20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,189 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+
+use lib ("$FindBin::RealBin/../../PerlLib/");
+use Ascii_genome_illustrator;
+use Cwd;
+
+my $usage = "usage: $0 refseqs.fa target.fa min_per_id [min_pct_aligned]\n\n";
+
+my $REFSEQS_FA = $ARGV[0] or die $usage;
+my $TARGET_FA = $ARGV[1] or die $usage;
+my $MIN_PER_ID = $ARGV[2] or die $usage;
+my $MIN_PCT_ALIGNED = $ARGV[3] || 0;
+
+main: {
+
+    
+    my $cmd = "blat $TARGET_FA $REFSEQS_FA -t=dna -q=dna -out=blast9 $TARGET_FA.blat.out";
+
+    &process_cmd($cmd);
+
+    # tried blastn, but it doesnt like the Trinity.fasta header format...
+    #my $cmd = "makeblastdb -in trinity_out_dir/Trinity.fasta -dbtype nucl";    
+    #$cmd = " blastn -db trinity_out_dir/Trinity.fasta -query refseqs.fa -outfmt 6 > blast.blastn.out";
+    #&process_cmd($cmd);
+    
+    &generate_ascii_illustration("$TARGET_FA.blat.out");
+    
+    exit(0);
+}
+
+####
+sub generate_ascii_illustration {
+    my ($align_out_file) = @_;
+
+    my %ref_seq_lengths = &get_seq_lengths($REFSEQS_FA);
+    my %target_seq_lengths = &get_seq_lengths($TARGET_FA);
+    
+    my @hits = &parse_align_out($align_out_file);
+    
+    ## Generate a reference view.
+    foreach my $ref_acc (keys %ref_seq_lengths) {
+        my $length = $ref_seq_lengths{$ref_acc};
+        my $ascii_illustration = new Ascii_genome_illustrator($ref_acc, 60);
+        
+        #$ascii_illustration->add_feature($ref_acc, 1, $length, "=");
+        
+        my @matches = grep { $_->{ref_acc} eq $ref_acc } @hits;
+        #@matches = reverse sort {$a->{bitscore}<=>$b->{bitscore}} @matches;
+        @matches = sort {$a->{ref_start}<=>$b->{ref_start}} @matches;
+
+
+        foreach my $match (@matches) {
+            
+            my $target_acc = $match->{target_acc};
+            my $target_start = $match->{target_start};
+            my $target_end = $match->{target_end};
+            my $per_id = $match->{per_id};
+            
+            if ($per_id < $MIN_PER_ID) { next; }
+
+            my $ref_start = $match->{ref_start};
+            my $ref_end = $match->{ref_end};
+
+            my $target_length = $target_seq_lengths{$target_acc};
+            my $pct_of_target_aligned = sprintf("%.2f", (abs($target_end-$target_start) + 1) / $target_length * 100);
+            
+            if ($pct_of_target_aligned < $MIN_PCT_ALIGNED) { next; }
+
+            my $target_feature_name = "$target_acc $target_start-$target_end:$target_length ($pct_of_target_aligned\% aln, $per_id\% ID)";
+
+            if ($target_start > $target_end) {
+                ($ref_start, $ref_end) = ($ref_end, $ref_start);
+            }
+            
+            $ascii_illustration->add_feature($target_feature_name, $ref_start, $ref_end, "-");
+            
+        }
+        
+        print $ascii_illustration->illustrate(1, $length);
+        print "\n"; # spacer
+        
+    }
+    
+    return;
+}
+
+####
+sub parse_align_out {
+    my ($align_out_file) = @_;
+    
+    my @alignments;
+
+    open (my $fh, $align_out_file) or die $!;
+    while (<$fh>) {
+        if (/^\#/) { next; }
+        chomp;
+
+=blast_outfmt6
+
+# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
+
+
+0       NM_012009_Sh2d1b1
+1       comp0_c0_seq1
+2       100.00
+3       1433
+4       0
+5       0
+6       1
+7       1433
+8       1
+9       1433
+10      0.0
+11      2647
+
+=cut
+
+        my @x = split(/\t/);
+        my ($ref_acc, $target_acc, $per_id, $align_len, $mismatches, $gaps, $ref_start, $ref_end, $target_start, $target_end, $evalue, $bitscore) = @x;
+        
+        my $struct = { target_acc => $target_acc,
+                       ref_acc => $ref_acc,
+                       
+                       per_id => $per_id,
+                       mismatches => $mismatches,
+                       gaps => $gaps,
+                       
+                       target_start => $target_start,
+                       target_end => $target_end,
+
+                       ref_start => $ref_start,
+                       ref_end => $ref_end,
+
+                       evalue => $evalue,
+                       bitscore => $bitscore,
+                   };
+
+        push (@alignments, $struct);
+    }
+
+    return(@alignments);
+
+}
+
+
+
+
+####
+sub get_seq_lengths {
+    my ($refseqs_fa) = @_;
+
+    my %lengths;
+    my $acc;
+    
+    open (my $fh, $refseqs_fa) or die $!;
+    while (<$fh>) {
+        if (/>(\S+)/) {
+            $acc = $1;
+        }
+        else {
+            my $seq = $_;
+            chomp $seq;
+            my $len = length($seq);
+            $lengths{$acc} += $len;
+        }
+    }
+    close $fh;
+    
+    return(%lengths);
+}
+    
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    my $ret = system($cmd);
+
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+    
+    return;
+}