npsearch 2.0.1 → 2.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -1,6 +0,0 @@
1
- >isotig00009_f2_3~~~ - S.P.=> Cleavage Site: 22:23 | D-value: 0.532
2
- MLKCFSIIMGLILLLEIGGGCA~~~IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLSCCGVNSYEDWDNNIYFNCSGPANNPEALWCAFLLLYTGSSKRSSQHPVRLWSSFPRTTKYFPHKDLHHWLCGYVYNVD
3
- >isotig00009_f3_7~~~ - S.P.=> Cleavage Site: 16:17 | D-value: 0.643
4
- MKTGIIIFISTVVVLP~~~ITLKPCGVPFSCCIPDQASGVANTQCGYGVRSPEQQNTFHTKIYTTGCADMFTMWINRYLYYIAGIAGVIVLVELFGFCFAHSLINDIKRQKARWAHR
5
- >isotig00016_f1_0~~~ - S.P.=> Cleavage Site: 23:24 | D-value: 0.592
6
- MNAGQIFIALMAQLFNACLLVSS~~~NFDSDIADSTLGKRSTGFVDTFGKRFVDSFGKRVDEFDYDHNGNYAEQSEQSSYISPQLKRGQKGLRSGSFIDAFGKRSSFQEVDEKRFADSFGKRFADSFGKRSPVGFVDTLGKRFAVSFGKRNTVGFVDTLGKRFADSFGKRSQQGFVDAFGKRYQGVY
@@ -1,6 +0,0 @@
1
- >isotig00009_f2_3~~~ - S.P.=> Cleavage Site: 22:23 | D-value: 0.532
2
- MLKCFSIIMGLILLLEIGGGCA~~~IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLSCCGVNSYEDWDNNIYFNCSGPANNPEALWCAFLLLYTGSSKRSSQHPVRLWSSFPRTTKYFPHKDLHHWLCGYVYNVD
3
- >isotig00009_f3_7~~~ - S.P.=> Cleavage Site: 16:17 | D-value: 0.643
4
- MKTGIIIFISTVVVLP~~~ITLKPCGVPFSCCIPDQASGVANTQCGYGVRSPEQQNTFHTKIYTTGCADMFTMWINRYLYYIAGIAGVIVLVELFGFCFAHSLINDIKRQKARWAHR
5
- >isotig00016_f1_0~~~ - S.P.=> Cleavage Site: 23:24 | D-value: 0.592
6
- MNAGQIFIALMAQLFNACLLVSS~~~NFDSDIADSTLGKRSTGFVDTFGKRFVDSFGKRVDEFDYDHNGNYAEQSEQSSYISPQLKRGQKGLRSGSFIDAFGKRSSFQEVDEKRFADSFGKRFADSFGKRSPVGFVDTLGKRFAVSFGKRNTVGFVDTLGKRFADSFGKRSQQGFVDAFGKRYQGVY
@@ -1,37 +0,0 @@
1
- <!DOCTYPE html>
2
- <html>
3
- <head>
4
- <title>Results</title>
5
- <meta content='text/html; charset=utf-8' http-equiv='Content-Type'>
6
- <style>
7
- .id {font-weight: bold;}
8
- .signalp {color:#007AC0; font-weight: bold;}
9
- .motif {color:#00B050; font-weight: bold;}
10
- .glycine {color:#FFC000; font-weight: bold;}
11
- .phenylalanine {color:#FF00EB; font-weight: bold;}
12
- .gkr {color:#FF0000; font-weight: bold;}
13
- .cysteine {color:#00B050;}
14
- p {word-wrap: break-word; font-family:Courier New, Courier, Mono;}
15
- </style>
16
- </head>
17
- <body>
18
- <p>
19
- <span class='id'>isotig00009_f2_3</span>
20
- <span>- S.P.=> Cleavage Site: 22:23 | D-value: 0.532</span>
21
- <br>
22
- <span class='signalp'>MLKCFSIIMGLILLLEIGGGCA</span><span>IYFYRAQIQAQFQKSLTDVTITDYRENADFQDLIDALQSGLS<span class="cysteine">C</span><span class="cysteine">C</span>GVNSYEDWDNNIYFN<span class="cysteine">C</span>SGPANNPEALW<span class="cysteine">C</span>AFLLLYTGSS<span class="motif">KR</span>SSQ<span class="motif">HPVR</span>LWSSFPRTTKYFPHKDLHHWL<span class="cysteine">C</span>GYVYNVD</span>
23
- </p>
24
- <p>
25
- <span class='id'>isotig00009_f3_7</span>
26
- <span>- S.P.=> Cleavage Site: 16:17 | D-value: 0.643</span>
27
- <br>
28
