aai 0.5.1 → 0.5.2
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- checksums.yaml +4 -4
- data/lib/aai.rb +28 -18
- data/lib/aai/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 7ad0d928493f79c8941621c5a60c434eab14d210
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4
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+
data.tar.gz: 64f0ddaac0103bf9413302cc6fc42b85d694e645
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 3ea7855a5732a973b543bc17841c21ff256828ee750acc02ebe49b4e26462f9065c245d9907f3a00afaf8e2cfc6f70f8c936c1372bc46f7e9540356de1198d60
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7
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+
data.tar.gz: 7cfba7f20566fc6f9c6177ce5bcc758a816e1c9e8ee65c9c2938e5dfd0b4a25ebfed0e34be1c209a164729d1b385d11f41dc3105646fb4bf2cbf0be7170b9285
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data/lib/aai.rb
CHANGED
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@@ -53,18 +53,16 @@ module Aai
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53
53
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[first_files[idx], second_files[idx], outf_names[idx]]
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54
54
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end
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55
55
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56
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-
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57
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-
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58
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-
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59
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-
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60
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-
out = infiles[2]
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56
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+
Parallel.each(args, in_processes: cpus) do |infiles|
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57
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+
query = infiles[0]
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58
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+
db = infiles[1]
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59
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+
out = infiles[2]
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61
60
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62
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-
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63
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-
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64
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-
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61
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+
cmd = "diamond blastp --threads 1 --outfmt 6 " +
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62
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+
"--query #{query} --db #{db} --out #{out} " +
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63
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+
"--evalue #{EVALUE_CUTOFF}"
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65
64
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66
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-
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67
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-
end
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65
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+
Process.run_and_time_it! "Diamond blast", cmd
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68
66
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end
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69
67
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70
68
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outf_names
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@@ -80,13 +78,11 @@ module Aai
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80
78
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suffix = BLAST_DB_SUFFIX
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81
79
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outfiles = fnames.map { |fname| fname + suffix }
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82
80
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83
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-
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84
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-
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85
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-
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86
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-
"--db #{fname}#{BLAST_DB_SUFFIX}"
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81
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+
Parallel.each(fnames, in_processes: cpus) do |fname|
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82
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+
cmd = "diamond makedb --threads 1 --in #{fname} " +
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83
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+
"--db #{fname}#{BLAST_DB_SUFFIX}"
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87
84
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|
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88
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-
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89
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-
end
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85
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+
Process.run_and_time_it! "Make db", cmd
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90
86
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end
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91
87
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92
88
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outfiles
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@@ -125,7 +121,14 @@ module Aai
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125
121
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126
122
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def get_best_hits fnames, seq_lengths
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|
127
123
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best_hits = {}
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128
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-
fnames.
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124
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+
num_fnames = fnames.count
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|
125
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+
log_every = num_fnames > 10 ? num_fnames / 10 : 1
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126
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+
fnames.each_with_index do |fname, idx| # blast files
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127
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+
if (idx % log_every).zero?
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|
128
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+
AbortIf.logger.debug { "Working on blastp file " +
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129
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+
"##{idx} of #{num_fnames}"}
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130
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+
end
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131
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+
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129
132
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File.open(fname, "rt").each_line do |line|
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130
133
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ary = line.chomp.split "\t"
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131
134
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@@ -217,7 +220,14 @@ module Aai
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217
220
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one_way_hits = one_way_best_hits best_hits
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218
221
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genome_pair_keys = one_way_hits.keys.map { |pair| pair.sort }.uniq
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219
222
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220
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-
genome_pair_keys.
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223
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+
num_genome_pairs = genome_pair_keys.count
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224
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+
log_every = num_genome_pairs > 10 ? num_genome_pairs / 10 : 1
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225
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+
genome_pair_keys.each_with_index do |pair_key, idx|
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226
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+
if (idx % log_every).zero?
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227
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+
AbortIf.logger.debug { "Working on genome pair ##{idx} of " +
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228
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+
"#{num_genome_pairs}" }
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|
229
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+
end
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|
230
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+
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221
231
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if one_way_hits.has_key?(pair_key) &&
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222
232
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one_way_hits.has_key?(pair_key.reverse)
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223
233
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data/lib/aai/version.rb
CHANGED