From a2ef9179b47fb0eaba78712220a1173fba0ffc5b Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Thu, 28 Jul 2016 09:10:49 +0800 Subject: [PATCH] Add pypy in README --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 4b26f1f..2e4d524 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,7 @@ Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 50 * stable: [0.5.0 (released on 2016-07-22)](https://github.com/OpenGene/AfterQC/archive/Release-0.5.0.zip) # Dependency: -`AfterQC` uses `editdistance` module for performance, if you are using pure `python`, install it using `pip`: +`AfterQC` uses `editdistance` module for performance, if you are using native `python`, install it using `pip`: ```shell pip install editdistance ``` @@ -27,6 +27,11 @@ If you failed to install `editdistance` with `pip`, you can run `make` in the `A ***WARNING: If you don't install or build `editdistance` module, `AfterQC` will use a python implementation of editdistance, but it will be extremely slow.*** +# pypy support +* Can be `3X` faster than native `python` +* Run `make` in `AfterQC` folder to build `editdistance` because it is not easy to install it from `pypy pip` +* All figures will not be generated with `pypy`, because `matplotlib` and `PIL` are not supported by `pypy` + # Simple usage: * Prepare your fastq files in a folder * For single-end sequencing, the filenames in the folder should be `*R1*`, otherwise you should specify `--read1_flag`