count_seqs.py –

Description:

Usage: count_seqs.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_fps

The input filepaths (comma-separated)

[OPTIONAL]

-o, --output_fp

The output filepath [default: write to stdout]

--suppress_errors

Suppress warnings about missing files [default: False]

Output:

Count the sequences in a fasta file and write results to stdout.

count_seqs.py -i in.fasta

Count the sequences in a fasta file and a fastq file and write results to file. Note that fastq files can only be processed if they end with .fastq – all other files are assumed to be fasta.

count_seqs.py -i in1.fasta,in2.fastq -o seq_counts.txt

Count the sequences all .fasta files in current directory and write results to stdout. Note that -i option must be quoted.

count_seqs.py -i "*.fasta"