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comparison ragoo.pl @ 0:90611c479c08 draft

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author dereeper
date Mon, 21 Jun 2021 21:10:57 +0000
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children 6a1c9991b723
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-1:000000000000 0:90611c479c08
1 #!/usr/bin/perl
2
3 use strict;
4
5 my $scaffolds= $ARGV[0];
6 my $reference = $ARGV[1];
7 my $output = $ARGV[2];
8 my $output2 = $ARGV[3];
9
10 my $tmpdir = "tmpdir$$";
11
12 mkdir($tmpdir);
13
14
15 my ($sc) = split(",",$scaffolds);
16 $scaffolds = $sc;
17
18 system("cp -rf $scaffolds $tmpdir/scaffolds.fa");
19 system("cp -rf $reference $tmpdir/reference.fa");
20 chdir($tmpdir);
21 system("ragoo.py scaffolds.fa reference.fa");
22
23
24 my %hash;
25 my $id;
26 open(F,"ragoo_output/ragoo.fasta");
27 while(<F>){
28 if (/>(.*)/){$id = $1;}
29 else{
30 $hash{$id}.= $_;
31 }
32 }
33 close(F);
34
35 open(O,">$output");
36 foreach my $id(keys(%hash)){
37 print O ">$id\n";
38 my $seq = $hash{$id};
39 for (my $i =0; $i <= length($seq); $i =$i+80){
40 my $subseq = substr($seq,$i,80);
41 print O "$subseq\n";
42 }
43 }
44 close(O);
45
46 open(O,">$output2");
47 foreach my $id(keys(%hash)){
48 if ($id =~/Chr0_RaGOO/){
49 next;
50 }
51 print O ">$id\n";
52 my $seq = $hash{$id};
53 for (my $i =0; $i <= length($seq); $i =$i+80){
54 my $subseq = substr($seq,$i,80);
55 print O "$subseq\n";
56 }
57 }
58 close(O);