BioDSL 1.0.1 → 1.0.2
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- checksums.yaml +4 -4
- data/.gitignore +1 -0
- data/BioDSL.gemspec +1 -1
- data/Gemfile +6 -0
- data/README.md +289 -155
- data/Rakefile +18 -16
- data/lib/BioDSL.rb +1 -1
- data/lib/BioDSL/cary.rb +78 -53
- data/lib/BioDSL/command.rb +2 -2
- data/lib/BioDSL/commands.rb +1 -1
- data/lib/BioDSL/commands/add_key.rb +1 -1
- data/lib/BioDSL/commands/align_seq_mothur.rb +4 -4
- data/lib/BioDSL/commands/analyze_residue_distribution.rb +5 -5
- data/lib/BioDSL/commands/assemble_pairs.rb +13 -13
- data/lib/BioDSL/commands/assemble_seq_idba.rb +7 -9
- data/lib/BioDSL/commands/assemble_seq_ray.rb +13 -13
- data/lib/BioDSL/commands/assemble_seq_spades.rb +4 -4
- data/lib/BioDSL/commands/classify_seq.rb +8 -8
- data/lib/BioDSL/commands/classify_seq_mothur.rb +5 -5
- data/lib/BioDSL/commands/clip_primer.rb +7 -7
- data/lib/BioDSL/commands/cluster_otus.rb +5 -5
- data/lib/BioDSL/commands/collapse_otus.rb +2 -2
- data/lib/BioDSL/commands/collect_otus.rb +2 -2
- data/lib/BioDSL/commands/complement_seq.rb +4 -4
- data/lib/BioDSL/commands/count.rb +1 -1
- data/lib/BioDSL/commands/count_values.rb +2 -2
- data/lib/BioDSL/commands/degap_seq.rb +6 -7
- data/lib/BioDSL/commands/dereplicate_seq.rb +1 -1
- data/lib/BioDSL/commands/dump.rb +2 -2
- data/lib/BioDSL/commands/filter_rrna.rb +4 -4
- data/lib/BioDSL/commands/genecall.rb +7 -7
- data/lib/BioDSL/commands/grab.rb +1 -1
- data/lib/BioDSL/commands/index_taxonomy.rb +3 -3
- data/lib/BioDSL/commands/mask_seq.rb +4 -4
- data/lib/BioDSL/commands/mean_scores.rb +2 -2
- data/lib/BioDSL/commands/merge_pair_seq.rb +3 -3
- data/lib/BioDSL/commands/merge_table.rb +1 -1
- data/lib/BioDSL/commands/merge_values.rb +1 -1
- data/lib/BioDSL/commands/plot_heatmap.rb +4 -5
- data/lib/BioDSL/commands/plot_histogram.rb +4 -4
- data/lib/BioDSL/commands/plot_matches.rb +5 -5
- data/lib/BioDSL/commands/plot_residue_distribution.rb +6 -6
- data/lib/BioDSL/commands/plot_scores.rb +7 -7
- data/lib/BioDSL/commands/random.rb +1 -1
- data/lib/BioDSL/commands/read_fasta.rb +9 -9
- data/lib/BioDSL/commands/read_fastq.rb +16 -16
- data/lib/BioDSL/commands/read_table.rb +2 -3
- data/lib/BioDSL/commands/reverse_seq.rb +4 -4
- data/lib/BioDSL/commands/slice_align.rb +4 -4
- data/lib/BioDSL/commands/slice_seq.rb +3 -3
- data/lib/BioDSL/commands/sort.rb +1 -1
- data/lib/BioDSL/commands/split_pair_seq.rb +6 -7
- data/lib/BioDSL/commands/split_values.rb +2 -2
- data/lib/BioDSL/commands/trim_primer.rb +13 -8
- data/lib/BioDSL/commands/trim_seq.rb +5 -5
- data/lib/BioDSL/commands/uchime_ref.rb +6 -6
- data/lib/BioDSL/commands/uclust.rb +5 -5
- data/lib/BioDSL/commands/unique_values.rb +1 -1
- data/lib/BioDSL/commands/usearch_global.rb +2 -2
- data/lib/BioDSL/commands/usearch_local.rb +2 -2
- data/lib/BioDSL/commands/write_fasta.rb +7 -9
- data/lib/BioDSL/commands/write_fastq.rb +4 -4
- data/lib/BioDSL/commands/write_table.rb +3 -3
- data/lib/BioDSL/commands/write_tree.rb +2 -3
- data/lib/BioDSL/config.rb +2 -2
- data/lib/BioDSL/csv.rb +8 -10
- data/lib/BioDSL/debug.rb +1 -1
- data/lib/BioDSL/fasta.rb +54 -40
- data/lib/BioDSL/fastq.rb +35 -32
- data/lib/BioDSL/filesys.rb +56 -47
- data/lib/BioDSL/fork.rb +1 -1
- data/lib/BioDSL/hamming.rb +1 -1
- data/lib/BioDSL/helpers.rb +1 -1
- data/lib/BioDSL/helpers/aux_helper.rb +1 -1
- data/lib/BioDSL/helpers/email_helper.rb +1 -1
- data/lib/BioDSL/helpers/history_helper.rb +1 -1
- data/lib/BioDSL/helpers/log_helper.rb +1 -1
- data/lib/BioDSL/helpers/options_helper.rb +1 -1
- data/lib/BioDSL/helpers/status_helper.rb +1 -1
- data/lib/BioDSL/html_report.rb +1 -1
