Module: MiGA::Common::Format
- Included in:
- MiGA
- Defined in:
- lib/miga/common/format.rb
Overview
General formatting functions shared throughout MiGA.
Instance Method Summary collapse
-
#clean_fasta_file(file) ⇒ Object
Cleans a FastA file in place.
-
#seqs_length(file, format, opts = {}) ⇒ Object
Calculates the average and standard deviation of the sequence lengths in a FastA or FastQ file (supports gzipped files).
-
#tabulate(header, values, tabular = false) ⇒ Object
Tabulates an
values
, and Array of Arrays, all with the same number of entries asheader
.
Instance Method Details
#clean_fasta_file(file) ⇒ Object
Cleans a FastA file in place.
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# File 'lib/miga/common/format.rb', line 27 def clean_fasta_file(file) tmp_fh = nil tmp_path = nil begin if file =~ /\.gz/ tmp_path = Tempfile.new('MiGA.gz').tap(&:close).path File.unlink tmp_path tmp_path += '.gz' tmp_fh = Zlib::GzipWriter.open(tmp_path, 9) fh = Zlib::GzipReader.open(file) else tmp_fh = Tempfile.new('MiGA') tmp_path = tmp_fh.path fh = File.open(file, 'r') end buffer = ''.dup fh.each_line do |ln| ln.chomp! if ln =~ /^>\s*(\S+)(.*)/ id, df = $1, $2 tmp_fh.print buffer.wrap_width(80) buffer = ''.dup tmp_fh.puts ">#{id.gsub(/[^A-Za-z0-9_\|\.]/, '_')}#{df}" else buffer << ln.gsub(/[^A-Za-z\.\-]/, '') end end tmp_fh.print buffer.wrap_width(80) tmp_fh.close fh.close FileUtils.mv(tmp_path, file) ensure begin tmp_fh.close unless tmp_fh.nil? File.unlink(tmp_path) unless tmp_path.nil? rescue end end end |
#seqs_length(file, format, opts = {}) ⇒ Object
Calculates the average and standard deviation of the sequence lengths in a FastA or FastQ file (supports gzipped files). The format
must be a Symbol, one of :fasta
or :fastq
. Additional estimations can be controlled via the opts
Hash. Supported options include:
-
:n50
: Include the N50 and the median (in bp) -
:gc
: Include the G+C content (in %) -
:x
: Include the undetermined bases content (in %) -
:skew
: Include G-C and A-T sequence skew (in %; forces gc: true). See definition used here in DOI:10.1177/117693430700300006
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# File 'lib/miga/common/format.rb', line 77 def seqs_length(file, format, opts = {}) opts[:gc] = true if opts[:skew] fh = file =~ /\.gz/ ? Zlib::GzipReader.open(file) : File.open(file, 'r') l = [] gc = 0 xn = 0 t = 0 c = 0 i = 0 # <- Zlib::GzipReader doesn't set `$.` fh.each_line do |ln| i += 1 if (format == :fasta and ln =~ /^>/) or (format == :fastq and (i % 4) == 1) l << 0 elsif format == :fasta or (i % 4) == 2 l[l.size - 1] += ln.chomp.size gc += ln.scan(/[GCgc]/).count if opts[:gc] xn += ln.scan(/[XNxn]/).count if opts[:x] if opts[:skew] t += ln.scan(/[Tt]/).count c += ln.scan(/[Cc]/).count end end end fh.close o = { n: l.size, tot: l.inject(0, :+), max: l.max } return o if o[:tot].zero? o[:avg] = o[:tot].to_f / l.size o[:var] = l.map { |a| a**2 }.inject(:+).to_f / l.size - o[:avg]**2 o[:sd] = Math.sqrt o[:var] o[:gc] = 100.0 * gc / o[:tot] if opts[:gc] o[:x] = 100.0 * xn / o[:tot] if opts[:x] if opts[:skew] at = o[:tot] - gc o[:at_skew] = 100.0 * (2 * t - at) / at o[:gc_skew] = 100.0 * (2 * c - gc) / gc end if opts[:n50] l.sort! thr = o[:tot] / 2 pos = 0 l.each do |a| pos += a o[:n50] = a break if pos >= thr end o[:med] = o[:n].even? ? 0.5 * l[o[:n] / 2 - 1, 2].inject(:+) : l[(o[:n] - 1) / 2] end o end |
#tabulate(header, values, tabular = false) ⇒ Object
Tabulates an values
, and Array of Arrays, all with the same number of entries as header
. Returns an Array of String, one per line.
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# File 'lib/miga/common/format.rb', line 11 def tabulate(header, values, tabular = false) fields = [] fields << header.map(&:to_s) unless tabular && header.all?(&:nil?) fields << fields.first.map { |h| h.gsub(/\S/, '-') } unless tabular fields += values.map { |r| r.map { |cell| cell.nil? ? '?' : cell.to_s } } clen = tabular ? Array.new(header.size, 0) : fields.map { |r| r.map(&:length) }.transpose.map(&:max) fields.map do |r| (0..(clen.size - 1)).map do |col_n| col_n == 0 ? r[col_n].rjust(clen[col_n]) : r[col_n].ljust(clen[col_n]) end.join(tabular ? "\t" : ' ') end end |