fu count

fu-count

Counts sequences in FASTA, FASTQ files, compressed or not.

Simple usage

By default will print a tsv output with filename and counts:

fu-count data/c*

data/clonal.fa	4
data/comments.fasta	3
data/comments.fastq	n/a
data/compressed.fasta.gz	3
data/compressed.fastq.gz	3

Parameters

• Filename options:

    -a, --abspath
        Print the absolute path of the filename (the absolute path is always
        the table key, but if relative paths are supplied, they will be
        printed).

    -b, --basename
        Print the filename without the path.

    -d, --thousandsep
        Print reads number with a "," used as thousand separator

• Output format

    Default output format is the filename and reads counts, tab separated.
    Options formatting either filename ("-a", "-b") and reads counts ("-d")
    will still work.

    -t, --tsv and -c, --csv
        Print a tabular output either tab separated (with "-t") or comma
        separated (with "-c").

    -j, --json
        Print full output in JSON format.

    -p, --pretty
        Same as JSON but in "pretty" format.

    -x, --screen
        This feature requires Term::ASCIITable. Print an ASCII-art table like:

          .---------------------------------------------------.
          | # | Name                     | Seqs | Gz | Parser |
          +---+--------------------------+------+----+--------+
          | 1 | data/comments.fasta      |    3 |  0 | FASTX  |
          | 2 | data/comments.fastq      |    3 |  0 | FASTQ  |
          | 3 | data/compressed.fasta.gz |    3 |  1 | FASTX  |
          | 4 | data/compressed.fastq.gz |    3 |  1 | FASTQ  |
          '---+--------------------------+------+----+--------'

• Sorting

    -s, --sortby
        Sort by field: 'order' (default, that is the order of the input files
        as supplied by the user), 'count' (number of sequences), 'name'
        (filename). By default will be descending for numeric fields,
        ascending for 'path'. See "-r, --reverse".

    -r, --reverse
        Reverse the sorting order.

• Other

    -f, --fastx
        Force FASTX reader also for files ending by .fastq or .fq (by default
        would use getFastqRead() )

    -v, --verbose
        Increase verbosity

    -h, --help
        Display this help page