20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,53 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+my $usage = "\n\n\tusage: $0 acc_list_file.txt target_db.fasta\n\n";
+
+my $acc_list_file = $ARGV[0] or die $usage;
+my $target_db = $ARGV[1] or die $usage;
+
+
+main: {
+
+    my $samtools = `sh -c "command -v samtools"`;
+    unless ($samtools =~ /\w/) {
+        die "Error, need samtools in your PATH setting.";
+    }
+    chomp $samtools;
+
+    my @accs = `cat $acc_list_file`;
+    chomp @accs;
+    
+    if (! -s "$target_db.fasta.fai") {
+        my $cmd = "$samtools faidx $target_db";
+        my $ret = system $cmd;
+        if ($ret) {
+            die "Error, cmd: $cmd died with ret $ret";
+        }
+    }
+    
+    my $ret = 0;
+    
+    foreach my $acc (@accs) {
+        $acc =~ s/\s//g;
+
+        unless ($acc =~ /\w/) { next; } 
+
+        my $cmd = "$samtools faidx $target_db \"$acc\"";
+        
+        my $result = `$cmd`;
+        if ($result) {
+            print $result;
+        }
+        else {
+            print STDERR "No entry retrieved for acc: $acc\n";
+            $ret = 1;
+        }
+    }
+
+    exit($ret);
+
+}
+