miga-base 1.0.5.2 → 1.1.0.0

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.
@@ -226,7 +226,7 @@ def kmer_extract(input_files):
226
226
  line = line.strip().split()
227
227
  protein_name = line[0]
228
228
  model_name = line[3]
229
- score = line[8]
229
+ score = float(line[8])
230
230
  if model_name in positive_matches:
231
231
  if score > positive_matches[model_name][1]:
232
232
  positive_matches[model_name] = [protein_name, score]
@@ -141,32 +141,43 @@ module MiGA::DistanceRunner::Commands
141
141
  ##
142
142
  # Execute a FastAAI command
143
143
  def fastaai_cmd(targets)
144
- qry_idx = dataset.result(:essential_genes).file_path(:fastaai_index)
144
+ qry_idx = dataset.result(:essential_genes).file_path(:fastaai_index_2)
145
145
  return nil unless qry_idx
146
146
 
147
- # Run FastAAI
148
- File.open(f1 = tmp_file, 'w') { |fh| fh.puts qry_idx }
149
- File.open(f2 = tmp_file, 'w') do |fh|
150
- targets.each do |target|
151
- target_idx = target&.result(:essential_genes)&.file_path(:fastaai_index)
152
- fh.puts target_idx if target_idx
153
- end
147
+ # Merge databases
148
+ donors = []
149
+ targets.each do |target|
150
+ tgt_idx = target&.result(:essential_genes)&.file_path(:fastaai_index_2)
151
+ donors << tgt_idx if tgt_idx
154
152
  end
153
+ return nil if donors.empty?
155
154
  run_cmd <<~CMD
156
- FastAAI --qd "#{f1}" --rd "#{f2}" --output "#{f3 = tmp_file}" \
157
- --threads #{opts[:thr]}
155
+ FastAAI merge_db --donors "#{donors.join(',')}" \
156
+ --recipient "#{f1 = tmp_file}" --threads #{opts[:thr]}
157
+ CMD
158
+
159
+ # Run FastAAI
160
+ run_cmd <<~CMD
161
+ FastAAI db_query --query "#{qry_idx}" --target "#{f1}" \
162
+ --output "#{f2 = tmp_file}" --threads #{opts[:thr]} \
163
+ --do_stdev
158
164
  CMD
159
165
 
160
166
  # Save values in the databases
161
167
  haai_data = {}
162
168
  aai_data = {}
163
- File.open(f3, 'r') do |fh|
169
+ # Ugly workaround to the insistence of FastAAI to not provide the files
170
+ # I ask for ;-)
171
+ qry_results = File.basename(qry_idx, '.faix') + '_results.txt'
172
+ out_file = File.join(f2, 'results', qry_results)
173
+ File.open(out_file, 'r') do |fh|
164
174
  fh.each do |ln|
165
175
  out = ln.chomp.split("\t")
166
176
  haai_data[out[1]] = [
167
177
  out[2].to_f * 100, out[3].to_f * 100, out[4].to_i, out[5].to_i
168
178
  ]
169
- aai_data[out[1]] = [out[6].to_f, 0, 0, 0] if out[6] !~ /^>/
179
+ out[6] = (out[6] =~ /^>/) ? 95.0 : out[6].to_f
180
+ aai_data[out[1]] = [out[6], 0, 0, 0]
170
181
  end
171
182
  end
172
183
  puts "Results: #{haai_data.size} | Inferences: #{aai_data.size}"
@@ -174,7 +185,7 @@ module MiGA::DistanceRunner::Commands
174
185
  batch_data_to_db(:aai, aai_data)
175
186
 
176
187
  # Cleanup
177
- [f1, f2, f3].each { |i| File.unlink(i) }
188
+ [f1, f2].each { |i| FileUtils.rm_r(i) }
178
189
  end
179
190
 
