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توضیحات

Various bioinformatics pipelines.

ویژگی	مقدار
سیستم عامل	-
نام فایل	cdpipelines-0.0.7
نام	cdpipelines
نسخه کتابخانه	0.0.7
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Christopher DeBoever
ایمیل نویسنده	cdeboever3@gmail.com
آدرس صفحه اصلی	https://github.com/cdeboever3/cdpipelines
آدرس اینترنتی	https://pypi.org/project/cdpipelines/
مجوز	MIT

cdpipelines =========== This repository holds various bioinformatics pipelines. Dependencies ------------ Many of the pipeline dependencies can be obtained using the ``prepare`` submodule (see below). Additionally, a working Python environment is needed along with some of the common scientific python packages. I recommend using `Anaconda python <https://store.continuum.io/cshop/anaconda/>`__ since it includes most of the needed packages. If you are using Anaconda, I'd recommend making new environments for different projects. Besides the default Anaconda packages, you will need the following (available through ``conda`` or ``pip``): - HTSeq - pandas - pysam (this is available through conda but currently it's an old version so you have to get it using ``pip``) - PyVCF ``rpy2`` ~~~~~~~~ Installing ``rpy2`` can be tricky. Different versions of ``R`` and ``rpy2`` don't work well together, so it's recommended to make a local installation of ``R`` using the ``prepare`` submodule and compile ``rpy2`` against this installation. You can install ``R`` using ``prepare.download_r`` and install ``rpy2`` using ``prepare.download_install_rpy2``. ``prepare.download_install_rpy2`` will prompt you to set your PATH, LDFLAGS, and LD\_LIBRARY\_PATH to correctly install ``rpy2``. After installing ``rpy2``, you need to set your PATH and LD\_LIBRARY\_PATH using these commands for every bash session where you want to use this ``rpy2``. I'd recommend putting the commands in a file that you source every time you load the project's Anaconda environment. Submodules ---------- ``general`` ~~~~~~~~~~~ ``general`` contains methods used in multiple pipelines. Some pipelines use similar but different versions of some methods, so the pipelines will have their own versions of those methods. Sometimes it may make sense to add options to a particular method that is used in multiple pipelines (where each pipeline has slightly different versions) and add the method into ``general``. ``prepare`` ~~~~~~~~~~~ The ``prepare`` module contains functions for downloading various software and reference files needed for the different pipelines. ``rnaseq`` ~~~~~~~~~~ This pipeline currently starts from fastq files and has two steps. For detailed information on each step, so the docstrings for each method. The first step is ``align_and_sort`` which (optionally) removes duplicates, aligns the reads, and makes coverage bigwig files for use with the UCSC genome browser or IGV. The read alignments are output in both genomic and transcriptomic coordinates. The second step is ``get_counts`` which counts reads overlapping genes for gene differential expression and exonic bins for use with DEXSeq.

نحوه نصب

نصب پکیج whl cdpipelines-0.0.7:

pip install cdpipelines-0.0.7.whl

نصب پکیج tar.gz cdpipelines-0.0.7:

pip install cdpipelines-0.0.7.tar.gz