- <span class='signalp'>MKTGIIIFISTVVVLP</span><span>ITLKP<span class="cysteine">C</span>GVPFS<span class="cysteine">C</span><span class="cysteine">C</span>IPDQASGVANTQ<span class="cysteine">C</span>GYGVRSPEQQNTFHTKIYTTG<span class="cysteine">C</span>ADMFTMWINRYLYYIAGIAGVIVLVELFGF<span class="cysteine">C</span>FAHSLINDI<span class="motif">KR</span>QKARWAHR</span>
29
- </p>
30
- <p>
31
- <span class='id'>isotig00016_f1_0</span>
32
- <span>- S.P.=> Cleavage Site: 23:24 | D-value: 0.592</span>
33
- <br>
34
- <span class='signalp'>MNAGQIFIALMAQLFNACLLVSS</span><span>NFDSDIADSTL<span class="gkr">GKR</span>STGFVDTF<span class="gkr">GKR</span>FVDSF<span class="gkr">GKR</span>VDEFDYDHNGNYAEQSEQSSYISPQL<span class="motif">KR</span>GQ<span class="motif">KGLR</span>SGSFIDAF<span class="gkr">GKR</span>SSFQEVDE<span class="motif">KR</span>FADSF<span class="gkr">GKR</span>FADSF<span class="gkr">GKR</span>SPVGFVDTL<span class="gkr">GKR</span>FAVSF<span class="gkr">GKR</span>NTVGFVDTL<span class="gkr">GKR</span>FADSF<span class="gkr">GKR</span>SQQGFVDAF<span class="gkr">GKR</span>YQGVY</span>
35
- </p>
36
- </body>
37
- </html>
@@ -1,122 +0,0 @@
1
- #!/usr/bin/env ruby
2
- require 'coveralls'
3
- Coveralls.wear!
4
-
5
- require 'bio'
6
- require 'test/unit'
7
-
8
- require 'npsearch'
9
- require 'npsearch/arg_validator'
10
-
11
- class InputChanged
12
- # Changed to include the full entry definition rather than just the id. This
13
- # was necessary for when testing individual parts since this is changed in
14
- # pipeline
15
- def read(input_file)
16
- input_read = {}
17
- biofastafile = Bio::FlatFile.open(Bio::FastaFormat, input_file)
18
- biofastafile.each_entry do |entry|
19
- # entry.definition used instead of entry.id
20
- input_read[entry.definition] = entry.seq
21
- end
22
- input_read
23
- end
24
- end
25
-
26
- class UnitTests < Test::Unit::TestCase
27
- def setup # read all expected files
28
- @dir = 'test/files'
29
- @translation_test = NpSearch::Translation.new
30
- @analysis_test = NpSearch::Analysis.new
31
- @test_input1 = InputChanged.new
32
- @test_arg_vldr = NpSearch::ArgValidators.new(:is_verbose)
33
- @test_vldr = NpSearch::Validators.new
34
- @test_input_read = NpSearch::Input.read("#{@dir}/genetic.fa")
35
- @expected_translation = NpSearch::Input.read("#{@dir}/1_protein.fa")
36
- @expected_orf = NpSearch::Input.read("#{@dir}/2_orf.fa")
37
- @expected_sp_out_file = File.read("#{@dir}/3_signalp_out.txt")
38
- @expected_secretome = @test_input1.read("#{@dir}/4_secretome.fa")
39
- @expected_output = @test_input1.read("#{@dir}/5_output.fa")
40
- @motif = 'KK|KR|RR|R..R|R....R|R......R|' \
41
- 'H..R|H....R|H......R|K..R|K....R|K......R'
42
- @motif_ar = %w(KR Kr kr)
43
- @input_file_ar = ["#{@dir}/genetic.fa", "#{@dir}/protein.fa"]
44
- @input_file_ar_neg = ["#{@dir}/empty_file.fa",
45
- "#{@dir}/missing_input.fa", "#{@dir}/not_fasta.fa"]