- data/lib/BioDSL/math.rb +1 -1
- data/lib/BioDSL/mummer.rb +1 -1
- data/lib/BioDSL/pipeline.rb +1 -1
- data/lib/BioDSL/seq.rb +240 -231
- data/lib/BioDSL/seq/ambiguity.rb +1 -1
- data/lib/BioDSL/seq/assemble.rb +1 -1
- data/lib/BioDSL/seq/backtrack.rb +93 -76
- data/lib/BioDSL/seq/digest.rb +1 -1
- data/lib/BioDSL/seq/dynamic.rb +43 -55
- data/lib/BioDSL/seq/homopolymer.rb +34 -36
- data/lib/BioDSL/seq/kmer.rb +67 -50
- data/lib/BioDSL/seq/levenshtein.rb +35 -40
- data/lib/BioDSL/seq/translate.rb +64 -55
- data/lib/BioDSL/seq/trim.rb +60 -50
- data/lib/BioDSL/serializer.rb +1 -1
- data/lib/BioDSL/stream.rb +1 -1
- data/lib/BioDSL/taxonomy.rb +1 -1
- data/lib/BioDSL/test.rb +1 -1
- data/lib/BioDSL/tmp_dir.rb +1 -1
- data/lib/BioDSL/usearch.rb +1 -1
- data/lib/BioDSL/verbose.rb +1 -1
- data/lib/BioDSL/version.rb +2 -2
- data/test/BioDSL/commands/test_add_key.rb +1 -1
- data/test/BioDSL/commands/test_align_seq_mothur.rb +1 -1
- data/test/BioDSL/commands/test_analyze_residue_distribution.rb +1 -1
- data/test/BioDSL/commands/test_assemble_pairs.rb +1 -1
- data/test/BioDSL/commands/test_assemble_seq_idba.rb +1 -1
- data/test/BioDSL/commands/test_assemble_seq_ray.rb +1 -1
- data/test/BioDSL/commands/test_assemble_seq_spades.rb +1 -1
- data/test/BioDSL/commands/test_classify_seq.rb +1 -1
- data/test/BioDSL/commands/test_classify_seq_mothur.rb +1 -1
- data/test/BioDSL/commands/test_clip_primer.rb +1 -1
- data/test/BioDSL/commands/test_cluster_otus.rb +1 -1
- data/test/BioDSL/commands/test_collapse_otus.rb +1 -1
- data/test/BioDSL/commands/test_collect_otus.rb +1 -1
- data/test/BioDSL/commands/test_complement_seq.rb +1 -1
- data/test/BioDSL/commands/test_count.rb +1 -1
- data/test/BioDSL/commands/test_count_values.rb +1 -1
- data/test/BioDSL/commands/test_degap_seq.rb +1 -1
- data/test/BioDSL/commands/test_dereplicate_seq.rb +1 -1
- data/test/BioDSL/commands/test_dump.rb +1 -1
- data/test/BioDSL/commands/test_filter_rrna.rb +1 -1
- data/test/BioDSL/commands/test_genecall.rb +1 -1
- data/test/BioDSL/commands/test_grab.rb +1 -1
- data/test/BioDSL/commands/test_index_taxonomy.rb +1 -1
- data/test/BioDSL/commands/test_mask_seq.rb +1 -1
- data/test/BioDSL/commands/test_mean_scores.rb +1 -1
- data/test/BioDSL/commands/test_merge_pair_seq.rb +1 -1
- data/test/BioDSL/commands/test_merge_table.rb +1 -1
- data/test/BioDSL/commands/test_merge_values.rb +1 -1
- data/test/BioDSL/commands/test_plot_heatmap.rb +1 -1
- data/test/BioDSL/commands/test_plot_histogram.rb +1 -1
- data/test/BioDSL/commands/test_plot_matches.rb +1 -1
- data/test/BioDSL/commands/test_plot_residue_distribution.rb +1 -1
- data/test/BioDSL/commands/test_plot_scores.rb +1 -1
- data/test/BioDSL/commands/test_random.rb +1 -1
- data/test/BioDSL/commands/test_read_fasta.rb +1 -1
- data/test/BioDSL/commands/test_read_fastq.rb +1 -1
- data/test/BioDSL/commands/test_read_table.rb +1 -1
- data/test/BioDSL/commands/test_reverse_seq.rb +1 -1
- data/test/BioDSL/commands/test_slice_align.rb +1 -1
- data/test/BioDSL/commands/test_slice_seq.rb +1 -1
- data/test/BioDSL/commands/test_sort.rb +1 -1
- data/test/BioDSL/commands/test_split_pair_seq.rb +1 -1
- data/test/BioDSL/commands/test_split_values.rb +1 -1
- data/test/BioDSL/commands/test_trim_primer.rb +1 -1
- data/test/BioDSL/commands/test_trim_seq.rb +1 -1
- data/test/BioDSL/commands/test_uchime_ref.rb +1 -1
- data/test/BioDSL/commands/test_uclust.rb +1 -1
- data/test/BioDSL/commands/test_unique_values.rb +1 -1
- data/test/BioDSL/commands/test_usearch_global.rb +1 -1
- data/test/BioDSL/commands/test_usearch_local.rb +1 -1
- data/test/BioDSL/commands/test_write_fasta.rb +1 -1
