PLEASE SEE https://github.com/jts/ncov-tools for an updated version of the package.
The ncov_parser package provides a suite of tools to parse the files generated
in the Nextflow workflow and provide a QC summary file. The package requires
several files including:
- .variants.tsv
- .qc.csv
- .per_base_coverage.bed
- .primertrimmed.consensus.fa
- .fa
An optional metadata file with ct values can be included.
In addition, bedtools should be run to generate a
<sample>.per_base_coverage.bed file to generate mean and median depth of
coverage statistics.
After downloading the repository, the package can be installed using pip:
git clone [email protected]:rdeborja/ncov_parser.git
cd ncov_parser
pip install .
The library consists of several functions that can be imported.
from ncov.parser.qc import *
Similarly, you can import only those functions of interesting, this can include:
get_qc_data
get_total_variants
import_ct_data
is_variant_n
is_variant_iupac
count_iupac_in_fasta
get_fasta_sequence_length
is_base_masked
is_indel
is_indel_triplet
get_coverage_stats
create_qc_summary_line
write_qc_summary
write_qc_summary_header
collect_qc_summary_data
In the bin directory, several wrapper scripts exist to assist in generating
QC metrics.
To create sample level summary qc files, use the get_qc_summary.py script:
get_qc_summary.py --qc <sample>.qc.csv --variants <sample>.variants.tsv
--coverage <sample>.per_base_coverage.bed --meta <metadata>.tsv
--fasta <sample>.primertrimmed.consensus.fa --reference <reference genome>.fa
[--indel] [--mask_start 100] [--mask_end 50]
Note the --indel flag should only be present if indels will be used in the
calculation of variants.
Once this is complete, we can use the collect_qc_summary.py script to
aggregate the sample level summary files into a single run tab-separate file.
collect_qc_summary.py --path <path to sample.summary.qc.tsv files>
Note that this tool has been used in conjunction with the @jts ncov-tools
suite of tools.
MIT