-conda --dry-run --config \ + snakemake --cores 4 --use-conda --dry-run --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ samples_csv="test_samples_long.csv" \ - cleanup_processing='True' + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 echo "Running full test with FTP..." - snakemake --cores 10 --use-conda --config \ + snakemake --cores 4 --use-conda --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ samples_csv="test_samples_long.csv" \ - cleanup_processing='True' - + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 + ls tests/test_counts/test_out/results -l head tests/test_counts/test_out/results/SAMPLE_02/SAMPLE_02_counts_single_all.txt diff --git a/.github/workflows/test_push.yml b/.github/workflows/test_push.yml index 784efc6..6b1fcd9 100644 --- a/.github/workflows/test_push.yml +++ b/.github/workflows/test_push.yml @@ -11,12 +11,12 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - + - name: Setup Python for FTP server uses: actions/setup-python@v4 with: python-version: '3.x' - + - name: Install pyftpdlib and start FTP server run: | pip install pyftpdlib @@ -24,9 +24,9 @@ jobs: python ftp_server.py & echo $! > $GITHUB_WORKSPACE/ftp_server.pid sleep 3 - curl ftp://localhost:21/ || echo "FTP server connection test failed" + curl ftp://localhost:2121/ || echo "FTP server connection test failed" echo "FTP server started with PID: $(cat $GITHUB_WORKSPACE/ftp_server.pid)" - + - name: Install Miniforge and Snakemake shell: bash -l {0} run: | @@ -43,17 +43,19 @@ jobs: run: | source "${HOME}/conda/etc/profile.d/conda.sh" conda activate snakemake - + echo "Running dry-run test..." - snakemake --cores 10 --use-conda --dry-run --config \ + snakemake --cores 4 --use-conda --dry-run --config \ processing_dir="tests/test_counts/test_out/processing" \ results_dir="tests/test_counts/test_out/results" \ benchmark_dir="tests/test_counts/test_out/benchmarks" \ reference_fasta="tests/test_counts/genome/random_genome.fa" \ gtf_file="tests/test_counts/genome/annotation.gtf" \ - samples_csv="test_samples_long.csv" \ - cleanup_processing='True' - + samples_csv="test_samples_ftp_and_local.csv" \ + cleanup_processing='True' \ + cores_align=2 cores_coverage=2 cores_fastp=2 cores_featurecounts=2 \ + cores_flagstat=2 cores_nanopore_align=2 max_cores=2 + - name: Stop FTP server if: always() From 2ff4880e658167b8846f3b4a82e4f645563021ef Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 17:19:10 +0000 Subject: [PATCH 05/13] Convert GFF annotations upfront with validation --- Snakefile | 19 ++++++- envs/gffread.yaml | 6 +++ rules/common.smk | 5 ++ rules/processing/prepare_annotation.smk | 71 ++++++++++++++++++++++++ rules/qc/paired_rnaseq.smk | 18 +++---- rules/qc/single_rnaseq.smk | 18 +++---- rules/sample_utils.py | 72 +++++++++++++++++++++++-- 7 files changed, 186 insertions(+), 23 deletions(-) create mode 100644 envs/gffread.yaml create mode 100644 rules/processing/prepare_annotation.smk diff --git a/Snakefile b/Snakefile index 9ffdd8a..952c34c 100644 --- a/Snakefile +++ b/Snakefile @@ -106,8 +106,22 @@ except Exception as e: if "processing_genome_index" not in config: fasta_name = os.path.splitext(os.path.basename(config["reference_fasta"]))[0] config["processing_genome_index"] = os.path.join(config['processing_dir'], 'reference', fasta_name) + if "processing_annotation_source" not in config: + config["processing_annotation_source"] = os.path.join( + config['processing_dir'], 'reference', os.path.basename(config["gtf_file"]) + ) if "processing_gtf_file" not in config: - config["processing_gtf_file"] = os.path.join(config['processing_dir'], 'reference', os.path.basename(config["gtf_file"])) + gtf_basename = os.path.basename(config["gtf_file"]) + annotation_stem, annotation_ext = os.path.splitext(gtf_basename) + if annotation_stem.endswith(".gff"): + annotation_stem = os.path.splitext(annotation_stem)[0] + if annotation_ext.lower() in (".gff", ".gff3"): + derived_gtf = f"{annotation_stem}.gtf" + else: + derived_gtf = gtf_basename + config["processing_gtf_file"] = os.path.join( + config['processing_dir'], 'reference', derived_gtf + ) if "processing_reference_fasta" not in config: config["processing_reference_fasta"] = os.path.join( config['processing_dir'], 'reference', os.path.basename(config["reference_fasta"]) or "reference.fa" @@ -203,6 +217,9 @@ onstart: # Include common functions include: "rules/common.smk" +# Prepare annotation for downstream