QC parser for SMaHT
Parses outputs of different QC tools and unifies them for the SMaHT portal
Installation
Simply run pip install qc-parser to install the package. You need at least Python 3.8.
To develop this package, clone this repo, make sure poetry is installed on your system and run make install.
Usage
After installation the following command can be run from the command line:
parse-qc \
-n 'BAM Quality Metrics' \
--metrics samtools /PATH/samtools.stats.txt \
--metrics picard_CollectInsertSizeMetrics /PATH/picard_cis_metrics.txt \
--additional-files /PATH/additional_output_1.pdf \
--additional-files /PATH/additional_output_2.tsv \
--output-zip metrics.zip
--output-json qc_values.json
In this example, the tool will parse the Samtools output file /PATH/samtools.stats.txt and the Picard output file /PATH/picard_cis_metrics.txt. The values that are extracted from both files are specified in src/metrics_to_extract.py. All metrics are combined and stored in qc_values.json that is compatible with Tibanna_ff's generic QC functionality.
The metrics.zip will contain the following files:
samtools.stats.txt
picard_cis_metrics.txt
additional_output_1.pdf
additional_output_2.tsv
The currently supported QC tools are:
- samtools_stats (Samtools stats)
- picard_CollectAlignmentSummaryMetrics (Picard CollectAlignmentSummaryMetrics)
- picard_CollectInsertSizeMetrics (Picard CollectInsertSizeMetrics)
- picard_CollectWgsMetrics (Picard CollectWgsMetrics)
- bamstats (bamStats.py)
- fastqc (FastQC)
- rnaseqc (RNA-SeQC)
- nanoplot (NanoPlot)
- verifybamid2 (VerifyBamID2)
- kraken2 (Kraken2)
- mosdepth (mosdepth)
- somalier (Somalier)
- tissue_classifier (internal tissue classification tool for RNA-Seq data)
Development
If you want to extract a new metric from an already supported QC tool, add the metric to the src/metrics_to_extract.py in the appropriate section.
If you want to add suuport for a new QC tool, you need to add a parser to src/MetricsParser.py and add the metrics you want to extract from the tool to src/metrics_to_extract.py.
Tests
The command make test will run local tests.
Release files for qc-parser 0.8.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| qc_parser-0.8.3.tar.gz | 15.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| qc_parser-0.8.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 31.1 kB
Release files / qc_parser-0.8.3.tar.gz
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| Size | 15.0 kB |
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Release files / qc_parser-0.8.3-py3-none-any.whl
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