# npysearch
npysearch implements an efficient BLAST-like sequence comparison algorithm, written in C++11 and using native Python datatypes and bindings. npysearch is light-weight, fast, and dependency-free. The code base of npysearch is adapted from [nsearch](https://github.com/stevschmid/nsearch).
## Installation
### from pypi
```
pip install npysearch
```
### from github
```
# Clone repository from github
git clone https://github.com/jeevannavar/npysearch.git
# Install package using pip
pip install ./npysearch
```
## Examples
```Python
# Import npysearch package
import npysearch as npy
# Read query file into a dictionary
query = npy.read_fasta("npysearch/inst/extdata/query.fasta")
# Read database file into a dictionary
database = npy.read_fasta("npysearch/inst/extdata/db.fasta")
# BLAST the query against the database
results_dna = blast(query, database)
# BLAST protein sequence file against itself using filenames as blast function arguments
results_prot = blast(query = "npysearch/inst/extdata/prot.fasta",
database = "npysearch/inst/extdata/prot.fasta",
alphabet = "protein")
```
## Caveats
* The `blast` function automatically detects whether the query and database arguments were passed as string paths to fasta files or as dictionaries of sequences. Both of them need not be input as the same type.
* Use `help(npy)` (assuming you've imported npysearch as npy) to get a list of the functions included and their docstrings. For docstrings of specific functions, for example blast, use `help(npy.blast)`
没有合适的资源?快使用搜索试试~ 我知道了~
资源推荐
资源详情
资源评论
收起资源包目录
npysearch-1.2.0.tar.gz (56个子文件)
npysearch-1.2.0
MANIFEST.in 98B
PKG-INFO 2KB
pyproject.toml 136B
include
nsearch
Database
Kmers.h 2KB
GlobalSearch.h 8KB
Search.h 2KB
HSP.h 1KB
HitWriter.h 465B
Highscore.h 2KB
Sequence.h 6KB
Alphabet.h 639B
Alnout
Writer.h 9KB
FASTA
Reader.h 882B
Writer.h 610B
Alphabet
Protein.h 5KB
DNA.h 4KB
PairedEnd
Reader.h 1KB
Merger.h 7KB
Alignment
ExtendAlign.h 6KB
SegmentPair.h 390B
BandedAlign.h 9KB
Common.h 203B
Cigar.h 3KB
FASTQ
Reader.h 729B
QScore.h 3KB
Writer.h 507B
FileFormat.h 2KB
SequenceReader.h 998B
Utils.h 224B
TextReader.h 1KB
SequenceWriter.h 477B
CSV
Writer.h 5KB
Database.h 6KB
npysearch.egg-info
PKG-INFO 2KB
requires.txt 15B
not-zip-safe 1B
SOURCES.txt 2KB
top_level.txt 21B
dependency_links.txt 1B
LICENSE 1KB
src
_npysearch
Filter.h 200B
Filter.cpp 2KB
Search.h 371B
Search.cpp 11KB
FileFormat.h 2KB
Common.h 3KB
Merge.h 164B
WorkerQueue.h 3KB
TextReader.cpp 3KB
Merge.cpp 4KB
winstd.h 1KB
Stats.h 843B
npysearch
__init__.py 11KB
setup.cfg 38B
setup.py 2KB
README.md 2KB
共 56 条
- 1
资源评论
挣扎的蓝藻
- 粉丝: 13w+
- 资源: 15万+
上传资源 快速赚钱
- 我的内容管理 展开
- 我的资源 快来上传第一个资源
- 我的收益 登录查看自己的收益
- 我的积分 登录查看自己的积分
- 我的C币 登录后查看C币余额
- 我的收藏
- 我的下载
- 下载帮助
安全验证
文档复制为VIP权益,开通VIP直接复制
信息提交成功