milesroberts-123 / extract-sequence-lengths

Extract sequence lengths from a fasta file and save them to a tab-delimited text file in genome file format.

extract-sequence-lengths

Extract sequence lengths from a fasta file and save them to a tab-delimited text file in genome file format.

This script uses Biopython to calculate the lengths of sequences stored in a fasta file and then outputs those lengths to a text file in the format:

chr01 1234567
chr02 9876543
...
chrN  2468101

The output text file is suitable as input into other commands, including bedtools.

USAGE

The syntax of this script is as follows:

python3 extract_sequence_lengths.py <NAME OF FASTA FILE> <NAME YOU WANT FOR OUTPUT FILE>

For example this code:

python3 extract_sequence_lengths.py example_chromosomes.fasta example_chromosome_lengths.txt

will calculate the length of each sequence in example_chromosomes.fasta and save those lengths to the example_chromosome_lengths.txt file.

DEPENDENCIES

1. Biopython - Installation instructions here. Usually you just type:

pip install biopython

2. The sys python module, which usually ships with python installations.