steps (convert GFF->GTF, validate feature/attribute) +include: "rules/processing/prepare_annotation.smk" + # Build Bowtie2 indexes from the staged reference FASTA include: "rules/processing/build_bowtie_index.smk" diff --git a/envs/gffread.yaml b/envs/gffread.yaml new file mode 100644 index 0000000..df2a187 --- /dev/null +++ b/envs/gffread.yaml @@ -0,0 +1,6 @@ +name: gffread +channels: + - conda-forge + - bioconda +dependencies: + - gffread=0.12.7 diff --git a/rules/common.smk b/rules/common.smk index 8ffe26d..c8c4aa0 100644 --- a/rules/common.smk +++ b/rules/common.smk @@ -37,6 +37,11 @@ def get_bowtie2_index_files(): """Return the expected Bowtie2 index files within the processing directory.""" return [f"{config['processing_genome_index']}{ext}" for ext in BOWTIE2_INDEX_SUFFIXES] + +def get_annotation_gtf(wildcards=None): + """Return the staged annotation path used across the pipeline.""" + return config["processing_gtf_file"] + # Helper function to get results directory path def get_results_path(*args): """Get a path within the results directory specified in config""" diff --git a/rules/processing/prepare_annotation.smk b/rules/processing/prepare_annotation.smk new file mode 100644 index 0000000..6428a1d --- /dev/null +++ b/rules/processing/prepare_annotation.smk @@ -0,0 +1,71 @@ +""" +Prepare the annotation for downstream rules. + +* If the user supplies a GFF/GFF3 annotation, convert it to GTF via gffread. +* Validate that the configured feature and attribute exist in the final GTF. +""" + +import os +from pathlib import Path + +from sample_utils import validate_feature_attribute + +ANNOTATION_NEEDS_CONVERSION = config["processing_annotation_source"] != config["processing_gtf_file"] + + +def _annotation_source(wildcards=None): + return config["processing_annotation_source"] + + +def _annotation_gtf(wildcards=None): + return config["processing_gtf_file"] + + +def _validation_flag(wildcards=None): + return os.path.join(config["processing_dir"], "reference", ".annotation_validated") + + +def _validate(gtf_path, feature_type=None, attribute_type=None): + validate_feature_attribute( + gtf_path, + feature_type or config.get("feature_type"), + attribute_type or config.get("attribute_type"), + ) + + +if ANNOTATION_NEEDS_CONVERSION: + rule prepare_annotation: + input: + source=_annotation_source, + output: + gtf=_annotation_gtf, + flag=_validation_flag, + params: + feature_type=lambda wildcards: config.get("feature_type"), + attribute_type=lambda wildcards: config.get("attribute_type"), + threads: + 1 + conda: + "../../envs/gffread.yaml" + singularity: + config.get("singularity_image", "") + run: + shell("mkdir -p $(dirname {output.gtf})") + shell("gffread {input.source} -T -o {output.gtf}") + _validate(output.gtf, params.feature_type, params.attribute_type) + Path(output.flag).touch() +else: + rule prepare_annotation: + input: + gtf=_annotation_gtf, + output: + gtf=_annotation_gtf, + flag=_validation_flag, + params: + feature_type=lambda wildcards: config.get("feature_type"), + attribute_type=lambda wildcards: config.get("attribute_type"), + threads: + 1 + run: + _validate(input.gtf, params.feature_type, params.attribute_type) + Path(output.flag).touch() diff --git a/rules/qc/paired_rnaseq.smk b/rules/qc/paired_rnaseq.smk index a9b8ecb..0d02f4b 100644 --- a/rules/qc/paired_rnaseq.smk +++ b/rules/qc/paired_rnaseq.smk @@ -9,13 +9,13 @@ rule qualimap_rnaseq_paired: input: bam = get_picard_bam, bai = lambda wildcards: f"{get_picard_bam(wildcards)}.bai", - bamqc_flag = get_processing_path("{run_tag}/bamqc_complete.flag") + bamqc_flag = get_processing_path("{run_tag}/bamqc_complete.flag"), + gtf = get_annotation_gtf output: dir = directory(get_processing_path("{run_tag}/qc/{run_tag}_qualimap_rnaseq/")), flag = get_processing_path("{run_tag}/qc_paired_complete.flag") params: - memory = config.get("qualimap_memory", "10G"), - gtf = config["processing_gtf_file"] + memory = config.get("qualimap_memory", "10G") log: stderr = get_processing_path("{run_tag}/logs/qualimap_rnaseq.log"), stdout = get_processing_path("{run_tag}/logs/qualimap_rnaseq.stdout.log") @@ -36,20 +36,20 @@ rule qualimap_rnaseq_paired: # Log start echo "Running qualimap rnaseq (paired-end) on {wildcards.run_tag}" > {log.stderr} echo "Input BAM: {input.bam}" >> {log.stderr} - echo "GTF file: {params.gtf}" >> {log.stderr} + echo "GTF file: {input.gtf}" >> {log.stderr} echo "Output directory: {output.dir}" >> {log.stderr} echo "Java memory: {params.memory}" >> {log.stderr} - + # Check if GTF file exists - if [[ ! -f {params.gtf} ]]; then - echo "ERROR: GTF file {params.gtf} not found" >> {log.stderr} + if [[ ! -f {input.gtf} ]]; then + echo "ERROR: GTF file {input.gtf} not found" >> {log.stderr} exit 1 fi - + # Run qualimap rnaseq with paired-end option qualimap rnaseq --java-mem-size={params.memory} \\ -bam {input.bam} \\ - -gtf {params.gtf} \\ + -gtf {input.gtf} \\ -outdir {output.dir} \\ -outformat HTML \\ -pe \\ diff --git a/rules/qc/single_rnaseq.smk b/rules/qc/single_rnaseq.smk index 2e31a68..fa2891c 100644 --- a/rules/qc/single_rnaseq.smk +++ b/rules/qc/single_rnaseq.smk @@ -9,13 +9,13 @@ rule qualimap_rnaseq_single: input: bam = get_picard_bam, bai = lambda wildcards: f"{get_picard_bam(wildcards)}.bai", - bamqc_flag = get_processing_path("{run_tag}/bamqc_complete.flag") + bamqc_flag = get_processing_path("{run_tag}/bamqc_complete.flag"), + gtf = get_annotation_gtf output: dir = directory(get_processing_path("{run_tag}/qc/{run_tag}_qualimap_rnaseq/")), flag = get_processing_path("{run_tag}/qc_single_complete.flag") params: - memory = config.get("qualimap_memory", "10G"), - gtf = config["processing_gtf_file"] + memory = config.get("qualimap_memory", "10G") log: stderr = get_processing_path("{run_tag}/logs/qualimap_rnaseq.log"), stdout = get_processing_path("{run_tag}/logs/qualimap_rnaseq.stdout.log") @@ -36,20 +36,20 @@ rule qualimap_rnaseq_single: # Log start echo "Running qualimap rnaseq (single-end) on {wildcards.run_tag}" > {log.stderr} echo "Input BAM: {input.bam}" >> {log.stderr} - echo "GTF file: {params.gtf}" >> {log.stderr} + echo "GTF file: {input.gtf}" >> {log.stderr} echo "Output directory: {output.dir}" >> {log.stderr} echo "Java memory: {params.memory}" >> {log.stderr} - + # Check if GTF file exists - if [[ ! -f {params.gtf} ]]; then - echo "ERROR: GTF file {params.gtf} not found" >> {log.stderr} + if [[ ! -f {input.gtf} ]]; then + echo "ERROR: GTF file {input.gtf} not found" >> {log.stderr} exit 1 fi - + # Run qualimap rnaseq without paired-end option qualimap rnaseq --java-mem-size={params.memory} \\ -bam {input.bam} \\ - -gtf {params.gtf} \\ + -gtf {input.gtf} \\ -outdir {output.dir} \\ -outformat HTML \\ > {log.stdout} 2>> {log.stderr} diff --git a/rules/sample_utils.py b/rules/sample_utils.py index f1939ba..b529611 100644 --- a/rules/sample_utils.py +++ b/rules/sample_utils.py @@ -1,6 +1,7 @@ """ Utility functions for sample handling in the RNA-seq pipeline. """ +import gzip import os import pandas as pd import shutil @@ -35,10 +36,21 @@ def copy_reference_files(config): fasta_stem = os.path.splitext(fasta_stem)[0] target_fasta = os.path.join(target_dir, fasta_basename) target_genome_base = os.path.join(target_dir, fasta_stem) - target_gtf_file = os.path.join(target_dir, os.path.basename(src_gtf_file)) + + annotation_basename = os.path.basename(src_gtf_file) + annotation_stem, annotation_ext = os.path.splitext(annotation_basename) + if annotation_stem.endswith(".gff"): + annotation_stem = os.path.splitext(annotation_stem)[0] + + target_annotation_source = os.path.join(target_dir, annotation_basename) + if annotation_ext.lower() in (".gff", ".gff3"): + target_gtf_file = os.path.join(target_dir, f"{annotation_stem}.gtf") + else: + target_gtf_file = target_annotation_source config["processing_reference_fasta"] = target_fasta config["processing_genome_index"] = target_genome_base + config["processing_annotation_source"] = target_annotation_source config["processing_gtf_file"] = target_gtf_file if not os.path.exists(target_fasta): @@ -48,10 +60,10 @@ def copy_reference_files(config): except Exception as e: print(f"Warning: Failed to copy FASTA file {src_fasta}: {e}") - if not os.path.exists(target_gtf_file): - print(f"Copying GTF file from {src_gtf_file} to {target_gtf_file}") + if not os.path.exists(target_annotation_source): + print(f"Copying GTF file from {src_gtf_file} to {target_annotation_source}") try: - shutil.copy2(src_gtf_file, target_gtf_file) + shutil.copy2(src_gtf_file, target_annotation_source) except Exception as e: print(f"Warning: Failed to copy GTF file: {e}") @@ -283,6 +295,58 @@ def validate_reference_inputs(config): print(f"Found reference FASTA at {fasta_path} and GTF at {gtf_path}") + +def validate_feature_attribute(gtf_path, feature_type, attribute_key): + """Ensure the requested feature and