NAME

fu-count - A FASTA/FASTQ sequence counter

SYNOPSIS

fu-count [options] [FILE1 FILE2 FILE3...]

DESCRIPTION

This program parses a list of FASTA/FASTQ files printing the number of sequences found in each file. Reads both uncompressed and GZipped files. Default output is the filename, tab, sequence count. Can be changed with options.

The table "key" is the absolute path of each input file, but the printed name can be changed with options.

PARAMETERS

FILE NAME

• -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

MODERN ALTERNATIVE

This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis. This suite is maintained for the higher portability of Perl scripts under certain circumstances.

SeqFu is available at https://github.com/telatin/seqfu2, and can be installed with BioConda conda install -c bioconda seqfu

CITING

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059