++ed by:
PROCH

1 PAUSE user
2 non-PAUSE users.

Andrea Telatin ⚗️
and 1 contributors

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 0.80

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,
  #               'min' => 4,
  #               'max' => 65,
  #               'dirname' => 'data',
  #               'size' => 130,
  #               'seqs' => 6,
  #               'filename' => 'small_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; 

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 (int)

the actual N50

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

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)

Implementation (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.

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