1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
|
#!/usr/bin/env perl
use strict;
use warnings;
use FindBin;
## we delete all files we don't need in this directory. Be careful in case users try running it somewhere else, outside this dir.
chdir $FindBin::RealBin or die "error, cannot cd to $FindBin::RealBin";
my @files_to_keep = qw (cleanme.pl
README
reads.left.fq.gz
reads.right.fq.gz
runMe.sh
__indiv_ex_sample_derived
misc_run_tests
run_abundance_estimation_procedure.sh
reads2.left.fq.gz
reads2.right.fq.gz
longReads.fa
Makefile
test_FL.sh
reads.left.fa.gz
reads.right.fa.gz
samples.SE.txt
samples.PE.txt
);
my %keep = map { + $_ => 1 } @files_to_keep;
`rm -rf ./trinity_out_dir` if (-d "trinity_out_dir");
`rm -rf ./bowtie_out` if (-d "bowtie_out");
`rm -rf ./RSEM.stat` if (-d "RSEM.stat");
`rm -rf ./trinity_single_outdir` if (-d "trinity_single_outdir");
`rm -rf ./bowtie_single_outdir` if (-d "bowtie_single_outdir");
`rm -rf ./normalized_reads_test` if (-d "normalized_reads_test");
`rm -rf ./collectl` if (-d "collectl");
`rm -rf ./trin_w_jaccard` if (-d "trin_w_jaccard");
`rm -rf ./trin_SE_outdir` if (-d "trin_SE_outdir");
`rm -rf ./trin_test_no_qtrim`;
`rm -rf ./trinity_test_no_qtrim` if (-d "trinity_test_no_qtrim");
`rm -rf ./trinity_w_jaccard` if (-d "trinity_w_jaccard");
`rm -rf ./__test_trinity*`;
`rm -rf ./trinity_trim_and_norm_outdir`;
`rm -rf ./RSEM_outdir`;
`rm -rf ./eXpress_outdir`;
`rm -rf ./eXpress_PE`;
`rm -rf ./kallisto_PE`;
`rm -rf ./RSEM_PE`;
`rm -rf ./test_trinity_long_reads`;
`rm -rf ./test_trinity_bowtie2`;
`rm -rf ./trinity_test_samples_SE`;
`rm -rf ./trinity_test_samples_PE`;
`rm -rf ./trinity_out_dir_monitored`;
`rm -rf ./trinity_piecemeal`;
`rm -rf ./trinity_test_samples_PE_min_kmer_cov_3`;
`rm -rf ./trinity_complete`;
foreach my $file (<*>) {
if (! $keep{$file}) {
print STDERR "-removing file: $file\n";
unlink($file);
}
}
exit(0);
|
