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"