20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,192 @@
+#!/usr/local/bin/perl -w
+
+# lightweight fasta reader capabilities:
+package Fasta_reader;
+
+use strict;
+use warnings;
+use Carp;
+
+sub new {
+    my ($packagename, $fastaFile) = @_;
+
+	## note: fastaFile can be a filename or an IO::Handle
+	
+
+    my $self = { fastaFile => undef,,
+				 fileHandle => undef };
+
+    bless ($self, $packagename);
+    
+    ## create filehandle
+    my $filehandle = undef;
+    
+	if (ref $fastaFile eq 'IO::Handle') {
+		$filehandle = $fastaFile;
+	}
+	else {
+		if ($fastaFile =~ /\.gz$/) {
+            open ($filehandle, "gunzip -c $fastaFile | ") or confess "Error, cannot open file $fastaFile using 'gunzip -c'";
+        }
+        else {
+            open ($filehandle, $fastaFile) or die "Error: Couldn't open $fastaFile\n";
+        }
+		$self->{fastaFile} = $fastaFile;
+	}
+	
+	$self->{fileHandle} = $filehandle;
+
+    return ($self);
+}
+
+
+
+#### next() fetches next Sequence object.
+sub next {
+    my $self = shift;
+    my $orig_record_sep = $/;
+    $/="\n>";
+    my $filehandle = $self->{fileHandle};
+    my $next_text_input = <$filehandle>;
+    
+	if (defined($next_text_input) && $next_text_input !~ /\w/) {
+		## must have been some whitespace at start of fasta file, before first entry.
+		## try again:
+		$next_text_input = <$filehandle>;
+	}
+	
+	my $seqobj = undef;
+    
+	if ($next_text_input) {
+		$next_text_input =~ s/^>|>$//g; #remove trailing > char.
+		$next_text_input =~ tr/\t\n\000-\037\177-\377/\t\n/d; #remove cntrl chars
+		my ($header, @seqlines) = split (/\n/, $next_text_input);
+		my $sequence = join ("", @seqlines);
+		$sequence =~ s/\s//g;
+		
+		$seqobj = Sequence->new($header, $sequence);
+    }
+    
+    $/ = $orig_record_sep; #reset the record separator to original setting.
+    
+    return ($seqobj); #returns null if not instantiated.
+}
+
+
+#### finish() closes the open filehandle to the query database.
+sub finish {
+    my $self = shift;
+    my $filehandle = $self->{fileHandle};
+    close $filehandle;
+    $self->{fileHandle} = undef;
+}
+
+####
+sub retrieve_all_seqs_hash {
+	my $self = shift;
+
+	my %acc_to_seq;
+	
+	while (my $seq_obj = $self->next()) {
+		my $acc = $seq_obj->get_accession();
+		my $sequence = $seq_obj->get_sequence();
+
+		$acc_to_seq{$acc} = $sequence;
+	}
+
+	return(%acc_to_seq);
+}
+
+
+
+##############################################
+package Sequence;
+use strict;
+
+sub new {
+    my ($packagename, $header, $sequence) = @_;
+    
+    ## extract an accession from the header:
+    my ($acc, $rest) = split (/\s+/, $header, 2);
+        
+    my $self = { accession => $acc,
+		 header => $header,
+		 sequence => $sequence,
+		 filename => undef };
+    bless ($self, $packagename);
+    return ($self);
+}
+
+####
+sub get_accession {
+    my $self = shift;
+    return ($self->{accession});
+}
+
+####
+sub get_header {
+    my $self = shift;
+    return ($self->{header});
+}
+
+####
+sub get_sequence {
+    my $self = shift;
+    return ($self->{sequence});
+}
+
+#### 
+sub get_FASTA_format {
+    my $self = shift;
+    my %settings = @_;
+
+    my $fasta_line_len = $settings{fasta_line_len} || 60;
+    
+    my $header = $self->get_header();
+    my $sequence = $self->get_sequence();
+    if ($fasta_line_len > 0) {
+        $sequence =~ s/(\S{$fasta_line_len})/$1\n/g;
+        chomp $sequence;
+    }
+    my $fasta_entry = ">$header\n$sequence\n";
+    return ($fasta_entry);
+}
+
+
+####
+sub write_fasta_file {
+    my $self = shift;
+    my $filename = shift;
+
+    my ($accession, $header, $sequence) = ($self->{accession}, $self->{header}, $self->{sequence});
+    
+	my $fasta_entry = $self->get_FASTA_format();
+	
+    my $tempfile;
+    if ($filename) {
+		$tempfile = $filename;
+    } else {
+		my $acc = $accession;
+		$acc =~ s/\W/_/g;
+		$tempfile = "$acc.fasta";
+    }
+    
+    open (TMP, ">$tempfile") or die "ERROR! Couldn't write a temporary file in current directory.\n";
+    print TMP $fasta_entry;
+    close TMP;
+    return ($tempfile);
+}
+
+####
+sub get_core_read_name {
+    my $self = shift;
+    
+    my $acc = $self->get_accession();
+    $acc =~ s|/[12]$||;
+    return($acc);
+}
+
+
+1; #EOM
+
+