46
- @cut_off_ar = [622, 10, 2, 1]
47
- @cut_off_ar_neg = [-10, 'hello', -5, 0]
48
- end
49
-
50
- def test_motif
51
- (0..2).each do |i|
52
- test_run = @test_arg_vldr.arg(@motif_ar[i], @input_file_ar[0], @dir,
53
- @cut_off_ar[0], FALSE, nil, 'help_banner')
54
- assert_equal('genetic', test_run)
55
- end
56
- end
57
-
58
- def test_input_file
59
- test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
60
- @cut_off_ar[0], FALSE, nil, 'help_banner')
61
- assert_equal('genetic', test_run)
62
- test_run1 = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[1], @dir,
63
- @cut_off_ar[0], FALSE, nil, 'help_banner')
64
- assert_equal('protein', test_run1)
65
- (0..2).each do |i|
66
- test_run2 = lambda do
67
- @test_arg_vldr.arg(@motif_ar[0], @input_file_ar_neg[i], @dir,
68
- @cut_off_ar[0], FALSE, nil, 'help_banner')
69
- end
70
- assert_raise(ArgumentError) { test_run2 }
71
- end
72
- end
73
-
74
- def test_orf_min_length
75
- (0..3).each do |i|
76
- test_run = @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
77
- @cut_off_ar[i], FALSE, nil, 'help_banner')
78
- assert_equal('genetic', test_run)
79
- end
80
- (0..3).each do |i|
81
- test_run1 = lambda do
82
- @test_arg_vldr.arg(@motif_ar[0], @input_file_ar[0], @dir,
83
- @cut_off_ar_neg[i], FALSE, nil, 'help_banner')
84
- end
85
- assert_raise(ArgumentError) { test_run1 }
86
- end
87
- end
88
-
89
- # => Test if the output directory validator works, in ensuring whether an
90
- # output directory can be found.
91
- def test_output_dir_validator
92
- assert_equal(nil, @test_vldr.output_dir(@dir))
93
- end
94
-
95
- # => Test if the translation method works properly - assert that the produced
96
- # translation is equal to the expected translation hash
97
- def test_translate
98
- translation_hash_test = NpSearch::Translation.translate(@test_input_read)
99
- assert_equal(@expected_translation, translation_hash_test)
100
- end
101
-
102
- # => Test if the extract_orf method works properly - assert that the produced
103
- # orf hash is equal to the expected orf hash.
104
- # => In orf method, an array is produced while in the expected file read, an
105
- # array isn't produced, thus it s necessary to remove "[ ]" from both end.
106
- def test_extract_orf
107
- orf_hash_test = NpSearch::Translation.extract_orf(@expected_translation, 10)
108
- assert_equal(@expected_orf.to_s, orf_hash_test.to_s.gsub('["', '"')
109
- .gsub('"]', '"'))
110
- end
111
-
112
- def test_parse
113
- secretome = NpSearch::Analysis.parse("#{@dir}/3_signalp_out.txt",
114
- @expected_orf, @motif)
115
- assert_equal(@expected_secretome, secretome)
116
- end
117
-
118
- def test_flattener
119
- flattened_output_test = NpSearch::Analysis.flattener(@expected_secretome)
120
- assert_equal(@expected_output, flattened_output_test)
121
- end
122
- end