A python tool to extract multiple fasta sequence records from multiFASTA file based on a list of record ids or a substring in the sequence header.
Written by: Li Chuin Chong and Yeo Keat Ee
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Download only the python code
wget https://raw.githubusercontent.com/ChongLC/seqExtractor/master/seqExtractor.py -
Download the entire repo
To use the seqExtractor, the following packages are needed to be installed:
- Biopython
- argparse
You can install these packages by using following command:
pip install -r requirements.txt
seqExtractor.py [-h] -i INPUT (-l ID_LIST | -s SUBSTRING) -o OUTPUT [-t THREADS] [-c]
Extract fasta sequence records from multiFASTA file based on a list of record ids or a substring in the sequence header
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Filename include extension of original FASTA file
-l ID_LIST, --id_list ID_LIST
Filename include extension of the sequence ID list
-s SUBSTRING, --substring SUBSTRING
Substring to search for in the sequence header
-o OUTPUT, --output OUTPUT
Filename include extension of output FASTA file
-t THREADS, --threads THREADS
Number of threads to use (default: 1)
-c, --case_insensitive
Make the substring search case insensitive (default: False)
-e, --exclude
Make the output FASTA file only contains excluded result (default: False)
There are two ways to use seqExtractor tool:
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Extract sequences based on a list of sequence IDs:
python seqExtractor.py -i input.fasta -l id_list.txt -o output.fasta -t 4 -
Extract sequences based on a substring in the sequence header:
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case sensitive (by default)
python seqExtractor.py -i input.fasta -s Belgium -o output.fasta -t 4 -
case insensitive
python seqExtractor.py -i input.fasta -s belgium -o output.fasta -t 4 --case-insensitive
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Inspired by faSomeRecords from Santiago Sanchez-Ramirez, which firstly created by kentUtils in C++ version.
Or would like a feature added? Or maybe drop some feedback? Just open a new issue or send an email to us (lichuinchong@gmail.com).