20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,183 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use File::Basename;
+use Cwd;
+
+use Carp;
+use Getopt::Long qw(:config no_ignore_case bundling pass_through);
+
+
+my $usage = <<__EOUSAGE__;
+
+######################################################################
+#
+#  Required:
+#  --genome <string>           target genome to align to
+#  --transcripts <string>      cdna sequences to align
+#
+#  Optional:
+#  --gtf <string>              gene structure annotations in gtf format
+#  --CPU <int>                 number of threads (default: 2)
+#  -o|--output <string>        bam output filename (default: basename(transcripts).mm2.bam)
+#
+#  -I|--max_intron_length <int>   maximum intron length (default: 100000)
+#
+#  --incl_out_gff3             include gff3 formatted output file for alignments.
+#  --allow_secondary           allow secondary alignments (default secondary=no)
+#
+#  --eqx                       include --eqx flag
+#  --cs                        include long format via --cs w/ minimap2
+#  --hq                        pacbio CCS reads (--splice:hq for mm2)
+#
+#######################################################################
+
+
+__EOUSAGE__
+
+    ;
+
+my $genome;
+my $transcripts;
+my $gtf;
+my $CPU = 2;
+
+my $help_flag;
+my $output;
+my $max_intron_length = 100000;
+my $incl_out_gff3;
+my $allow_secondary = 0;
+my $include_cs_flag = 0;
+my $include_eqx_flag = 0;
+my $include_hq_flag = 0;
+
+&GetOptions( 'h' => \$help_flag,
+             'genome=s' => \$genome,
+             'transcripts=s' => \$transcripts,
+             'gtf=s' => \$gtf,
+             'CPU=i' => \$CPU,
+             'o|output=s' => \$output,
+             'I|max_intron_length=i' => \$max_intron_length,
+             'incl_out_gff3' => \$incl_out_gff3,
+             'allow_secondary' => \$allow_secondary,
+             'cs' => \$include_cs_flag,
+             'hq' => \$include_hq_flag,
+    );
+
+
+if ($help_flag) {
+    die $usage;
+}
+
+
+unless ($genome && $transcripts) {
+    die $usage;
+}
+
+
+my $include_cs_param = "";
+my $include_cs_token = "";
+if ($include_cs_flag) {
+    $include_cs_param = "--cs";
+    $include_cs_token = ".cs";
+}
+
+my $include_eqx_param = "";
+my $include_eqx_token = "";
+if ($include_eqx_flag) {
+    $include_eqx_param = "--eqx";
+    $include_eqx_token = ".eqx";
+}
+
+
+my $include_hq_param = "";
+my $include_hq_token = "";
+if ($include_hq_flag) {
+    $include_hq_param = ":hq";
+    $include_hq_token = ".hq";
+}
+
+
+unless ($output) {
+    $output = basename($transcripts) . ".mm2${include_cs_token}${include_eqx_token}${include_hq_token}.bam";
+}
+
+
+
+
+main: {
+
+	
+    my $genomeBaseDir = dirname($genome);
+    my $genomeName = basename($genome);
+    my $mm2_idx = "$genomeBaseDir/$genomeName" . ".mm2";
+    
+    my $cwd = cwd();
+
+    my $splice_file = "$mm2_idx.splice.bed";
+
+    unless (-e $mm2_idx) {
+        
+        my $cmd = "minimap2 -d $mm2_idx $genome";
+        &process_cmd($cmd);
+    }
+
+    
+    if ($gtf && ! -s $splice_file) {
+	my $cmd = "paftools.js gff2bed $gtf > $splice_file";
+	&process_cmd($cmd);
+    }
+	
+	
+    ## run minimap2
+
+    my $splice_param = "";
+    if ($splice_file) {
+        $splice_param = "--junc-bed $splice_file";
+    }
+
+    my $secondary = ($allow_secondary) ? "" : "--secondary=no";
+
+    my $cmd = "minimap2 --sam-hit-only  -ax splice$include_hq_param $splice_param $secondary -t $CPU -u b -G $max_intron_length $include_cs_param $include_eqx_param $mm2_idx $transcripts > $output.tmp.sam";
+    &process_cmd($cmd);
+
+    $cmd = "samtools view -Sb -T $genome $output.tmp.sam -o $output.tmp.unsorted.bam";
+    &process_cmd($cmd);
+
+    $cmd = "samtools sort $output.tmp.unsorted.bam -o $output";
+    &process_cmd($cmd);
+
+    $cmd = "samtools index $output";
+    #&process_cmd($cmd);
+    `$cmd`; # ignore error that occurs if file is too big.
+
+    if ($incl_out_gff3) {
+        $cmd = "$FindBin::Bin/SAM_to_gff3.minimap2.pl $output > $output.gff3";
+        &process_cmd($cmd);
+    }
+
+    unlink("$output.tmp.sam", "$output.tmp.unsorted.bam");
+    
+	exit(0);
+}
+
+####
+sub process_cmd {
+	my ($cmd) = @_;
+	
+	print STDERR "CMD: $cmd\n";
+	#return;
+
+	my $ret = system($cmd);
+	if ($ret) {
+		die "Error, cmd: $cmd died with ret ($ret)";
+	}
+
+	return;
+}
+
+
+