This project provides scripts for analyzing the probe files for an NGS capture library and creating input files for various programs (picard, bedtools, etc)
Table of Contents
- Python 3.3+
- Tested on Linux and OS X.
- bedtools >= 2.26
Clone the project from the git repository:
cd ~/src git clone [email protected]:sheenams/ngs_capture_qc.git cd ngs_capture_qc python3 -m venv capqc-env source capqc-env/bin/activate pip install -r requirements.txt
The capqc script provides the different scripts used to process
the original probe file. To run capqc:
% ./capqc -h
The expected order of operations: 1. ./capqc refgene_to_bed [-h] refgene output
- created BED format of refgene, if one isn't available already
create_files and summarize_assay expect refgene in bed format.
- ./capqc summarize_assay [-h] [--outdir OUTDIR] bed genes refgene_bed bedtools
- overall_summary (unique bases targeted, coding bases targeted, refgenes with at least 1 base targeted, probes outside of coding)
- preferred refgene summary (total_bases_targeted,length_of_gene,fraction_of_gene_covered,exons_with_coverage)
- other refgene summary (total_bases_targeted,length_of_gene,fraction_of_gene_covered,exons_with_coverage)
./capqc filter_refgene [-h] refgene genes outfile - the refgene file input for this is NOT bed format - this will validated preferred transcripts and create the filtered refgene file for use in CNV calling
./capqc parse_refgene_positions [-h] refgene outfile - parse the filtered refgene file (NOT BED FORMAT) and report start/stop position for each gene
./capqc xlsxmaker [-h] -o OUTFILE infiles [infiles ...] - per refgene summary - other genes that are covered - overall summary - refgene position information
./capqc capqc create_files [-h] probefile refgene_bed bedtools outdir - creates the following files:
- clean bed (probes merged, deduplicated and annotated)
- picard bed (probes in format required by Picard)
Commands are constructed as follows. Every command starts with the
name of the script, followed by an "action" followed by a series of
required or optional "arguments". The name of the script, the action,
and options and their arguments are entered on the command line
separated by spaces. Help text is available for both the cap_qc
script and individual actions using the -h or --help options:
% capqc -h
usage: capqc [-h] [-V] [-v] [-q]
{help,create_files,filter_refgene,refgene_to_bed,summarize_assay}
...
Utilities for the ngs_capture_qc scripts
positional arguments:
{help,create_files,filter_refgene,refgene_to_bed,summarize_assay}
help Detailed help for actions using `help <action>`
create_files Script to create specifically formatted files from the
original probes file
filter_refgene Filter a file containing the refgene annotation table,
limiting to
refgene_to_bed Convert UCSC refgene.txt files to BED format, for use
in summarize_assay script
xlsxmaker Create xlsx workbook from all output files
summarize_assay Given probe reference file, list of preferred
transcripts and refgene.bed,
parse_refgene_positions
Parse the filtered refgene file and report chrm:start-
stop for each gene
optional arguments:
-h, --help show this help message and exit
-V, --version Print the version number and exit
-v, --verbose Increase verbosity of screen output (eg, -v is
verbose, -vv more so)
-q, --quiet Suppress output
We use abbrevited git sha hashes to identify the software version:
% ./capqc -V 0309.004ecac
Unit tests are implemented using the unittest module in the Python
standard library. The tests subdirectory is itself a Python
package that imports the local version (ie, the version in the project
directory, not the version installed to the system) of the cap_qc
package. All unit tests can be run like this:
% ./testall ................... ---------------------------------------------------------------------- Ran 19 tests in 4.624s OK
Copyright (c) 2019 Sheena Todhunter
Released under the MIT License:
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.