- data/test/BioDSL/commands/test_write_fastq.rb +1 -1
- data/test/BioDSL/commands/test_write_table.rb +1 -1
- data/test/BioDSL/commands/test_write_tree.rb +1 -1
- data/test/BioDSL/helpers/test_options_helper.rb +3 -3
- data/test/BioDSL/seq/test_assemble.rb +58 -56
- data/test/BioDSL/seq/test_backtrack.rb +83 -81
- data/test/BioDSL/seq/test_digest.rb +47 -45
- data/test/BioDSL/seq/test_dynamic.rb +66 -64
- data/test/BioDSL/seq/test_homopolymer.rb +35 -33
- data/test/BioDSL/seq/test_kmer.rb +29 -28
- data/test/BioDSL/seq/test_translate.rb +44 -42
- data/test/BioDSL/seq/test_trim.rb +59 -57
- data/test/BioDSL/test_cary.rb +1 -1
- data/test/BioDSL/test_command.rb +2 -2
- data/test/BioDSL/test_csv.rb +34 -31
- data/test/BioDSL/test_debug.rb +31 -31
- data/test/BioDSL/test_fasta.rb +30 -29
- data/test/BioDSL/test_fastq.rb +27 -26
- data/test/BioDSL/test_filesys.rb +28 -27
- data/test/BioDSL/test_fork.rb +29 -28
- data/test/BioDSL/test_math.rb +31 -30
- data/test/BioDSL/test_mummer.rb +1 -1
- data/test/BioDSL/test_pipeline.rb +1 -1
- data/test/BioDSL/test_seq.rb +42 -41
- data/test/BioDSL/test_serializer.rb +35 -33
- data/test/BioDSL/test_stream.rb +28 -27
- data/test/BioDSL/test_taxonomy.rb +38 -37
- data/test/BioDSL/test_test.rb +32 -31
- data/test/BioDSL/test_tmp_dir.rb +1 -1
- data/test/BioDSL/test_usearch.rb +28 -27
- data/test/BioDSL/test_verbose.rb +32 -31
- data/test/helper.rb +34 -31
- metadata +3 -2
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# #
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data/lib/BioDSL/commands/dump.rb
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# This software is part of the BioDSL
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# This software is part of the BioDSL (www.BioDSL.org). #
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# #
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# @return [Dump] Returns an instance of the Dump class.
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@options = options
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check_options
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def record2entry(record, i)
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if record.key? :SEQ
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unless @filter.include? i
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output << record
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# Set the default option values.
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@options[:type] ||= :dna
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entry = BioDSL::Seq.new(seq_name: i, seq: record[:SEQ])
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fasta_io.puts entry.to_fasta
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data/lib/BioDSL/commands/grab.rb
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create_output_dir
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check_output_files
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@index
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@index = BioDSL::Taxonomy::Index.new(options)
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# Return command lambda for index_taxonomy.
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# Set default options.
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def defaults
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# Mask sequence in given record.
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@@ -180,10 +180,10 @@ module BioDSL
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def defaults