attribute exist in a GTF/GFF3 file.""" + + if not feature_type or not attribute_key: + raise ValueError( + "ERROR: feature_type and attribute_type must be set in the config to validate the annotation." + ) + + found_feature = False + found_attribute = False + open_func = gzip.open if gtf_path.endswith(".gz") else open + + with open_func(gtf_path, "rt") as handle: + for line in handle: + if not line or line.startswith("#"): + continue + + parts = line.rstrip("\n").split("\t") + if len(parts) < 9 or parts[2] != feature_type: + continue + + found_feature = True + attributes = parts[8] + + for field in attributes.split(";"): + field = field.strip() + if not field: + continue + + if " " in field: + key, _ = field.split(" ", 1) + elif "=" in field: + key, _ = field.split("=", 1) + else: + continue + + if key == attribute_key: + found_attribute = True + break + + if found_attribute: + break + + if not found_feature: + raise ValueError(f"ERROR: Feature type '{feature_type}' not found in {gtf_path}.") + + if not found_attribute: + raise ValueError( + f"ERROR: Attribute '{attribute_key}' not found for feature type '{feature_type}' in {gtf_path}." + ) + def is_sample_completed(config, sample, samples_df): """Check if a sample has already been processed""" try: From 4245612c985bfa3e823602c7a22b0266232e3748 Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 17:25:10 +0000 Subject: [PATCH 06/13] Fix prepare_annotation rule outputs --- rules/processing/prepare_annotation.smk | 29 +++++++++---------------- 1 file changed, 10 insertions(+), 19 deletions(-) diff --git a/rules/processing/prepare_annotation.smk b/rules/processing/prepare_annotation.smk index 6428a1d..72657fc 100644 --- a/rules/processing/prepare_annotation.smk +++ b/rules/processing/prepare_annotation.smk @@ -10,19 +10,10 @@ from pathlib import Path from sample_utils import validate_feature_attribute -ANNOTATION_NEEDS_CONVERSION = config["processing_annotation_source"] != config["processing_gtf_file"] - - -def _annotation_source(wildcards=None): - return config["processing_annotation_source"] - - -def _annotation_gtf(wildcards=None): - return config["processing_gtf_file"] - - -def _validation_flag(wildcards=None): - return os.path.join(config["processing_dir"], "reference", ".annotation_validated") +ANNOTATION_SOURCE = config["processing_annotation_source"] +ANNOTATION_GTF = config["processing_gtf_file"] +VALIDATION_FLAG = os.path.join(config["processing_dir"], "reference", ".annotation_validated") +ANNOTATION_NEEDS_CONVERSION = ANNOTATION_SOURCE != ANNOTATION_GTF def _validate(gtf_path, feature_type=None, attribute_type=None): @@ -36,10 +27,10 @@ def _validate(gtf_path, feature_type=None, attribute_type=None): if ANNOTATION_NEEDS_CONVERSION: rule prepare_annotation: input: - source=_annotation_source, + source=ANNOTATION_SOURCE, output: - gtf=_annotation_gtf, - flag=_validation_flag, + gtf=ANNOTATION_GTF, + flag=VALIDATION_FLAG, params: feature_type=lambda wildcards: config.get("feature_type"), attribute_type=lambda wildcards: config.get("attribute_type"), @@ -57,10 +48,10 @@ if ANNOTATION_NEEDS_CONVERSION: else: rule prepare_annotation: input: - gtf=_annotation_gtf, + gtf=ANNOTATION_GTF, output: - gtf=_annotation_gtf, - flag=_validation_flag, + gtf=ANNOTATION_GTF, + flag=VALIDATION_FLAG, params: feature_type=lambda wildcards: config.get("feature_type"), attribute_type=lambda wildcards: config.get("attribute_type"), From 97e49c3448de727cf7b32cf881f667549367cbe5 Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 17:33:07 +0000 Subject: [PATCH 07/13] Fix prepare_annotation cycle for native GTF inputs --- rules/processing/prepare_annotation.smk | 1 - tests/test_counts/genome/test.gff | 9 ++++++ tests/test_counts/gff_config.yaml | 37 +++++++++++++++++++++++++ 3 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 tests/test_counts/genome/test.gff create mode 100644 tests/test_counts/gff_config.yaml diff --git a/rules/processing/prepare_annotation.smk b/rules/processing/prepare_annotation.smk index 72657fc..4c1c1f3 100644 --- a/rules/processing/prepare_annotation.smk +++ b/rules/processing/prepare_annotation.smk @@ -50,7 +50,6 @@ else: input: gtf=ANNOTATION_GTF, output: - gtf=ANNOTATION_GTF, flag=VALIDATION_FLAG, params: feature_type=lambda wildcards: config.get("feature_type"), diff --git a/tests/test_counts/genome/test.gff b/tests/test_counts/genome/test.gff new file mode 100644 index 0000000..541aa8d --- /dev/null +++ b/tests/test_counts/genome/test.gff @@ -0,0 +1,9 @@ +test_genome Prediction transcript 11 500 . + . transcript_id "gene1.1"; gene_id "gene1"; +test_genome Prediction exon 11 500 . + . transcript_id "gene1.1"; gene_id "gene1"; +test_genome Prediction CDS 11 500 . + 0 transcript_id "gene1.1"; gene_id "gene1"; +test_genome Prediction transcript 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; +test_genome Prediction exon 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; +test_genome Prediction CDS 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; +test_genome Prediction transcript 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; +test_genome Prediction exon 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; +test_genome Prediction CDS 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; \ No newline at end of file diff --git a/tests/test_counts/gff_config.yaml b/tests/test_counts/gff_config.yaml new file mode 100644 index 0000000..3a12649 --- /dev/null +++ b/tests/test_counts/gff_config.yaml @@ -0,0 +1,37 @@ +# Test configuration using GFF annotation to exercise conversion +processing_dir: "tests/test_counts/test_out_gff/processing" +results_dir: "tests/test_counts/test_out_gff/results" +benchmark_dir: "tests/test_counts/test_out_gff/benchmarks" + +samples_csv: "test_samples_long.csv" +selected_samples: [] + +reference_fasta: "tests/test_counts/genome/random_genome.fa" +gtf_file: "tests/test_counts/genome/test.gff" + +cores_align: 4 +cores_coverage: 4 +cores_flagstat: 4 +cores_featurecounts: 4 +cores_fastp: 4 +cores_default: 1 +max_cores: 4 +feature_type: "CDS" +attribute_type: "gene_id" + +remove_duplicates: False +qualimap_memory: "2G" + +coverage_bin_size: 50 +coverage_normalize: "RPKM" +min_mapping_quality: 2 + +copy_fastq: False +copy_bam: False +copy_benchmarks: False +copy_logs: False +cleanup_processing: False + +max_resources: + network: 2 + io: 1000 From cce8b4d6ebe00cefc68bbf631b39e28607093ea7 Mon Sep 17 00:00:00 2001 From: mtinti Date: Mon, 15 Dec 2025 17:39:01 +0000 Subject: [PATCH 08/13] Update GFF test fixture --- tests/test_counts/genome/test.gff | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/tests/test_counts/genome/test.gff b/tests/test_counts/genome/test.gff index 541aa8d..137830f 100644 --- a/tests/test_counts/genome/test.gff +++ b/tests/test_counts/genome/test.gff @@ -1,9 +1,15 @@ -test_genome Prediction transcript 11 500 . + . transcript_id "gene1.1"; gene_id "gene1"; -test_genome Prediction exon 11 500 . + . transcript_id "gene1.1"; gene_id "gene1"; -test_genome Prediction CDS 11 500 . + 0 transcript_id "gene1.1"; gene_id "gene1"; -test_genome Prediction transcript 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; -test_genome Prediction exon 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; -test_genome Prediction CDS 2001 2500 . + . transcript_id "gene2.1"; gene_id "gene2"; -test_genome Prediction transcript 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; -test_genome Prediction exon 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; -test_genome Prediction CDS 4001 4500 . + . transcript_id "gene3.1"; gene_id "gene3"; \ No newline at end of file +##gff-version 3 +##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=185431 +##sequence-region test_genome 1 5000 +test_genome Prediction protein_coding_gene 11 500 . - . ID=gene1;description=test_desc gene1;ebi_biotype=protein_coding +test_genome Prediction mRNA 11 500 . - . ID=gene1:mRNA;Parent=gene1;description=test_desc gene1;gene_ebi_biotype=protein_coding +test_genome Prediction exon 11 500 . - . ID=exon_gene1:mRNA-E1;Parent=gene1:mRNA;gene_id=gene1 +test_genome Prediction CDS 11 500 . - 0 ID=gene1:mRNA-p1-CDS1;Parent=gene1:mRNA;gene_id=gene1;protein_source_id=gene1:mRNA-p1 +test_genome Prediction protein_coding_gene 2001 2500 . - . ID=gene2;description=test_desc gene2;ebi_biotype=protein_coding +test_genome Prediction mRNA 2001 2500 . - . ID=gene2:mRNA;Parent=gene1;description=test_desc gene2;gene_ebi_biotype=protein_coding +test_genome Prediction exon 2001 2500 . - . ID=exon_gene2:mRNA-E1;Parent=gene2:mRNA;gene_id=gene2 +test_genome Prediction CDS 2001 2500 . - 0 ID=gene2:mRNA-p1-CDS1;Parent=gene2:mRNA;gene_id=gene2;protein_source_id=gene2:mRNA-p1 +test_genome Prediction protein_coding_gene 4001 4500 . - . ID=gene3;description=test_desc gene3;ebi_biotype=protein_coding +test_genome Prediction mRNA 4001 4500 . - . ID=gene3:mRNA;Parent=gene1;description=test_desc gene3;gene_ebi_biotype=protein_coding +test_genome Prediction exon 4001 4500 . - . 