20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,200 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Fasta_reader;
+use File::Basename;
+
+
+my $usage = "usage: $0 isoform.EXPR.matrix Trinity.fasta [by=transcript|gene (default:transcript)]\n\n"
+    . "\t note, use the isoform.EXPR.matrix file regardiess of wehther you choose transcript | gene feature type to explore.\n\n";
+
+
+my $matrix_file = $ARGV[0] or die $usage;
+my $fasta_file = $ARGV[1] or die $usage;
+my $by_feature_type = $ARGV[2] || "transcript";
+
+
+unless (-s $matrix_file) {
+    die "Error, cannot locate matrix file: $matrix_file";
+}
+unless (-s $fasta_file) {
+    die "Error, cannot locate fasta file: $fasta_file";
+}
+
+unless ($by_feature_type =~ /^(transcript|gene)$/) {
+    die "Error, cannot discern feature type: [$by_feature_type] ";
+}
+
+my %trans_lengths;
+{
+    my $fasta_reader = new Fasta_reader($fasta_file);
+    while (my $seq_obj = $fasta_reader->next()) {
+        
+        my $acc = $seq_obj->get_accession();
+        my $sequence = $seq_obj->get_sequence();
+        
+        my $seq_len = length($sequence);
+
+        $trans_lengths{$acc} = $seq_len;
+    }
+}
+
+open (my $fh, $matrix_file) or die $!;
+my $header = <$fh>;
+
+my %gene_to_trans;
+
+my $sum_expr = 0;
+
+
+my $feature_type = "transcript";
+
+while (<$fh>) {
+    chomp;
+    my @x = split(/\t/);
+    my $acc = shift @x; # gene accession
+    my $max_expr = 0;
+    my $trans_sum_expr = 0;
+    while (@x) {
+        my $expr = shift @x;
+        
+        $trans_sum_expr += $expr;
+        $sum_expr += $expr;    
+
+        if ($expr > $max_expr) {
+            $max_expr = $expr;
+        }
+    }
+    
+    my $seq_len = $trans_lengths{$acc} or die "Error, no seq length for acc: $acc.  Be sure to give the isoform.TPM expression matrix as input parameter";
+
+    my $gene_id = $acc;
+
+    
+    if ($by_feature_type =~ /gene/) {
+        if ($acc =~ /^(\S+)_i\d+/) {
+            $gene_id = $1;
+            $feature_type = "gene";
+        }
+        else {
+            die "Error, by_feature_type is gene, but cannot extract gene_id from $acc ";
+        }
+    }
+    
+    push (@{$gene_to_trans{$gene_id}}, { acc => $acc,
+                                         len => $seq_len,
+                                         sum_expr => $trans_sum_expr,
+                                         max_expr => $max_expr,
+          });
+    
+}
+
+my @genes;
+
+## make expression weighted gene length
+foreach my $gene (keys %gene_to_trans) {
+    my @trans_structs = @{$gene_to_trans{$gene}};
+
+    my $sum_expr = 0;
+    my $sum_expr_n_len = 0;
+    my $max_expr = 0;
+    foreach my $trans_struct (@trans_structs) {
+        my $len = $trans_struct->{len};
+        my $expr = $trans_struct->{sum_expr} || 1;
+        $sum_expr_n_len += $len * $expr;
+        $sum_expr += $expr;
+
+        my $m_expr = $trans_struct->{max_expr};
+        if ($m_expr > $max_expr) {
+            $max_expr = $m_expr;
+        }
+        
+    }
+    
+    my $gene_len = $sum_expr_n_len / $sum_expr;
+    
+    push (@genes, { acc => $gene,
+                    sum_expr => $sum_expr,
+                    len => $gene_len,
+                    max_expr => $max_expr } );
+}
+
+
+@genes = reverse sort { $a->{sum_expr} <=> $b->{sum_expr}
+                        ||
+                            $a->{len} <=> $b->{len} } @genes;
+
+
+
+## write output table
+
+
+my $E_file = basename($matrix_file) . ".by-$feature_type.E-inputs";
+open (my $ofh, ">$E_file") or die $!;
+print $ofh join("\t", "#Ex", "acc", "length", "max_expr_over_samples", "sum_expr_over_samples") . "\n";
+
+print "Ex\tExN50\tnum_${feature_type}s\n";
+
+my $prev_pct = 0;
+my $sum = 0;
+my @captured;
+while (@genes) {
+    
+    my $t = shift @genes;
+
+    $sum += $t->{sum_expr};
+
+    my $pct = int($sum/$sum_expr * 100);
+    
+    print $ofh join("\t", $pct, $t->{acc}, int($t->{len}), sprintf("%.3f", $t->{max_expr}), sprintf("%.3f", $t->{sum_expr})) . "\n";
+    
+    if ($prev_pct > 0 && $pct > $prev_pct) {
+        
+                        
+        my $N50 = int(&calc_N50(@captured));
+        my $num_trans = scalar(@captured);
+        
+        print "$prev_pct\t$N50\t$num_trans\n";
+    }
+    
+    $prev_pct = $pct;
+    
+    push (@captured, $t);
+}
+
+# do last one
+
+my $N50 = &calc_N50(@captured);
+my $num_genes = scalar(@captured);
+print "100\t$N50\t$num_genes\n";
+
+
+exit(0);
+
+
+####
+sub calc_N50 {
+    my @entries = @_;
+    
+    @entries = reverse sort {$a->{len}<=>$b->{len}} @entries;
+    
+    my $sum_len = 0;
+    foreach my $entry (@entries) {
+        $sum_len += $entry->{len};
+    }
+
+    my $loc_sum = 0;
+    foreach my $entry (@entries) {
+        $loc_sum += $entry->{len};
+        if ($loc_sum / $sum_len * 100 >= 50) {
+            return($entry->{len});
+        }
+    }
+
+    return(-1); # error
+}
+