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@@ -147,9 +147,9 @@ module BioDSL
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# Set default options.
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def defaults
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+
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+
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|
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# Given a record with a sequence count its residues.
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@@ -157,12 +157,12 @@ module BioDSL
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# @param record [Hash] BioDSL record
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|
def count_residues(record)
|
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|
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|
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|
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|
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|
record[:SEQ].upcase.chars.each_with_index do |char, i|
|
|
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|
c = char.to_sym
|
|
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|
@counts[i][c] += 1
|
|
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|
-
@total[i]
|
|
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|
+
@total[i] += 1
|
|
166
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|
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|
|
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|
end
|
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|
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|
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@@ -21,7 +21,7 @@
|
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# #
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# This software is part of the BioDSL
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# #
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|
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@@ -113,7 +113,7 @@ module BioDSL
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STATS = %i(records_in records_out sequences_in sequences_out residues_in
|
|
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|
residues_out)
|
|
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|
|
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|
-
SCORES_MAX = 100_000
|
|
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|
+
SCORES_MAX = 100_000 # Maximum score string length.
|
|
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|
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|
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|
# Constructor for PlotScores.
|
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#
|
|
@@ -180,9 +180,9 @@ module BioDSL
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|
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|
def default
|
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|
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|
|
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|
-
@options[:title]
|
|
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|
-
@options[:xlabel]
|
|
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|
-
@options[:ylabel]
|
|
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|
+
@options[:title] ||= 'Mean Quality Scores'
|
|
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|
+
@options[:xlabel] ||= 'Sequence Position'
|
|
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|
+
@options[:ylabel] ||= 'Mean Score'
