qc-parser 0.5.0

Parses outputs of different QC tools and unifies them for the SMaHT portal

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)

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.