aai 0.2.2 → 0.3.0
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- checksums.yaml +4 -4
- data/exe/aai +6 -2
- data/lib/aai.rb +5 -4
- 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: 27ae62f0f9faca6746e563c76f8ca78376cd7e06
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4
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+
data.tar.gz: 0766cf35cf6654147d7a07261f2e4c9cef610062
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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: 4ab936b2f2a91c5b1415e2adf552a809b65487e0d6b3b611cc6551b28686109e6d402e9452cb1e6229b3c78fa16356837e1013bde573954db0f77ecfd53027e3
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7
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+
data.tar.gz: ed52d87efbcdb2aed8bd9ecb7f8da62cceb029e44a4e4f1cc61d55b777dbeb6f711583f51e065a527267edbcba381cb1f511c982785bd05624532124e6ed8a8a
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data/exe/aai
CHANGED
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@@ -33,6 +33,7 @@ opts = Trollop.options do
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33
33
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Options:
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34
34
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EOS
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35
35
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36
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+
opt(:cpus, "Number of CPUs to use", type: :integer, default: 1)
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36
37
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opt(:infiles, "Input files", type: :strings)
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37
38
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opt(:outdir, "Output directory", type: :string, default: ".")
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38
39
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opt(:basename, "Base name for output file", type: :string,
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@@ -52,9 +53,12 @@ FileUtils.mkdir_p opts[:outdir]
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52
53
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53
54
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seq_lengths, clean_fnames = Aai.process_input_seqs! opts[:infiles]
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54
55
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55
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-
blast_db_basenames = Aai.make_blastdbs! clean_fnames
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56
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+
blast_db_basenames = Aai.make_blastdbs! clean_fnames,
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57
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+
opts[:cpus]
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56
58
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57
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-
btabs = Aai.blast_permutations! clean_fnames,
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59
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+
btabs = Aai.blast_permutations! clean_fnames,
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60
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+
blast_db_basenames,
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61
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+
opts[:cpus]
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58
62
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59
63
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best_hits = Aai.get_best_hits btabs, seq_lengths
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60
64
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data/lib/aai.rb
CHANGED
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@@ -21,7 +21,7 @@ module Aai
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21
21
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EVALUE_CUTOFF = 1e-3
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22
22
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LENGTH_CUTOFF = 70 # actually is 70 percent
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23
23
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24
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-
def blast_permutations! fastas, blast_dbs
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24
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+
def blast_permutations! fastas, blast_dbs, cpus=4
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25
25
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file_permutations = one_way_combinations fastas, blast_dbs, true
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26
26
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file_permutations = file_permutations.select do |f1, f2|
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27
27
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genome_from_fname(f1) != genome_from_fname(f2)
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@@ -54,7 +54,7 @@ module Aai
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54
54
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end
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55
55
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56
56
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Time.time_it "Running blast jobs" do
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57
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-
Parallel.each(parallel_args) do |infiles|
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57
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+
Parallel.each(parallel_args, in_processes: cpus) do |infiles|
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58
58
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query = infiles[0]
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59
59
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db = infiles[1]
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60
60
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out = infiles[2]
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@@ -70,14 +70,15 @@ module Aai
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70
70
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# Make blast dbs given an array of filenames.
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71
71
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#
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72
72
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# @param fnames [Array<String>] an array of filenames
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73
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+
# @param cpus [Integer] number of cpus to use
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73
74
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#
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74
75
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# @return [Array<String>] blast db basenames
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75
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-
def make_blastdbs! fnames
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76
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+
def make_blastdbs! fnames, cpus=4
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76
77
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suffix = BLAST_DB_SUFFIX
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77
78
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outfiles = fnames.map { |fname| fname + suffix }
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78
79
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79
80
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Time.time_it "Making blast databases" do
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80
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-
Parallel.each(fnames) do |fname|
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81
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+
Parallel.each(fnames, in_processes: cpus) do |fname|
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81
82
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cmd = "makeblastdb -in #{fname} -out #{fname}#{BLAST_DB_SUFFIX} -dbtype prot"
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82
83
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83
84
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Process.run_it! cmd
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data/lib/aai/version.rb
CHANGED