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z92nlg;$AnPMK%(g7A0={4TXCb?_LBGK?PgWxmJmePoRlOG#uiJ!%Kr3Ztnx*ed7b$ zeH*l5l&$Yx8$)B@nY@BdL^=1>rC~5@fZ+sxKFxmDj;i)>&b^-!x`L(+@%s;AZY$?( z`&0+H(pMpH?#d0$x#Lp*1+?D0yf?_F?$y!G@#gPmc{yd z@U(DpPlz@UjAp`?M3@6VBm~osxQQ|K&d!D5<9!F2{{*#Rb`Y^)NWcuH(R`%UYV=R? z2#xJM!u%fLdXLEeSZ~#YH6MEqYWg%EAJ!IYnm=wXgQWX}7DnmE7xkoOMDy{WX0OKb MWJ os.path.getmtime(target_fasta): + needs_fasta_copy = True + print(f"Source FASTA is newer than cached copy, updating...") + + if needs_fasta_copy: print(f"Copying FASTA file from {src_fasta} to {target_fasta}") try: shutil.copy2(src_fasta, target_fasta) except Exception as e: print(f"Warning: Failed to copy FASTA file {src_fasta}: {e}") + # Copy annotation if it doesn't exist or if source is newer + needs_annotation_copy = False if not os.path.exists(target_annotation_source): - print(f"Copying GTF file from {src_gtf_file} to {target_annotation_source}") + needs_annotation_copy = True + elif os.path.getmtime(src_gtf_file) > os.path.getmtime(target_annotation_source): + needs_annotation_copy = True + print(f"Source annotation is newer than cached copy, updating...") + + if needs_annotation_copy: + print(f"Copying annotation file from {src_gtf_file} to {target_annotation_source}") try: shutil.copy2(src_gtf_file, target_annotation_source) except Exception as e: - print(f"Warning: Failed to copy GTF file: {e}") + print(f"Warning: Failed to copy annotation file: {e}") def create_sample_directories(config, sample_name): """Create the necessary directory structure for a specific sample""" diff --git a/tests/.DS_Store b/tests/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..384b3be5e5ee244f5219a9bd364c577cc8a0fd5b GIT binary patch literal 6148 zcmeHKyG{c^3>-s>NNG~0++W}iR#Er@J^+-2F5-$K{Z)JypO*2XAUfzm6OAQ%cD{$d z(|#CEULunMQa}nw0VyB_Zlpjp*5&F(_vsobAO-G60slTUx??Y#664ds5F-F_!E_kc zF-s7eCy2dpN@Rv+NhK!LYQ(UlGvBJN7fy*uht=?5^<=9F#p3C_zePE$Cn`z-DR8a8 zV{X^p|DWl9%>UOU?WBMdxGM#0v3uEV`AXGWXD{cyw$b0{Uh_?N<2on|(T<7Hj=Ax6 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Program:featureCounts v2.1.1; Command:"featureCounts" "-p" "-B" "-C" "-M" "-O" "--countReadPairs" "-T" "8" "-t" "CDS" "-g" "gene_id" "-a" "tests/test_counts/test_out/processing/reference/test.gtf" "-o" "tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01_counts_paired_all.txt" "tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01.picard.bam" +Geneid Chr Start End Strand Length tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01.picard.bam +gene1 test_genome;test_genome;test_genome 11;2001;4001 500;2500;4500 -;-;- 1490 20 diff --git a/tests/test_counts/test_out/results/SAMPLE_01/SAMPLE_01_counts_paired_unique.txt b/tests/test_counts/test_out/results/SAMPLE_01/SAMPLE_01_counts_paired_unique.txt new file mode 100644 index 0000000..84e8e19 --- /dev/null +++ b/tests/test_counts/test_out/results/SAMPLE_01/SAMPLE_01_counts_paired_unique.txt @@ -0,0 +1,3 @@ +# Program:featureCounts v2.1.1; Command:"featureCounts" "-p" "-B" "-C" "-O" "--countReadPairs" "-T" "8" "-t" "CDS" "-g" "gene_id" "-Q" "2" "-a" "tests/test_counts/test_out/processing/reference/test.gtf" "-o" "tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01_counts_paired_unique.txt" "tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01.picard.bam" +Geneid Chr Start End Strand Length tests/test_counts/test_out/processing/SAMPLE_01/SAMPLE_01.picard.bam +gene1 test_genome;test_genome;test_genome 11;2001;4001 500;2500;4500 -;-;- 1490 20 diff --git a/tests/test_counts/test_out/results/SAMPLE_01/SAMPLE_01_unique.bw b/tests/test_counts/test_out/results/SAMPLE_01/SAMPLE_01_unique.bw new file mode 100644 index 0000000000000000000000000000000000000000..93bacb0883bf9def5b6b20e7ff40396f34184837 GIT binary patch literal 833 zcmY%U)8E0uz{n86$N&cYP&$+e!bc_zpmGci2+;=|5cW!_`j=SrAyf~2R);W#9~xeT z6*@97DA<|TvN(O&KI@0!*=pyBJ*O%_!Nm>4pdf+;9ZWYPP^2WaxFkM3H7`Fm6(kHY z8m6pbj_t*TT!#WA+8!3W6bK(aw#xHhj)}yP9aC91Ur!JbTzq0v_yg7%M@*Xod(${Qmmp!