Added module assemblathon_stats

.editorconfig

@@ -30,3 +30,7 @@ indent_style = unset
 # ignore python
 [*.{py}]
 indent_style = unset
+
+# ignore perl
+[*.{pl,pm}]
+indent_size = unset

bin/FAlite_a93cba2.pm

@@ -0,0 +1,128 @@
+package FAlite_a93cba2;
+use strict;
+sub new {
+	my ($class, $fh) = @_;
+	if (ref $fh !~ /GLOB/)
+		{die ref $fh, "\n", "FAlite_a93cba2 ERROR: expect a GLOB reference\n"}
+	my $this = bless {};
+	$this->{FH} = $fh;
+	while(<$fh>) {last if $_ =~ /\S/} # not supposed to have blanks, but...
+	my $firstline = $_;
+	if (not defined $firstline) {warn "FAlite_a93cba2: Empty\n"; return $this}
+	if ($firstline !~ /^>/) {warn "FAlite_a93cba2: Not FASTA formatted\n"; return $this}
+	$this->{LASTLINE} = $firstline;
+	chomp $this->{LASTLINE};
+	return $this;
+}
+sub nextEntry {
+	my ($this) = @_;
+	return 0 if not defined $this->{LASTLINE};
+	my $fh = $this->{FH};
+	my $def = $this->{LASTLINE};
+	my @seq;
+	my $lines_read = 0;
+	while(<$fh>) {
+		$lines_read++;
+		if ($_ =~ /^>/) {
+			$this->{LASTLINE} = $_;
+			chomp $this->{LASTLINE};
+			last;
+		}
+		push @seq, $_;
+	}
+	return 0 if $lines_read == 0;
+	chomp @seq;
+	my $entry = FAlite_a93cba2::Entry::new($def, \@seq);
+	return $entry;
+}
+
+package FAlite_a93cba2::Entry;
+use overload '""' => 'all';
+sub new {
+	my ($def, $seqarry) = @_;
+	my $this = bless {};
+	$this->{DEF} = $def;
+	$this->{SEQ} = join("", @$seqarry);
+	$this->{SEQ} =~ s/\s//g; # just in case more spaces
+	return $this;
+}
+sub def {shift->{DEF}}
+sub seq {shift->{SEQ}}
+sub all {my $e = shift; return $e->{DEF}."\n".$e->{SEQ}."\n"}
+
+1;
+
+__END__
+
+=head1 NAME
+
+FAlite_a93cba2;
+
+=head1 SYNOPSIS
+
+ use FAlite_a93cba2;
+ my $fasta = new FAlite_a93cba2(\*STDIN);
+ while(my $entry = $fasta->nextEntry) {
+     $entry->def;
+     $entry->seq;
+ }
+
+=head1 DESCRIPTION
+
+FAlite_a93cba2 is a package for parsing FASTA files and databases. The FASTA format is
+widely used in bioinformatics. It consists of a definition line followed by
+sequence with an arbitrary number of lines and line lengths.
+
+A FASTA file looks like this:
+
+ >identifier descriptive text
+ GAATTC
+
+A FASTA database looks like this:
+
+ >identifier1 some text describing this entry
+ GAATTC
+ ACTAGT
+ >identifier2 some text describing this entry
+ AAACCT
+ GCTAAT
+
+=head2 Object
+
+FAlite_a93cba2 has two kinds of objects, the file and the entry.
+
+ my $fasta_file = new FAlite_a93cba2(\*STDIN); # or any other filehandle
+ $entry = $fasta_file->nextEntry; # single fasta fle
+ while(my $entry = $fasta_file->nextEntry) {
+     # canonical form of use for fasta database
+ }
+
+The entry has two attributes (def and seq).
+
+ $entry->def; # access the def line
+ $entry->seq; # access the sequence
+ "$entry";    # overload to fasta file ($entry->def . "\n" . $entry->seq)
+
+=head1 AUTHOR
+
+Ian Korf (ikorf@sapiens.wustl.edu, http://sapiens.wustl.edu/~ikorf)
+
+=head1 ACKNOWLEDGEMENTS
+
+This software was developed at the Genome Sequencing Center at Washington
+Univeristy, St. Louis, MO.
+
+=head1 COPYRIGHT
+
+Copyright (C) 1999 Ian Korf. All Rights Reserved.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+
+
+
+
+