lsa 0.1.0 → 0.1.1
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/lib/lsa.rb +4 -6
- data/lib/lsa/version.rb +1 -1
- data/test_files/mapping_with_bad_group_name.txt +4 -0
- metadata +3 -4
- data/test_files/#cluster_file.txt# +0 -3
- data/test_files/.#cluster_file.txt +0 -1
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: bce829681f089991e590e51004e9f005aeeaf5fd
|
|
4
|
+
data.tar.gz: f593d26fb0b6acfcc6fab9b78a9ffaefc42e2e1e
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: ed48ee109b8b9716f1d0005b6115a40afb4497da06222d12f935662aead64534b3e5d0ba2c8e24be2f9f1e260281b2124cf5e1c835080b1ff0120a14543de109
|
|
7
|
+
data.tar.gz: 81a6f135ec5217025dbcc4ba16620ccb8292454d6b91453e5fd4cb2ee446dcb891f065c0c1eab345e510bf7bc838fe934c4a68d2374255f71cb729c2a3d34377
|
data/lib/lsa.rb
CHANGED
|
@@ -4,26 +4,24 @@ require "abort_if"
|
|
|
4
4
|
|
|
5
5
|
include AbortIf
|
|
6
6
|
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
7
|
module Lsa
|
|
11
|
-
|
|
12
8
|
def clean_str str
|
|
13
9
|
str.strip.gsub(/[^\p{Alnum}_]+/, "_").gsub(/_+/, "_")
|
|
14
10
|
end
|
|
15
11
|
|
|
16
|
-
|
|
17
12
|
def parse_mapping_file mapping_fname, mmseqs_final_outf
|
|
18
13
|
data_labels = []
|
|
19
14
|
label2outf = {}
|
|
20
15
|
doc2new_doc = {}
|
|
21
16
|
File.open(mapping_fname, "rt").each_line.with_index do |line, idx|
|
|
22
17
|
if idx.zero?
|
|
23
|
-
|
|
18
|
+
current_label, *data_labels = line.chomp.split("\t").map do |str|
|
|
24
19
|
clean_str str
|
|
25
20
|
end
|
|
26
21
|
|
|
22
|
+
abort_if data_labels.any? { |label| label == "original" },
|
|
23
|
+
"Illegal data label: 'original'. Please change it."
|
|
24
|
+
|
|
27
25
|
abort_unless data_labels.uniq.count == data_labels.count,
|
|
28
26
|
"The data labels are not unique in #{mapping_fname}"
|
|
29
27
|
|
data/lib/lsa/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: lsa
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.1.
|
|
4
|
+
version: 0.1.1
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Ryan Moore
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: exe
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2017-
|
|
11
|
+
date: 2017-08-10 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: abort_if
|
|
@@ -109,14 +109,13 @@ files:
|
|
|
109
109
|
- lib/lsa.rb
|
|
110
110
|
- lib/lsa/version.rb
|
|
111
111
|
- lsa.gemspec
|
|
112
|
-
- test_files/#cluster_file.txt#
|
|
113
|
-
- test_files/.#cluster_file.txt
|
|
114
112
|
- test_files/cluster_file_another_group.txt
|
|
115
113
|
- test_files/cluster_file_group.txt
|
|
116
114
|
- test_files/cluster_file_original.txt
|
|
117
115
|
- test_files/e_coli.faa.gz
|
|
118
116
|
- test_files/m_mazei.faa.gz
|
|
119
117
|
- test_files/mapping.txt
|
|
118
|
+
- test_files/mapping_with_bad_group_name.txt
|
|
120
119
|
- test_files/s_flexneri.faa.gz
|
|
121
120
|
- test_files/small/e_coli.faa.gz
|
|
122
121
|
- test_files/small/m_mazei.faa.gz
|
|
@@ -1 +0,0 @@
|
|
|
1
|
-
test_files/moorer@roaming-254-155.host.udel.edu.943
|