Fasta Tools

Fasta Tools- in Java Language

Fasta Tools- in Python Language

Below, listed some script that accomplish trivial tasks. Follow the link, copy the whole text and paste into a text file. Rename the text file to relevant script name. Do not forget to set the executable flag for the file.

On a Linux/ Unix environment, you simply install biopython package, then from a terminal run the script. All scripts will complain from wrongly set arguments, and will try to recommend a solution or at least direct you to the it.

  • Generate fasta and qual files from a fastq file

This script extracts sequence and quality informations from a fastq formatted file. Sequences and quality values are written into files separately, as fasta and qual files.

Results will be written into the same directory where fastq file resides. Get the script from here..

Usage: python ./ fastqfile

  • Generate stats from a fasta file

This script outputs basic statistics of a fasta formatted file. Outputted stats are as follows: sequence count, longest, shortest, average sequence length, N50 length, standart deviation of sequences' length and cumulative base count of all sequences.

Results will be written onto terminal screen (stdout). Get the script from here..

Usage: python ./ fastafile

more to be added..