fasta_motif_sliding_generator 0.0.1

checksums.yaml

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+SHA512:
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data/lib/fasta_motif_sliding_generator.rb

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+class FastaMotifSlidingGenerator
+=begin
+ a fasta class to make genomic sliding window for the 
+  if you have a binding site and you want to prepare 
+  the motifs for the binding site as a sliding window
+  you can also use the same. You can also search the 
+  sliding window motifs starting with the particular tag
+  to see how many of them are generated. 
+=end
+  def initialize(fasta_sequence, takeiter, motif)
+  @fasta = fasta_sequence
+  @take = takeiter.to_i
+  @motif = motif.to_s
+  end
+  def sequencechunk
+    fasta_block = @fasta.split(//)
+    fasta_chunk_sequences = []
+    for i in 0..fasta_block.length-@take
+      fasta_chunk_sequences.push(fasta_block.slice(i,i-i+@take).join)
+    end
+  return fasta_chunk_sequences
+  end
+  def returnmotif
+    fasta_block = @fasta.split(//)
+    fasta_chunk_sequences = []
+    for i in 0..fasta_block.length-@take
+        fasta_chunk_sequences.push(fasta_block.slice(i,i-i+@take).join)
+    fasta_motifs = []
+    fasta_chunk_sequences.each{|fasta| puts fasta_motifs.push(fasta) if fasta.start_with?(@motif)}
+    end
+    return fasta_motifs
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: fasta_motif_sliding_generator
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Gaurav Sablok
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2023-09-01 00:00:00.000000000 Z
+dependencies: []
+description:
+email:
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/fasta_motif_sliding_generator.rb
+homepage: https://github.com/sablokgaurav/pacbio_oxford_assembly_binding_ruby_motif_scanner
+licenses:
+- MIT
+metadata: {}
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.4.19
+signing_key:
+specification_version: 4
+summary: Generates the sliding iterable for the given fasta stretch and check its
+  starting motifs
+test_files: []