Mercurial > repos > fubar > microsatbed

annotate seqrequester/src/tests/summarizeTest.pl @ 1:1085e094cf5f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
author fubar
date Sat, 13 Jul 2024 12:39:06 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
1 #!/usr/bin/env perl
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
2 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
3 # Generates a FASTA with sequence of a known length, to test
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
4 # `seqrequester summarize`.
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
5 #
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
6
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
7 use strict;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
8
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
9 my $prefix = shift @ARGV;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
10 my @lengths;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
11 my $tLength = 0;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
12
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
13 die "usage: $0 output-prefix\n" if ($prefix eq "");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
14
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
15 my $seqidx = "aaaa";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
16 my $seqnum = "000000";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
17
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
18 open(F, "> $prefix.fasta");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
19 for (my $n=0; $n < 100000; $n++) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
20 my $small = rand(1);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
21 my $lseed = rand(1);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
22 my $length;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
23
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
24 if ($small < 0.0000) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
25 $length = int($lseed * 128 * 1048576) + 128 * 1048576;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
26 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
27 elsif ($small < 0.9) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
28 $length = int($lseed * 30) + 1;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
29 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
30 else {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
31 $length = int($lseed * 1024) + 1024;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
32 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
33
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
34 push @lengths, $length;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
35 $tLength += $length;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
36
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
37 my $rem = $length % 10;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
38
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
39 my $seq = "$seqidx$seqnum"; $seqidx++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
40
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
41 print F ">", $n+1, "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
42 while ($length > 0) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
43 print F $seq;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
44 $seq++;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
45 $length -= 5;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
46 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
47 print F "z" x $rem;
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
48 print F "\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
49
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
50 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
51 close(F);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
52
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
53 open(F, "> $prefix.lengths");
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
54 foreach my $l (@lengths) {
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
55 print F "$l\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
56 }
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
57 close(F);
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
58
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
59 print STDERR "Wrote ", scalar(@lengths), " sequences with total length $tLength.\n";
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
60
1085e094cf5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 7ceb6658309a7ababe622b5d92e729e5470e22f0-dirty
fubar
parents:
diff changeset
61 exit(0);