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# `seqsearch` version 1.2.1
`seqsearch` is a python package for dealing sequence similarity searches (e.g. BLAST on DNA sequences) and automation.
It has many convenience methods that can automatically launch several types of search algorithms, as well as quick installation of sequence reference databases.
## Prerequisites
Since `seqsearch` is written in python, it is compatible with all operating systems: Linux, macOS and Windows. The only prerequisite is `python3` (which is often installed by default) along with the `pip3` package manager.
To check if you have `python3` installed, type the following on your terminal:
$ python3 -V
If you do not have `python3` installed, please refer to the section [obtaining python3](docs/installing_tips.md#obtaining-python3).
To check you have `pip3` installed, type the following on your terminal:
$ pip3 -V
If you do not have `pip3` installed, please refer to the section [obtaining pip3](docs/installing_tips.md#obtaining-pip3).
## Installing
To install the `seqsearch` package, simply type the following commands on your terminal:
$ pip3 install --user seqsearch
Alternatively, if you want to install it for all users of the system:
$ sudo pip3 install seqsearch
## Usage
Bellow are some examples to illustrate the various ways there are to use this package.
### Searches
You can parallelize BLAST searches by splitting the input into several files. It's easier to chop-up the input, because database chopping requires message passing across the nodes like mpiblast does (when and if it works).
Input chopping is fine as long as the database to search against fits in the RAM of the nodes. If the input is small and the database is large you can always switch them one for the other (in most cases).
# This example is not completed yet. TODO.
### Databases
# This example is not completed yet. TODO.
## Extra documentation
More documentation is available at:
<http://xapple.github.io/seqsearch/seqsearch>
This documentation is simply generated with:
$ pdoc --html --output-dir docs --force seqsearch
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资源分类:Python库 所属语言:Python 资源全名:seqsearch-1.2.1.tar.gz 资源来源:官方 安装方法:https://lanzao.blog.csdn.net/article/details/101784059
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seqsearch-1.2.1.tar.gz (29个子文件)
seqsearch-1.2.1
MANIFEST.in 37B
PKG-INFO 3KB
setup.cfg 38B
seqsearch.egg-info
PKG-INFO 3KB
requires.txt 87B
SOURCES.txt 725B
top_level.txt 10B
dependency_links.txt 1B
setup.py 822B
seqsearch
search
vsearch.py 1KB
parallel.py 5KB
ncbi.py 3KB
__init__.py 7KB
blast.py 9KB
hmmer.py 4KB
__init__.py 169B
databases
pr_two.py 3KB
silva_mothur.py 3KB
nr.py 813B
silva.py 3KB
refseq.py 1KB
__init__.py 4KB
pfam.py 4KB
tigrfam.py 2KB
string.py 3KB
nt.py 3KB
foraminifera.py 4KB
README.md 2KB
LICENSE.txt 1KB
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