-wPS_?j)3r%&JU|8ea8vYhub!qdaVH1$>+>))1~x60V(6OaC_lpovr 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+div.header div.rel { + margin-top: 1em; +} + +div.header div.rel a { + color: #fcaf3e; + letter-spacing: .1em; + text-transform: uppercase; +} + +p.logo { + float: right; +} + +img.logo { + border: 0; +} + + +/* Content */ +div.content-wrapper { + background-color: white; + padding-top: 20px; + padding-bottom: 20px; +} + +div.document { + width: 50em; + float: left; +} + +div.body { + padding-right: 2em; + text-align: justify; +} + +div.document h1 { + line-height: 120%; +} + +div.document ul { + margin: 1.5em; + list-style-type: square; +} + +div.document dd { + margin-left: 1.2em; + margin-top: .4em; + margin-bottom: 1em; +} + +div.document .section { + margin-top: 1.7em; +} +div.document .section:first-child { + margin-top: 0px; +} + +div.document div.highlight { + padding: 3px; + background-color: #eeeeec; + border-top: 2px solid #dddddd; + border-bottom: 2px solid #dddddd; + margin-top: .8em; + margin-bottom: .8em; +} + +div.document h2 { + margin-top: .7em; +} + +div.document p { + margin-bottom: .5em; +} + +div.document li.toctree-l1 { + margin-bottom: 1em; +} + +div.document .descname { + font-weight: bold; +} + +div.document .docutils.literal { + background-color: #eeeeec; + padding: 1px; +} + +div.document .docutils.xref.literal { + background-color: transparent; + padding: 0px; +} + +div.document blockquote { + margin: 1em; +} + +div.document ol { + margin: 1.5em; +} + + +/* Sidebar */ + +div.sidebar { + width: 20em; + float: right; + font-size: .9em; +} + +div.sidebar a, div.header a { + text-decoration: none; +} + +div.sidebar a:hover, div.header a:hover { + text-decoration: underline; +} + +div.sidebar h3 { + color: #2e3436; + text-transform: uppercase; + font-size: 130%; + letter-spacing: .1em; +} + +div.sidebar ul { + list-style-type: none; +} + +div.sidebar li.toctree-l1 a { + display: block; + padding: 1px; + border: 1px solid #dddddd; + background-color: #eeeeec; + margin-bottom: .4em; + padding-left: 3px; + color: #2e3436; +} + +div.sidebar li.toctree-l2 a { + background-color: transparent; + border: none; + margin-left: 1em; + border-bottom: 1px solid #dddddd; +} + +div.sidebar li.toctree-l3 a { + background-color: transparent; + border: none; + margin-left: 2em; + border-bottom: 1px solid #dddddd; +} + +div.sidebar li.toctree-l2:last-child a { + border-bottom: none; +} + +div.sidebar li.toctree-l1.current a { + border-right: 5px solid #fcaf3e; +} + +div.sidebar li.toctree-l1.current li.toctree-l2 a { + border-right: none; +} + +div.sidebar input[type="text"] { + width: 170px; +} + +div.sidebar input[type="submit"] { + width: 30px; +} + + +/* Footer */ + +div.footer-wrapper { + background: url(bgfooter.png) top left repeat-x; + border-top: 4px solid #babdb6; + padding-top: 10px; + padding-bottom: 10px; + min-height: 80px; +} + +div.footer, div.footer a { + color: #888a85; +} + +div.footer .right { + text-align: right; +} + +div.footer .left { + text-transform: uppercase; +} + + +/* Styles copied from basic theme */ + +img.align-left, .figure.align-left, object.align-left { + clear: left; + float: left; + margin-right: 1em; +} + +img.align-right, .figure.align-right, object.align-right { + clear: right; + float: right; + margin-left: 1em; +} + +img.align-center, .figure.align-center, object.align-center { + display: block; + margin-left: auto; + margin-right: auto; +} + +img.align-center-qualimap { + display: block; + margin-left: auto; + margin-right: auto; + width: 100% +} + +.align-left { + text-align: left; +} + +.align-center { + text-align: center; +} + +.align-right { + text-align: right; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li div.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable dl, table.indextable dd { + margin-top: 0; + margin-bottom: 0; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +/* -- viewcode extension ---------------------------------------------------- */ + +.viewcode-link { + float: right; +} + +.viewcode-back { + float: right; + 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list-style: none; +} + +div.related li { + display: inline; +} + +div.related li.right { + float: right; + margin-right: 5px; +} + +/* -- sidebar --------------------------------------------------------------- */ + +div.sphinxsidebarwrapper { + padding: 10px 5px 0 10px; +} + +div.sphinxsidebar { + float: left; + width: 0px; + margin-left: -100%; + font-size: 90%; +} + +div.sphinxsidebar ul { + list-style: none; +} + +div.sphinxsidebar ul ul, +div.sphinxsidebar ul.want-points { + margin-left: 20px; + list-style: square; +} + +div.sphinxsidebar ul ul { + margin-top: 0; + margin-bottom: 0; +} + +div.sphinxsidebar