From 0d8cd3adf0db362ae3c1211bddfeafbd17f91c35 Mon Sep 17 00:00:00 2001 From: Matt Shirley Date: Fri, 4 Sep 2015 12:01:53 -0400 Subject: [PATCH] Update parser and README --- README.md | 67 +++++++++++++++++++++++++++------------------------ fastqp/cli.py | 1 - 2 files changed, 36 insertions(+), 32 deletions(-) diff --git a/README.md b/README.md index 3f6b653..5c02b76 100644 --- a/README.md +++ b/README.md @@ -33,41 +33,46 @@ Note: BAM file support requires [samtools](http://samtools.sourceforge.net) Usage ----- - simple NGS read quality assessment using Python - - positional arguments: - input input file (one of .sam, .bam, or .fastq(.gz) or stdin - (-)) - - optional arguments: - -h, --help show this help message and exit - -q, --quiet do not print any messages (default: False) - -s BINSIZE, --binsize BINSIZE - number of reads to bin for sampling (default: auto) - -n NREADS, --nreads NREADS - number of reads sample from input (default: 2000000) - -k {2,3,4,5,6,7,8,9,10}, --kmer {2,3,4,5,6,7,8,9,10} - length of kmer for over-repesented kmer counts - (default: 5) - -o OUTPUT, --output OUTPUT - base name for output files (default: plot) - -ll LEFTLIMIT, --leftlimit LEFTLIMIT - leftmost cycle limit (default: 1) - -rl RIGHTLIMIT, --rightlimit RIGHTLIMIT - rightmost cycle limit (-1 for none) (default: -1) - --aligned only aligned reads (default: False) - --unaligned only unaligned reads (default: False) - --nofigures don't produce figures (default: False) - --nokmer do not count kmers (default: False) - --gemstone reads have convolution string (default: False) +```shell +usage: fastqp [-h] [-q] [-s BINSIZE] [-a NAME] [-n NREADS] [-p BASE_PROBS] [-k {2,3,4,5,6,7}] [-o OUTPUT] + [-ll LEFTLIMIT] [-rl RIGHTLIMIT] [-mq MEDIAN_QUAL] [--aligned-only | --unaligned-only] [-d] + input + +simple NGS read quality assessment using Python + +positional arguments: + input input file (one of .sam, .bam, .fq, or .fastq(.gz) or stdin (-)) + +optional arguments: + -h, --help show this help message and exit + -q, --quiet do not print any messages (default: False) + -s BINSIZE, --binsize BINSIZE + number of reads to bin for sampling (default: auto) + -a NAME, --name NAME sample name identifier for text and graphics output (default: input file name) + -n NREADS, --nreads NREADS + number of reads sample from input (default: 2000000) + -p BASE_PROBS, --base-probs BASE_PROBS + probabilites for observing A,T,C,G,N in reads (default: 0.25,0.25,0.25,0.25,0.1) + -k {2,3,4,5,6,7}, --kmer {2,3,4,5,6,7} + length of kmer for over-repesented kmer counts (default: 5) + -o OUTPUT, --output OUTPUT + base name for output files (default: fastqp_figures) + -ll LEFTLIMIT, --leftlimit LEFTLIMIT + leftmost cycle limit (default: 1) + -rl RIGHTLIMIT, --rightlimit RIGHTLIMIT + rightmost cycle limit (-1 for none) (default: -1) + -mq MEDIAN_QUAL, --median-qual MEDIAN_QUAL + median quality threshold for failing QC (default: 30) + --aligned-only only aligned reads (default: False) + --unaligned-only only unaligned reads (default: False) + -d, --count-duplicates + calculate sequence duplication rate (default: False) +``` Changes ------- -New in 0.1.5: - -- Added `.fq` as acceptable file extension. (Thanks @danielecook) -- Added cycle-specific kmer plots +See [releases page](https://github.com/mdshw5/fastqp/releases) for details. Examples -------- diff --git a/fastqp/cli.py b/fastqp/cli.py index d25c8d9..5e1feda 100644 --- a/fastqp/cli.py +++ b/fastqp/cli.py @@ -345,7 +345,6 @@ def main(): align_group = parser.add_mutually_exclusive_group() align_group.add_argument('--aligned-only', action="store_true", default=False, help="only aligned reads (default: %(default)s)") align_group.add_argument('--unaligned-only', action="store_true", default=False, help="only unaligned reads (default: %(default)s)") - parser.add_argument('--no-figures', action="store_true", default=False, help="don't produce figures (default: %(default)s)") parser.add_argument('-d', '--count-duplicates', action="store_true", default=False, help="calculate sequence duplication rate (default: %(default)s)") args = parser.parse_args()