Fastaselect

Find sequences from a large fasta file by names，length and keywords.

Usage

fastaselect.py [-h] -o OUTPUT -i INPUT [-k KEYWORD] [-n NAME] [-m MIN]  

optional arguments:  
  -h, --help            show this help message and exit  
  -o OUTPUT, --output OUTPUT  
                        The output file  
  -i INPUT, --input INPUT  
                        The input file  
  -k KEYWORD, --keyword KEYWORD   Find special sequence compliance with your matching rules  
  -n NAME, --name NAME  A file contain the sequence name you want to extract  
  -m MIN, --min MIN     Minimum length  

Example:

Find sequence longer than 500bp

$python fastaselect.py -o output.fasta -i input.fasta -m 500  

Find sequence by keywords or regular expression

$python fastaselect.py -o output.fasta -i input.fasta -k ^\w.*\d  

Find squence by sequence name

$cat name.txt  
seq1  
seq2  
seq3  
seq4

$python fastaselect.py -o output.fasta -i input.fasta -n name.txt  

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Please note that the file path is differenc in windows and linux:
Windows: C:\\your\\file\\path\\file.fasta
Linux: /home/your/file/path/file.fasta

zhutao@cau.edu.cn for help #######################################################################################