Unfortunately, getting a read from a FASTA file can be challenging for large files if you try to open it in text edit.
Have you generated an alignment file and got frustrated because the query sequence was not in the output? This tutorial shows how to retrieve the sequence from the FASTA using a single awk line.
Why would I want to Get Read from a FASTA in One Line?
There are several reasons why someone might want to read from a FASTA file in one line:
- Efficiency: Reading the file in one line can be faster and more memory-efficient compared to reading it line by line.
- Parsing: In some cases, reading the entire FASTA file in one line makes it easier to parse and process the data.
- Simplicity: Reading the entire file in one line can simplify the code and make it easier to understand.
- Convenience: In some situations, it may be more convenient to have the entire FASTA file in a single string, rather than in multiple lines.
However, it’s important to note that reading the entire FASTA file into memory in one line may not be feasible for very large files. In such cases, reading the file line by line may be the more appropriate approach.
Single Line to Extract a Sequence from FASTA
First and fore more, awk can be simply used to access the sequence from a FASTA file assuming that the sequence id is known for the target sequence – this can be easily obtained from the output of BLAST, DIAMOND, BWA, etc
$ awk -v seq="TARGETED_ID" -v RS='>' '$1 == seq {print RS $0}' YOUR_FASTA
Finally, I hope this is useful for you – it has been for me over the years.
Extracting more than one Sequence
In the case of more than one sequence is needed, I would recommend using seqtk with the following command line which requires a file defining with sequences that should be pulled out.
$ seqtk subseq {FASTA/FASTQ/FASTQ_GZ} {LIST_IDS} > {OUTPUT_FILE}
More Resources
Here are three of my favorite Python Bioinformatics Books in case you want to learn more about it.
- Python for the Life Sciences: A Gentle Introduction to Python for Life Scientists Paperback by Alexander Lancaster
- Bioinformatics with Python Cookbook by Tiago Antao
- Bioinformatics Programming Using Python: Practical Programming for Biological Data by Mitchell L. Model