|
|
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186
|
end
|
|
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|
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|
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|
# Collect plot data from a given record.
|
|
@@ -196,7 +196,7 @@ module BioDSL
|
|
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|
|
|
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|
score_vec = NArray.to_na(scores, 'byte') - Seq::SCORE_BASE
|
|
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|
@scores_vec[0...scores.length] += score_vec
|
|
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|
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@count_vec[0...scores.length]
|
|
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|
+
@count_vec[0...scores.length] += 1
|
|
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200
|
|
|
201
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|
@max = scores.length if scores.length > @max
|
|
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|
end
|
|
@@ -212,7 +212,7 @@ module BioDSL
|
|
|
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|
|
|
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|
# Prepare data to plot.
|
|
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|
def prepare_plot_data
|
|
215
|
-
@max = 1 if @max == 0
|
|
215
|
+
@max = 1 if @max == 0 # ugly fix to avaid index error
|
|
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216
|
|
|
217
217
|
count_vec = @count_vec[0...@max].to_f
|
|
218
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|
count_vec *= (Seq::SCORE_MAX / @count_vec.max(0).to_f)
|
|
@@ -21,7 +21,7 @@
|
|
|
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|
# #
|
|
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# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
|
|
23
23
|
# #
|
|
24
|
-
# This software is part of the BioDSL
|
|
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|
+
# This software is part of the BioDSL (www.BioDSL.org). #
|
|
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|
# #
|
|
26
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|
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
|
|
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|
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@@ -21,7 +21,7 @@
|
|
|
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|
# #
|
|
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# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
|
|
23
23
|
# #
|
|
24
|
-
# This software is part of the BioDSL
|
|
24
|
+
# This software is part of the BioDSL (www.BioDSL.org). #
|
|
25
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|
# #
|
|
26
26
|
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
|
|
27
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|
|
|
@@ -142,11 +142,11 @@ module BioDSL
|
|
|
142
142
|
|
|
143
143
|
input.each do |record|
|
|
144
144
|
output << record
|
|
145
|
-
@status[:records_in]
|
|
145
|
+
@status[:records_in] += 1
|
|
146
146
|
|
|
147
147
|
if record[:SEQ]
|
|
148
148
|
@status[:sequences_in] += 1
|
|
149
|
-
@status[:residues_in]
|
|
149
|
+
@status[:residues_in] += record[:SEQ].length
|
|
150
150
|
end
|
|
151
151
|
end
|
|
152
152
|
end
|
|
@@ -165,9 +165,9 @@ module BioDSL
|
|
|
165
165
|
break if @count == first
|
|
166
166
|
output << entry.to_bp
|
|
167
167
|
|
|
168
|
-
@status[:records_out]
|
|
168
|
+
@status[:records_out] += 1
|
|
169
169
|
@status[:sequences_out] += 1
|
|
170
|
-
@status[:residues_out]
|
|
170
|
+
@status[:residues_out] += entry.length
|
|
171
171
|
|
|
172
172
|
@count += 1
|
|
173
173
|
end
|
|
@@ -200,9 +200,9 @@ module BioDSL
|
|
|
200
200
|
input.each do |entry|
|
|
201
201
|
output << entry.to_bp
|
|
202
202
|
|
|
203
|
-
@status[:records_out]
|
|
203
|
+
@status[:records_out] += 1
|
|
204
204
|
@status[:sequences_out] += 1
|
|
205
|
-
@status[:residues_out]
|
|
205
|
+
@status[:residues_out] += entry.length
|
|
206
206
|
end
|
|
207
207
|
end
|
|
208
208
|
|
|
@@ -213,9 +213,9 @@ module BioDSL
|
|
|
213
213
|
@buffer.each do |entry|
|
|
214
214
|
output << entry.to_bp
|
|
215
215
|
|
|
216
|
-
@status[:records_out]
|
|
216
|
+
@status[:records_out] += 1
|
|
217
217
|
@status[:sequences_out] += 1
|
|
218
|
-
@status[:residues_out]
|
|
218
|
+
@status[:residues_out] += entry.length
|
|
219
219
|
end
|
|
220
220
|
end
|
|
221
221
|
end
|