NAME

Proch::N50 - a small module to calculate N50 (total size, and total number of sequences) for a FASTA or FASTQ file. It's easy to install, with minimal dependencies.

VERSION

version 1.5.0

SYNOPSIS

use Proch::N50 qw(getStats getN50);
my $filepath = '/path/to/assembly.fasta';

# Get N50 only: getN50(file) will return an integer
print "N50 only:\t", getN50($filepath), "\n";

# Full stats
my $seq_stats = getStats($filepath);
print Data::Dumper->Dump( [ $seq_stats ], [ qw(*FASTA_stats) ] );
# Will print:
# %FASTA_stats = (
#               'N50' => 65,
#               'N75' => 50,
#               'N90' => 4,
#               'min' => 4,
#               'max' => 65,
#               'dirname' => 'data',
#               'auN' => 45.02112,
#               'size' => 130,
#               'seqs' => 6,
#               'filename' => 'test.fa',
#               'status' => 1
#             );

# Get also a JSON object
my $seq_stats_with_JSON = getStats($filepath, 'JSON');
print $seq_stats_with_JSON->{json}, "\n";
# Will print:
# {
#    "status" : 1,
#    "seqs" : 6,
#    <...>
#    "filename" : "small_test.fa",
#    "N50" : 65,
# }
# Directly ask for the JSON object only:
my $json = jsonStats($filepath);
print $json;

NAME

Proch::N50 - a small module to calculate N50 (total size, and total number of sequences) for a FASTA or FASTQ file. It's easy to install, with minimal dependencies.

VERSION

version 1.4.2

METHODS

getN50(filepath)

This function returns the N50 for a FASTA/FASTQ file given, or 0 in case of error(s).

getStats(filepath, alsoJSON)

Calculates N50 and basic stats for <filepath>. Returns also JSON if invoked with a second parameter. This function return a hash reporting:

• size (int)

  total number of bp in the files

• N50, N75, N90 (int)

  the actual N50, N75, and N90 metrices

• auN (float)

  the area under the Nx curve, as described in https://lh3.github.io/2020/04/08/a-new-metric-on-assembly-contiguity. Returs with 5 decimal digits.

• min (int)

  Minimum length observed in FASTA/Q file

• max (int)

  Maximum length observed in FASTA/Q file

• seqs (int)

  total number of sequences in the files

• filename (string)

  file basename of the input file

• dirname (string)

  name of the directory containing the input file (as received)

• path (string)

  name of the directory containing the input file (resolved to its absolute path)

• json (string: JSON pretty printed)

  (pretty printed) JSON string of the object (only if JSON is installed)

jsonStats(filepath)

Returns the JSON string with basic stats (same as $result->{json} from getStats(File, JSON)). Requires JSON::PP installed.

_n50fromHash(hash, totalsize)

This is an internal helper subroutine that perform the actual N50 calculation, hence its addition to the documentation. Expects the reference to an hash of sizes $size{SIZE} = COUNT and the total sum of sizes obtained parsing the sequences file. Returns N50, min and max lengths.

Dependencies

Module (N50.pm)

• FASTX::Reader (required)
• JSON::PP, File::Basename (core modules)

Stantalone program (n50.pl)

• Term::ANSIColor

• JSON

  (optional) when using --format JSON

• Text::ASCIITable

  (optional) when using --format screen. This might be substituted by a different module in the future.

SUPPORT

This module and the n50 program have limited support. SeqFu (https://telatin.github.io/seqfu2) is a compiled suite of utilities that includes a seqfu stats module, a faster replacement for the n50 program.

If you are interested in contributing to the development of this module, or in reporting bugs, please refer to repository https://github.com/telatin/proch-n50/issues.

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