form { + margin-top: 10px; +} + +div.sphinxsidebar input { + border: 1px solid #98dbcc; + font-family: sans-serif; + font-size: 1em; +} + +div.sphinxsidebar #searchbox input[type="text"] { + width: 170px; +} + +div.sphinxsidebar #searchbox input[type="submit"] { + width: 30px; +} + +img { + border: 0; +} + +/* -- search page ----------------------------------------------------------- */ + +ul.search { + margin: 10px 0 0 20px; + padding: 0; +} + +ul.search li { + padding: 5px 0 5px 20px; + background-image: url(file.png); + background-repeat: no-repeat; + background-position: 0 7px; +} + +ul.search li a { + font-weight: bold; +} + +ul.search li div.context { + color: #888; + margin: 2px 0 0 30px; + text-align: left; +} + +ul.keywordmatches li.goodmatch a { + font-weight: bold; +} + +/* -- index page ------------------------------------------------------------ */ + +table.contentstable { + width: 90%; +} + +table.contentstable p.biglink { + line-height: 150%; +} + +a.biglink { + font-size: 1.3em; +} + +span.linkdescr { + font-style: italic; + padding-top: 5px; + font-size: 90%; +} + +/* -- general index --------------------------------------------------------- */ + +table.indextable { + width: 100%; +} + +table.indextable td { + text-align: left; + vertical-align: top; +} + +table.indextable dl, table.indextable dd { + margin-top: 0; + margin-bottom: 0; +} + +table.indextable tr.pcap { + height: 10px; +} + +table.indextable tr.cap { + margin-top: 10px; + background-color: #f2f2f2; +} + +img.toggler { + margin-right: 3px; + margin-top: 3px; + cursor: pointer; +} + +div.modindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +div.genindex-jumpbox { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; + margin: 1em 0 1em 0; + padding: 0.4em; +} + +/* -- general body styles --------------------------------------------------- */ + +a.headerlink { + visibility: hidden; +} + +h1:hover > a.headerlink, +h2:hover > a.headerlink, +h3:hover > a.headerlink, +h4:hover > a.headerlink, +h5:hover > a.headerlink, +h6:hover > a.headerlink, +dt:hover > a.headerlink { + visibility: visible; +} + +div.body p.caption { + text-align: inherit; +} + +div.body td { + text-align: left; +} + +.field-list ul { + padding-left: 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node.nextSibling)); + node.nodeValue = val.substr(0, pos); + } + } + else if (!jQuery(node).is("button, select, textarea")) { + jQuery.each(node.childNodes, function() { + highlight(this); + }); + } + } + return this.each(function() { + highlight(this); + }); +}; + +/** + * Small JavaScript module for the documentation. + */ +var Documentation = { + + init : function() { + this.fixFirefoxAnchorBug(); + this.highlightSearchWords(); + this.initIndexTable(); + }, + + /** + * i18n support + */ + TRANSLATIONS : {}, + PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; }, + LOCALE : 'unknown', + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext : function(string) { + var translated = Documentation.TRANSLATIONS[string]; + if (typeof translated == 'undefined') + return string; + return (typeof translated == 'string') ? translated : translated[0]; + }, + + ngettext : function(singular, plural, n) { + 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'...' : '') + + $.trim(text.substr(start, 240)) + + ((start + 240 - text.length) ? '...' : ''); + var rv = $('
').text(excerpt); + $.each(hlwords, function() { + rv = rv.highlightText(this, 'highlighted'); + }); + return rv; +} + + +/** + * Porter Stemmer + */ +var Stemmer = function() { + + var step2list = { + ational: 'ate', + tional: 'tion', + enci: 'ence', + anci: 'ance', + izer: 'ize', + bli: 'ble', + alli: 'al', + entli: 'ent', + eli: 'e', + ousli: 'ous', + ization: 'ize', + ation: 'ate', + ator: 'ate', + alism: 'al', + iveness: 'ive', + fulness: 'ful', + ousness: 'ous', + aliti: 'al', + iviti: 'ive', + biliti: 'ble', + logi: 'log' + }; + + var step3list = { + icate: 'ic', + ative: '', + alize: 'al', + iciti: 'ic', + ical: 'ic', + ful: '', + ness: '' + }; + + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, success: null, + dataType: "script", cache: true}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (var i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + }; + pulse(); + }, + + /** + * perform a search for something + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('

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