finishm 0.0.1 → 0.0.2

data/bin/scaffold_end_coverages.rb

@@ -1,69 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-require 'bio-logger'
-require 'bio-samtools'
-require 'bio'
-
-if __FILE__ == $0 #needs to be removed if this script is distributed as part of a rubygem
-  SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
-
-  # Parse command line options into the options hash
-  options = {
-    :logger => 'stderr',
-    :contig_end_length => 200,
-  }
-  o = OptionParser.new do |opts|
-    opts.banner = "
-      Usage: #{SCRIPT_NAME} <arguments>
-
-      Takes a sorted, indexed BAM file and outputs the coverages of each of the reference sequences\n\n"
-
-    opts.on("-b", "--bam BAM_FILE", "BAM file that defines overall mapping/coverage [required]") do |arg|
-      options[:bam_file] = arg
-    end
-    opts.on("-f", "--reference-fasta FASTA_FILE", "FASTA file of the reference [required]") do |arg|
-      options[:fasta_file] = arg
-    end
-
-    opts.on("-l", "--end-length LENGTH", "How far from the end to count [default: #{options[:contig_end_length]}]") do |arg|
-      options[:contig_end_length] = arg.to_i
-      raise "Inappropriate end length detected, I need a positive number, found #{options[:contig_end_length]} parsed from #{arg}" if options[:contig_end_length] < 1
-    end
-
-    # logger options
-    opts.separator "\n\tVerbosity:\n\n"
-    opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {Bio::Log::CLI.trace('error')}
-    opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
-    opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| Bio::Log::CLI.trace(s)}
-  end; o.parse!
-  if ARGV.length != 0 or options[:bam_file].nil? or options[:fasta_file].nil?
-    $stderr.puts o
-    exit 1
-  end
-  # Setup logging. bio-logger defaults to STDERR not STDOUT, I disagree
-  Bio::Log::CLI.logger(options[:logger]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
-
-
-  # open the BAM file for reading
-  bam = Bio::DB::Sam.new(:bam => options[:bam_file], :fasta => options[:fasta_file])
-  bam.open
-  puts %w(Reference StartCoverage EndCoverage).join("\t")
-  contigs_file = Bio::FlatFile.auto(options[:fasta_file])
-  contigs_file.each_entry do |record|
-    ref = record.definition
-    ref_length = record.length
-  #bam.each_reference do |ref, ref_length| #currently commented out because there is extraneous output on STDOUT if you use this
-    next if ref == '*' #Ignore umapped reads
-    # Coverage of the start
-    end_length = options[:contig_end_length]
-    end_length = ref_length if ref_length < options[:contig_end_length]
-
-    cov_start = bam.average_coverage(ref, 1, end_length)
-    cov_end = bam.average_coverage(ref, ref_length-end_length+1, end_length)
-    puts [
-      ref, cov_start, cov_end
-    ].join("\t")
-  end
-  exit
-end #end if running as a script

data/bin/trail_validator.rb

@@ -1,84 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'optparse'
-require 'bio-logger'
-require 'pp'
-
-SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = 'finishm'
-$:.unshift File.join(File.dirname(__FILE__),'..','lib')
-require 'priner'
-
-# Parse command line options into the options hash
-options = {
-  :logger => 'stderr',
-  :log_level => 'info',
-}
-
-o = OptionParser.new do |opts|
-  opts.banner = "
-    Usage: #{SCRIPT_NAME} --trails <trail(s) fasta> --kmer-abundances <abundances.csv>
-
-    Given an input kmer set of sequences then abundances space separated file, and a threshold, print out how many kmers are unique to different subsets of columns\n\n"
-
-  opts.on("--trails FASTA_FILE", "fasta file of trail(s) to be tested [required]") do |arg|
-    options[:trails_fasta_file] = arg
-  end
-  opts.on("--kmer-abundances FILE", "kmer multiple abundance file [required]") do |arg|
-    options[:kmer_multiple_abundance_file] = arg
-  end
-
-  #opts.separator "\nOptional arguments:\n\n"
-  opts.on("--output-kmer-coverages FILE", "output kmer coverages across each library across the contigs default: don't output]") do |arg|
-    options[:output_trail_kmer_coverage_file] = arg
-  end
-
-  # logger options
-  opts.separator "\nVerbosity:\n\n"
-  opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
-  opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
-  opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
-end; o.parse!
-if ARGV.length != 0 or options[:trails_fasta_file].nil? or options[:kmer_multiple_abundance_file].nil? or options[:output_trail_kmer_coverage_file].nil?
-  $stderr.puts "Options not correctly specified. Found:"
-  pp options
-  $stderr.puts o
-  exit 1
-end
-# Setup logging
-Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
-
-# read in fasta file of trails
-log.info "Reading trail sequences from #{options[:trails_fasta_file]}"
-fasta_seqs = {}
-Bio::FlatFile.foreach(options[:trails_fasta_file]) do |e|
-  name = e.definition
-  seq = e.seq.seq
-  fasta_seqs[name]=seq
-end
-
-log.info "Reading kmer abundances from #{options[:kmer_multiple_abundance_file]}.."
-kmer_hash = Bio::KmerMultipleAbundanceHash.parse_from_file options[:kmer_multiple_abundance_file]
-log.info "Finished reading the kmer abundances"
-
-if options[:output_trail_kmer_coverage_file]
-  log.info "Writing out kmer coverages to #{options[:output_trail_kmer_coverage_file]}.."
-  writer = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new
-  io = File.open(options[:output_trail_kmer_coverage_file],'w')
-  fasta_seqs.each do |name, seq|
-    log.debug "Writing coverages for #{name}"
-    writer.write_depths(io, name, seq, kmer_hash)
-  end
-  log.info "Finished writing"
-end
-
-#log.info "Filtering trail(s) based on kmer coverage, requiring each kmer in the path to have a minimum of #{options[:kmer_path_filter_min_coverage]} coverage in patterned reads, except for the #{options[:kmer_path_end_exclusion_length]}bp at the ends"
-#kmer_path_filter = Bio::AssemblyGraphAlgorithms::KmerCoverageBasedPathFilter.new
-#thresholds = desired_pattern.collect{|c| c == true ? 1 : 0}
-#log.info "Using thresholds for filtering: #{thresholds}"
-#trails = kmer_path_filter.filter(trails, kmer_hash, thresholds, :exclude_ending_length => options[:kmer_path_end_exclusion_length])
-#log.info "After filtering remained #{trails.length} trails"
-
-#trails.each_with_index do |trail, i|
-#  puts ">trail#{i+1}"
-#  puts trail.sequence
-#end