20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,176 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use Carp;
+
+use FindBin;
+use lib ("$FindBin::RealBin/../../PerlLib");
+use Fasta_reader;
+use Nuc_translator;
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+use Cwd;
+
+my $usage = <<__EOUSAGE__;
+
+
+##################################################################
+
+$0
+
+##################################################################
+#
+# Required:
+#
+#  --transcripts <string>       file containing target transcripts in fasta format
+#
+# Optional:
+#
+#  --read_length <int>          default: 76
+#
+#  --frag_length <int>             default: 300
+#
+#  --out_prefix <string>        default: 'reads'
+#
+#  --depth_of_cov <int>         default: 100  (100x targeted base coverage)
+#
+####
+#
+#  following wgsim options are pass-through:
+#
+# Options: 
+#    -e FLOAT      base error rate [0.020]
+#    -s INT        standard deviation [50]
+#    -r FLOAT      rate of mutations [0.0010]
+#    -R FLOAT      fraction of indels [0.15]
+#    -X FLOAT      probability an indel is extended [0.30]
+#    -S INT        seed for random generator [-1]
+#    -A FLOAT      disgard if the fraction of ambiguous bases higher than FLOAT [0.05]
+#    -h            haplotype mode
+#    -Z INT        strand specific mode: 1=FR, 2=RF
+#    -D            debug mode... highly verbose
+#
+#
+############################################################################################
+
+
+
+__EOUSAGE__
+
+    ;
+
+
+
+my $require_proper_pairs_flag = 0;
+
+my $transcripts;
+my $read_length = 76;
+my $frag_length = 300;
+my $help_flag;
+my $out_prefix = "reads";
+my $depth_of_cov = 100;
+
+&GetOptions ( 'help' => \$help_flag,
+              'transcripts=s' => \$transcripts,
+              'read_length=i' => \$read_length,
+              'frag_length=i' => \$frag_length,
+              'out_prefix=s' => \$out_prefix,
+              'depth_of_cov=i' => \$depth_of_cov,
+              
+              
+    );
+
+
+
+if ($help_flag) {
+    die $usage;
+}
+
+unless ($transcripts) { 
+    die $usage;
+}
+
+unless ($out_prefix =~ /^\//) {
+    $out_prefix = cwd() . "/$out_prefix";
+}
+
+main: {
+    
+    my $number_reads = &estimate_total_read_count($transcripts, $depth_of_cov, $read_length);
+    
+    my $cmd = "wgsim-trans -N $number_reads -1 $read_length -2 $read_length "
+        . " -d $frag_length "
+        . " @ARGV > $out_prefix.log"; # pass-through to wgsim
+    
+    
+    my $token = "wgsim_R${read_length}_F${frag_length}_D${depth_of_cov}";
+    if (grep { "-Z" } @ARGV) {
+        $token .= "_SS";
+    }
+    
+    
+    
+    my $left_prefix = "$out_prefix.$token.left";
+    my $right_prefix = "$out_prefix.$token.right";
+    
+    $cmd .= " $transcripts $left_prefix.fq $right_prefix.fq";
+    
+    &process_cmd($cmd);
+
+    # convert to fasta format
+    &process_cmd("$FindBin::Bin/../support_scripts/fastQ_to_fastA.pl -I $left_prefix.fq > $left_prefix.fa");
+
+    &process_cmd("$FindBin::Bin/../support_scripts/fastQ_to_fastA.pl -I $right_prefix.fq > $right_prefix.fa");
+
+    #unlink("$left_prefix.fq", "$right_prefix.fq");
+
+    open(my $ofh, ">$out_prefix.$token.info") or die "Error, cannot write to file: $out_prefix.$token.info";
+    print $ofh join("\t", $transcripts, "$left_prefix.fa", "$right_prefix.fa");
+    close $ofh;
+    
+    
+    exit(0);
+
+}
+
+
+####
+sub estimate_total_read_count {
+    my ($transcripts_fasta_file, $depth_of_cov, $read_length) = @_;
+
+    my $sum_seq_length = 0;
+    my $fasta_reader = new Fasta_reader($transcripts);
+    while (my $seq_obj = $fasta_reader->next()) {
+        my $sequence = $seq_obj->get_sequence();
+        $sum_seq_length += length($sequence);
+    }
+    
+    # DOC = num_reads * read_length * 2 / seq_length
+
+    # so, 
+
+    # num_reads = DOC * seq_length / 2 / read_length
+
+    my $num_reads = $depth_of_cov * $sum_seq_length / 2 / $read_length;
+
+    $num_reads = int($num_reads + 0.5);
+    
+    return($num_reads);
+}
+
+
+####
+sub process_cmd {
+    my ($cmd) = @_;
+
+    print STDERR "CMD: $cmd\n";
+
+    my $ret = system($cmd);
+
+    if ($ret) {
+        die "Error, cmd: $cmd died with ret $ret";
+    }
+
+    return;
+}
+