180
191
  ##
@@ -1,12 +1,12 @@
1
- Software Test exec Website Notes
2
- -------- --------- ------- -----
3
- Ruby ruby https://www.ruby-lang.org/ Required version: 2.3+
4
- Python python3 https://www.python.org/ Required version: 3+
1
+ Software Test exec Website Notes
2
+ -------- --------- ------- -----
3
+ Ruby ruby https://www.ruby-lang.org/ Required version: 2.3+
4
+ Python python3 https://www.python.org/ Required version: 3+
5
5
  R R http://www.r-project.org/
6
6
  SQLite3 sqlite3 https://www.sqlite.org/
7
7
  NCBI BLAST+ blastp ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
8
- DIAMOND diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.9.20+
9
- FastANI fastANI https://github.com/ParBLiSS/FastANI Required version: 1.1+
8
+ DIAMOND diamond http://ab.inf.uni-tuebingen.de/software/diamond Required version: v0.9.20+
9
+ FastANI fastANI https://github.com/ParBLiSS/FastANI Required version: 1.1+
10
10
  HMMer 3.0+ hmmsearch http://hmmer.janelia.org/software
11
11
  Bedtools bedtools http://bedtools.readthedocs.org/en/latest/
12
12
  Prodigal prodigal http://prodigal.ornl.gov
@@ -17,6 +17,6 @@ FaQCs (reads) FaQCs https://github.com/LANL-Bioinformatics/FaQCs
17
17
  Falco (reads) falco https://github.com/smithlabcode/falco
18
18
  Seqtk (reads) seqtk https://github.com/lh3/seqtk
19
19
  Fastp (reads) fastp https://github.com/OpenGene/fastp
20
- OpenJDK (rdp) java https://adoptopenjdk.net/ Any Java VM would work
20
+ Temurin (rdp) java https://adoptium.net/ Any Java VM would work
21
21
  MyTaxa (mytaxa) MyTaxa http://enve-omics.ce.gatech.edu/mytaxa
22
22
  Krona (mytaxa) ktImportText https://github.com/marbl/Krona/wiki
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.0.5.2
4
+ version: 1.1.0.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Luis M. Rodriguez-R
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2021-08-26 00:00:00.000000000 Z
11
+ date: 2021-10-28 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons
@@ -107,6 +107,7 @@ files:
107
107
  - README.md
108
108
  - Rakefile
109
109
  - bin/miga
110
+ - bin/miga-env
110
111
  - lib/miga.rb
111
112
  - lib/miga/_data/aai-intax-blast.tsv.gz
112
113
  - lib/miga/_data/aai-intax-diamond.tsv.gz
@@ -155,6 +156,7 @@ files:
155
156
  - lib/miga/cli/action/ln.rb
156
157
  - lib/miga/cli/action/ls.rb
157
158
  - lib/miga/cli/action/ncbi_get.rb
159
+ - lib/miga/cli/action/ncbi_get/downloads.rb
158
160
  - lib/miga/cli/action/new.rb
159
161
  - lib/miga/cli/action/next_step.rb
160
162
  - lib/miga/cli/action/option.rb
@@ -260,9 +262,10 @@ files:
260
262
  - utils/FastAAI/00.Libraries/01.SCG_HMMs/Archaea_SCG.hmm
261
263
  - utils/FastAAI/00.Libraries/01.SCG_HMMs/Bacteria_SCG.hmm
262
264
  - utils/FastAAI/00.Libraries/01.SCG_HMMs/Complete_SCG_DB.hmm
263
- - utils/FastAAI/FastAAI/FastAAI
265
+ - utils/FastAAI/FastAAI
266
+ - utils/FastAAI/FastAAI-legacy/FastAAI
267
+ - utils/FastAAI/FastAAI-legacy/kAAI_v1.0_virus.py
264
268
  - utils/FastAAI/README.md
265
- - utils/FastAAI/kAAI_v1.0_virus.py
266
269
  - utils/adapters.fa
267
270
  - utils/cleanup-databases.rb
268
271
  - utils/core-pan-plot.R