Metadata-Version: 2.1
Name: seqits
Version: 0.0.1
Summary: Tools for sequences process
Home-page: https://github.com/sfjdx1144/seqits
Author: Fujun Sun
Author-email: sfjdx1144@live.com
License: GPL-3.0 license
Platform: any
Requires-Python: >=3.4.0
Description-Content-Type: text/markdown
License-File: LICENSE

# Seqits

 Seqits provides several useful toosl for sequences processing. 

## Installation method

`pip install seqits `

## Tools

#### Seqits

`python -m seqits -v # display the version of Seqits`
`python -m seqits list # display all tools in Seqits`

#### randseq

This tool can generate cds or protein sequence(s) randamly.

| Arguments      | Description                                                    |
| -------------- |:--------------------------------------------------------------:|
| type           | nucl/prot, cds or protein sequence(s)                          |
| num            | number of sequences(s) to generate                             |
| out (optional) | output file, defaut: output.fa                                 |
| show(optional) | whether display the output on the screen or not, defaut: false |

e.g. `python -m seqits.randseq nucl 100 -o output.fa -s true`

#### search

This tool can search and extract  sequence(s) you want by  Gene ID or Gene Name.

| Arguments       | Description                                                                                                                                          |
| --------------- |:----------------------------------------------------------------------------------------------------------------------------------------------------:|
| input           | input raw fasta file                                                                                                                                 |
| gene            | input gene(s)                                                                                                                                        |
| type (optional) | string/file, type of input gene(s). For file, one gene one line; for string, gene(s) should be seperated with ',', default string                    |
| mode (optional) | fast/order, "fast" mode may faster than "order" mode, but "order" mode can display your output accoring to the order of input gene(s), default: fast |
| out (optional)  | output file, defaut: output.fa                                                                                                                       |
| show (optional) | whether display output on the screen or not, defaut: false                                                                                           |

e.g. `python -m seqits.search input.fa Gene1,Gene2,Gene3 --out output.fa`

#### formatseq

This tool can make format the fasta file.

| Arguments       | Description                                                |
| --------------- |:----------------------------------------------------------:|
| input           | input raw fasta file                                       |
| num (optional)  | number of characters per line, defaut: 60                  |
| out (optional)  | output file, defaut: output.fa                             |
| show (optional) | whether display output on the screen or not, defaut: false |

e.g. `python -m seqits.formatseq input.fa 100`




