20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,88 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Process_cmd;
+use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
+use Carp;
+
+
+my $CPU = 2;
+
+my $usage = <<__EOUSAGE__;
+
+############################################################################
+#
+#  --target <string>        target for alignment
+#
+#  --left <string>          read_1.fq
+#
+#  optional:
+#
+#  --right <string>         read_2.fq
+#
+#  --CPU <int>              number of threads (default: $CPU)
+#
+#  --max_hits <int>         default 10
+
+ usage: $0  --target target.seq --left reads_1.fq [--right reads_2.fq --CPU 8]
+    
+      and you can pipe it into samtools to make a bam file:
+   
+         | samtools view -@ 8 -Sb - | samtools sort -@ 8 -m 4G - -o bowtie2.coordSorted.bam
+
+#############################################################################
+
+
+
+__EOUSAGE__
+
+    ;
+
+    
+my $help_flag;
+my $target_seq;
+my $reads_1_fq;
+my $reads_2_fq;
+my $max_hits = 10;
+
+&GetOptions ( 'h' => \$help_flag,
+              'target=s' => \$target_seq,
+              'left=s' => \$reads_1_fq,
+              'right=s' => \$reads_2_fq,
+              'CPU=i' => \$CPU,
+              'max_hits=i' => \$max_hits,
+    );
+
+
+if ($help_flag) { die $usage; }
+
+unless ($target_seq && $reads_1_fq) { die $usage; }
+
+
+
+main: {
+
+    unless (-s "$target_seq.1.bt2") {
+        my $cmd = "bowtie2-build $target_seq $target_seq 1>&2 ";
+        &process_cmd($cmd);
+    }
+    
+    my $format = ($reads_1_fq =~ /\.fq|\.fastq/) ? "-q" : "-f";
+    
+    my $bowtie2_cmd = "bowtie2 --threads $CPU --local --no-unal -x $target_seq $format -k $max_hits";
+    if ($reads_2_fq) {
+        $bowtie2_cmd .= " -1 $reads_1_fq -2 $reads_2_fq ";
+    }
+    else {
+        $bowtie2_cmd .= " -U $reads_1_fq ";
+    }
+
+    
+    &process_cmd($bowtie2_cmd);
+    
+    exit(0);
+}
+