adding an auxiliary script: adjust_TY_annotation_for_gff3.pl

yjx1217 · Jan 30, 2023 · 8b90d42 · 8b90d42
1 parent ee9d9b0
commit 8b90d42
Showing 1 changed file with 111 additions and 0 deletions.
diff --git a/scripts/adjust_TY_annotation_for_gff3.pl b/scripts/adjust_TY_annotation_for_gff3.pl
@@ -0,0 +1,111 @@
+#!/usr/bin/perl
+use warnings;
+use strict;
+use Getopt::Long;
+
+##############################################################
+#  script: adjust_TY_annotation_for_gff3.pl
+#  author: Jia-Xing Yue (GitHub ID: yjx1217)
+#  last edited: 2023.01.30
+#  description: change TY4_soloLTR, TSU4_soloLTR, TY4_truncated, TSU4_truncated to TY4/TSU4_soloLTR, TY4/TSU4_soloLTR, TY4/TSU4_truncated, and TY4/TSU4_truncated respectively; remove "p" suffix after TY.
+#  example: perl adjust_TY4TSU4_annotation_for_gff3.pl -i input.gff3(.gz) -o output.gff3(.gz)
+##############################################################
+
+my ($input, $output);
+GetOptions('input|i:s' => \$input, # input TY list file
+	   'output|o:s' => \$output); # output TY GFF3 file
+
+my $input_fh = read_file($input);
+my $output_fh = write_file($output);
+while (<$input_fh>) {
+    chomp;
+    if ((/^\s*\#/) or (/^\#/)) {
+	print $output_fh "$_\n";
+    } else {
+	my $flag = 0;
+	my @line = split /\t/, $_;
+	my $chr = $line[0];
+	my $source = $line[1];
+	my $feature = $line[2];
+	my $start = $line[3];
+	my $end = $line[4];
+	my $score = $line[5];
+	my $strand = $line[6];
+	my $phase = $line[7];
+	my $attributes = $line[8];
+	if ($feature eq "mobile_element") {
+	    my ($mobile_element_type) = ($attributes =~ /mobile_element_type=([^;]+)/);
+	    $mobile_element_type =~ s/TY1p/TY1/gi;
+	    $mobile_element_type =~ s/TY2p/TY2/gi;
+	    $mobile_element_type =~ s/TY3p/TY3/gi;
+	    $mobile_element_type =~ s/TY4p/TY4/gi;
+	    $mobile_element_type =~ s/TY5p/TY5/gi;
+	    $mobile_element_type =~ s/TSU4p/TSU4/gi;
+	    $mobile_element_type =~ s/TSU4b/TSU4/gi;
+	    if (($mobile_element_type =~ /(TSU4|TY4|TY4\/TSU4|TSU4\/TY4)/) and ($mobile_element_type =~ /truncated/)) {
+		$mobile_element_type = "TY4/TSU4_truncated";
+	    } elsif (($mobile_element_type =~ /(TSU4|TY4|TY4\/TSU4|TSU4\/TY4)/) and ($mobile_element_type =~ /soloLTR/)) {
+		$mobile_element_type = "TY4/TSU4_soloLTR";
+	    }
+	    print $output_fh "$chr\t$source\tmobile_element\t$start\t$end\t$score\t$strand\t$phase\tID=$mobile_element_type:$chr:$start-$end:$strand;Name=$mobile_element_type:$chr:$start-$end:$strand;mobile_element_type=$mobile_element_type\n";
+	} else {
+	    print $output_fh "$_\n";
+	}
+    }
+}
+
+
+
+
+sub read_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /\.gz$/) {
+        open($fh, "gunzip -c $file |") or die "can't open pipe to $file";
+    } else {
+        open($fh, $file) or die "can't open $file";
+    }
+    return $fh;
+}
+
+sub write_file {
+    my $file = shift @_;
+    my $fh;
+    if ($file =~ /\.gz$/) {
+        open($fh, "| gzip -c >$file") or die "can't open $file\n";
+    } else {
+        open($fh, ">$file") or die "can't open $file\n";
+    }
+    return $fh;
+}  
+
+
+sub parse_fasta_file {
+    my $fh = shift @_;
+    my %seq;
+    my $seq_name = "";
+    my $flag = 0;
+    while (<$fh>) {
+	chomp;
+	if (/^\s*$/) {
+	    next;
+	} elsif (/^\s*#/) {
+	    next;
+	} elsif (/^>(\S+)/) {
+	    $seq_name = $1;
+	    $seq{$seq_name} = "";
+	} else {
+	    $seq{$seq_name} .= $_;
+	}
+  }
+    return %seq;
+}
+
+
+
+sub revcom {
+    my $seq = shift @_;
+    my $seq_revcom = reverse $seq;
+    $seq_revcom =~ tr/ATGCatgc/TACGtacg/;
+    return $seq_revcom;
+}