20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,126 @@
+package Fasta_retriever;
+
+use strict;
+use warnings;
+use Carp;
+use threads;
+use threads::shared;
+
+
+my $LOCKVAR :shared;
+our $DEBUG = 0;
+
+sub new {
+    my ($packagename) = shift;
+    my $filename = shift;
+    
+    unless ($filename) {
+        confess "Error, need filename as param";
+    }
+
+    my $self = { filename => $filename,
+                 acc_to_pos_index => undef,
+                 fh => undef,
+    };
+    
+    my %acc_to_pos_index :shared;
+
+    $self->{acc_to_pos_index} = \%acc_to_pos_index;
+        
+    bless ($self, $packagename);
+
+    $self->_init();
+
+
+    return($self);
+}
+
+
+sub _init {
+    my $self = shift;
+    
+    my $filename = $self->{filename};
+    
+    # use a samtools faidx index if available
+    my $index_file = "$filename.fai";
+    if (-s $index_file) {
+        open(my $fh, $index_file) or die "Error, cannot open file: $index_file";
+        while(<$fh>) {
+            chomp;
+            my @x = split(/\t/);
+            my $acc = $x[0];
+            my $file_pos = $x[2];
+            $self->{acc_to_pos_index}->{$acc} = $file_pos;
+        }
+        close $fh;
+    }
+    else {
+        print STDERR "-missing faidx file: $index_file, extracting positions directly.\n";
+        print STDERR "-Fasta_retriever:: begin initializing for $filename\n";
+    
+        open (my $fh, $filename) or die $!;
+        $self->{fh} = $fh;
+        while (<$fh>) {
+            if (/>(\S+)/) {
+                my $acc = $1;
+                my $file_pos = tell($fh);
+                $self->{acc_to_pos_index}->{$acc} = $file_pos;
+            }
+        }
+        print STDERR "-Fasta_retriever:: done initializing for $filename\n";
+    }
+    
+    return;
+}
+
+sub refresh_fh {
+    my $self = shift;
+    
+    open (my $fh, $self->{filename}) or die "Error, cannot open file : " . $self->{filename};
+    $self->{fh} = $fh;
+    
+    return $fh;
+}
+
+
+sub get_seq {
+    my $self = shift;
+    my $acc = shift;
+
+    unless (defined $acc) {
+        confess "Error, need acc as param";
+    }
+
+
+    my $seq = "";
+
+    {
+        lock $LOCKVAR;
+    
+        my $file_pos = $self->{acc_to_pos_index}->{$acc} or confess "Error, no seek pos for acc: $acc";
+        
+        my $fh = $self->refresh_fh();
+        seek($fh, $file_pos, 0);
+
+        print STDERR "seeking $acc -> $file_pos\n" if $DEBUG;
+        
+        while (<$fh>) {
+            if (/^>/) {
+                print STDERR "   reached $_, stopping\n" if $DEBUG;
+                last;
+            }
+            my $seq_part = $_;
+            $seq_part =~ s/\s//g;
+            $seq .= $seq_part;
+        }
+        print STDERR "-done seeking $acc\n\n" if $DEBUG;
+        
+    }    
+    
+    return($seq);
+}
+
+    
+
+1; #EOM
+