NAME
fu-count - A FASTA/FASTQ sequence counter
VERSION
version 1.5.7
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.
NAME
fu-count - A FASTA/FASTQ sequence counter
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This suite of tools has been superseded by SeqFu, a compiled program providing faster and safer tools for sequence analysis.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
AUTHOR
Andrea Telatin <andrea@telatin.com>
COPYRIGHT AND LICENSE
This software is Copyright (c) 2018-2022 by Andrea Telatin.
This is free software, licensed under:
The MIT (X11) License