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PROCH

1 PAUSE user
4 non-PAUSE users.

Andrea Telatin ⚗️
and 1 contributors

NAME

fqc - A FASTA/FASTQ sequence counter

VERSION

version 0.50

SYNOPSIS

  fqc [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

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2019 by Andrea Telatin.

This is free software, licensed under:

  The MIT (X11) License