truncate_fasta_qual_files.py – Generates filtered fasta and quality score files by truncating at the specified base position.

Description:

This module is designed to remove regions of poor quality in 454 sequence data. Drops in quality can be visualized with the quality_scores_plot.py module. The base position specified will be used as an index to truncate the sequence and quality scores, and all data at that base position and to the end of the sequence will be removed in the output filtered files.

Usage: truncate_fasta_qual_files.py [options]

Input Arguments:

Note

[REQUIRED]

-f, --fasta_fp

Fasta file. Needed to test for congruety between the number of nucleotides in the fasta file and quality scores in the qual file.

-q, --qual_fp

Quality score file used to generate histogram data.

-b, --base_pos

Nucleotide position to truncate the fasta and quality score files at.

[OPTIONAL]

-o, --output_dir

Output directory. Will be created if does not exist. [default: .]

Output:

Filtered versions of the input fasta and qual file (based on input name with ‘_filtered’ appended) will be generated in the output directory

Example:

Truncate the input fasta and quality files at base position 215, output to the filtered_seqs directory:

truncate_fasta_qual_files.py -f seqs.fna -q seqs.qual -b 215 -o filtered_seqs/