20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,99 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use lib ($ENV{EUK_MODULES});
+use Fasta_reader;
+
+
+my $usage = "usage: $0 transcripts.cdna.fasta\n\n";
+
+my $transcripts_fasta_file = $ARGV[0] or die $usage;
+
+my $graphs_per_dir = 100;
+
+
+main: {
+    
+    my $fasta_reader = new Fasta_reader($transcripts_fasta_file) or die $!;
+    
+    
+    my $count = 0;
+   
+    my %gene_to_seq;
+
+    while (my $seq_obj = $fasta_reader->next()) {
+        
+        my $accession = $seq_obj->get_accession();
+
+        my $sequence = $seq_obj->get_sequence();
+        
+        my ($trans, $gene) = split(/;/, $accession);
+
+
+        $gene_to_seq{$gene}->{$trans} = $sequence;
+
+    }
+
+    foreach my $gene (keys %gene_to_seq) {
+        
+        my $trans_href = $gene_to_seq{$gene};
+        
+        my @trans = keys %$trans_href;
+        unless (scalar @trans > 1) {
+            # want just alt-splice ones.
+            next; 
+        }
+
+        $gene =~ s/\W/_/g;
+        
+        
+        my $dir_no = int($count/$graphs_per_dir);
+        my $outdir = "gene_altSplice_graphs/g_$dir_no";
+        if (! -d $outdir) {
+            &process_cmd("mkdir -p $outdir");
+        }
+
+        my $fa_file = "$outdir/$gene.fa";
+        open (my $ofh, ">$fa_file") or die $!;
+        foreach my $trans_acc (keys %$trans_href) {
+
+            my $seq = $trans_href->{$trans_acc};
+            print $ofh ">$trans_acc\n$seq\n";
+            
+        }
+        
+        
+        close $ofh;
+
+        my $cmd = "~/SVN/trinityrnaseq/trunk/util/misc/Monarch --misc_seqs $fa_file --graph $fa_file.dot";
+        &process_cmd($cmd);
+
+        
+        $count++;
+    }
+
+
+    print STDERR "\n\nDone.\n\n";
+    
+    exit(0);
+}
+
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+    
+    return;
+
+
+}
@@ -0,0 +1,71 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use lib ($ENV{EUK_MODULES});
+use Fasta_reader;
+
+my $usage = "usage: $0 transcripts.cdna.fasta\n\n";
+
+my $transcripts_fasta = $ARGV[0] or die $usage;
+
+
+my $graphs_per_dir = 100;
+
+
+main: {
+    
+    my $fasta_reader = new Fasta_reader($transcripts_fasta) or die $!;
+    
+    
+    my $count = 0;
+   
+    while (my $seq_obj = $fasta_reader->next()) {
+        
+        my $accession = $seq_obj->get_accession();
+        $accession =~ s/\W/_/g;
+
+        my $sequence = $seq_obj->get_sequence();
+
+        my $dir_no = int($count/$graphs_per_dir);
+        my $outdir = "trans_graphs/g_$dir_no";
+        if (! -d $outdir) {
+            &process_cmd("mkdir -p $outdir");
+        }
+        
+        my $fa_file = "$outdir/$accession.fa";
+        open (my $ofh, ">$fa_file") or die $!;
+        print $ofh ">$accession\n$sequence\n";
+        close $ofh;
+
+        my $cmd = "~/SVN/trinityrnaseq/trunk/util/misc/Monarch --misc_seqs $fa_file --graph $fa_file.dot";
+        &process_cmd($cmd);
+
+        
+        $count++;
+    }
+
+
+    print STDERR "\n\nDone.\n\n";
+    
+    exit(0);
+}
+
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+    
+    my $ret = system($cmd);
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+    
+    return;
+
+
+}