From f56b93b0f2c8c0130ea459bbf78c3e5dca5e3c40 Mon Sep 17 00:00:00 2001 From: Vadim Nazarov Date: Wed, 19 Aug 2015 18:10:51 +0300 Subject: [PATCH] update readme a bit --- README.md | 23 ++++++++++++++++++----- 1 file changed, 18 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 796de07..ff904ec 100644 --- a/README.md +++ b/README.md @@ -149,7 +149,7 @@ Wow-wow, easy here. They are not implemented yet. python3 pyymir.py -* `python3 pyymir.py -v` - print the version of Ymir. +* `python3 pyymir.py -v` - print the current version of Ymir. * `python3 pyymir.py -a` - list all available algorithms for the statistical inference of marginal probabilities and their aliases. * `python3 pyymir.py -m` - list all available models and their aliases. * `python3 pyymir.py -f` - list all available converters for input formats and their aliases. @@ -161,15 +161,18 @@ Wow-wow, easy here. They are not implemented yet. After compiling an executable files will appear in the `build` folder. -You can download sample files with outputs from [tcR](https://imminfo.github.io/tcr/) package and [MiTCR](http://mitcr.milaboratory.com/) software from here [here](). +You can download sample files with outputs from [tcR](https://imminfo.github.io/tcr/) package and [MiTCR](http://mitcr.milaboratory.com/) software with + + curl -sL https://github.com/imminfo/ymir/releases/download/v1.0-pre3/example-files.zip > examples.zip + unzip examples.zip ### Compute generation probabilities of human TCR-alpha data from tcR output files -The most common task with generation probabilities is to compute them. +The most common task with generation probabilities is to compute them. python3 compute.py -i -f -m [-o ] [-p] [-l] -Run `python3 compute.py -h` to see a help message. +> Note: run `python3 compute.py -h` to see a help message. * `` - input file (text or gzipped) or a folder with input files (of the same format) or a list of space-separated files and/or folders in any combinations. * `` - format of input files (tcR, MiTCR, MiGEC, etc.) as an alias or as a Python 3 class from your module linked to the '$YMIR_HOME/converters' package. For a list of possible input formats and their aliases in this Ymir distribution run `$python3 pyymir.py -f`. @@ -178,19 +181,29 @@ Run `python3 compute.py -h` to see a help message. * `-p` - recompute or use predefined model's gene usage (default is to recompute, to change it add `-p` to your script call). * `-l` - add this to leave converted files (default is to remove converted files). +Example command to compute generation probabilities from tcR file: + python3 compute.py -i ./examples/tcr.htra.txt -f tcr -m htra ### Estimate human TCR-beta generation model parameters using EM-algorithm from MiTCR output files python3 inference.py -i ??? -f mitcr -m htrb -Run `python3 pyymir.py -f` to view all available models and their aliases. +> Note: run `python3 inference.py -h` to see a help message. + +Example command to perform statistical inference from MiTCR file: + + python3 inference.py -i ./examples/mitcr.htrb.txt -f mitcr -m htrb + +Run `python3 pyymir.py -m` to view all available models and their aliases. ### Generate artificial human TCR-alpha repertoire before selection python3 generate.py -c 500000 -m htra +> Note: run `python3 generate.py -h` to see a help message. + asdasd ---