# Error class for all exceptions to do with Usearch.
class UsearchError < StandardError; end
-SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
-
class Usearch
include Enumerable
@outfile = outfile
@options = options
@command = []
+
+ raise UsearchError, %{Empty input file -> "#{@infile}"} if File.size(@infile) == 0
end
# Method that calls Usearch sorting for sorting a FASTA file
# according to decending sequence length.
- def sort_length
- # usearch -sort seqs.fasta -output seqs.sorted.fasta
- if File.size(@infile) < SORT_LIMIT
- @command << "usearch --sort #{@infile} --output #{@infile}.sort"
- else
- @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
- end
+ def sortbylength
+ # usearch -sortbylength seqs.fasta -output seqs_sorted.fasta -minseqlength 64
+ @command << "usearch"
+ @command << "-sortbylength #{@infile}"
+ @command << "-output #{@infile}.sort"
execute
# Method that calls Usearch sorting for sorting a FASTA file
# according to cluster size.
- def sort_size
- # usearch -sortsize seqs.fasta -output seqs.sorted.fasta
- @command << "usearch --sortsize #{@infile} --output #{@infile}.sort"
+ def sortbysize
+ # usearch -sortbysize seqs.fasta -output seqs_sorted.fasta -minsize 4
+ @command << "usearch"
+ @command << "-sortbysize #{@infile}"
+ @command << "-output #{@infile}.sort"
execute
File.rename "#{@infile}.sort", @infile
end
- # Method to execute clustering de novo.
- def cluster
- @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
+ # Method to execute cluster_fast.
+ def cluster_fast
+ # usearch -cluster_fast query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc
+ @command << "usearch"
+ @command << "-cluster_fast #{@infile}"
+ @command << "-id #{@options[:identity]}"
+ @command << "-uc #{@outfile}"
+ @command << "-threads #{@options[:cpus]}"
- execute
+ execute
+ end
+
+ # Method to execute cluster_smallmem.
+ # NB sequences must be sorted with sortbylength or sortbysize.
+ def cluster_smallmem
+ # usearch -cluster_smallmem query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc
+ @command << "usearch"
+ @command << "-cluster_smallmem #{@infile}"
+ @command << "-id #{@options[:identity]}"
+ @command << "-uc #{@outfile}"
+ @command << "-strand both" if @options[:comp]
+
+ execute
end
- # Method to execute database search.
- def usearch
- @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
- @command << "--userfields target+tloz+thiz+query+bits+strand"
- @command << "--id #{@options[:identity]}" if @options.has_key? :identity
- @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
- @command << "--rev"
+ # Method to execute database local search.
+ def usearch_local
+ # usearch -usearch_local query.fasta -db proteins.udb -id 0.8 -alnout results.aln
+ # usearch -usearch_local query.fasta -db ESTs.fasta -id 0.9 -evalue 1e-6 -blast6out results.m8 -strand plus -maxaccepts 8 -maxrejects 256
+
+ @command << "usearch"
+ @command << "-usearch_local #{@infile}"
+ @command << "-db #{@options[:database]}"
+ @command << "-blast6out #{@outfile}"
+ @command << "-strand both"
+ @command << "-id #{@options[:identity]}" if @options[:identity]
+ @command << "-evalue #{@options[:e_val]}" if @options[:e_val]
+ @command << "-maxaccepts #{@options[:maxaccepts]}"
+ @command << "-threads #{@options[:cpus]}"
+
+ execute
+ end
- execute
+ # Method to execute database global search.
+ def usearch_global
+ # usearch -usearch_global query.fasta -db proteins.udb -id 0.8 -alnout results.aln
+ # usearch -usearch_global query.fasta -db ESTs.fasta -id 0.9 -blast6out results.m8 -strand plus -maxaccepts 8 -maxrejects 256
+
+ @command << "usearch"
+ @command << "-usearch_global #{@infile}"
+ @command << "-db #{@options[:database]}"
+ @command << "-blast6out #{@outfile}"
+ @command << "-strand both"
+ @command << "-id #{@options[:identity]}"
+ @command << "-evalue #{@options[:e_val]}" if @options[:e_val]
+ @command << "-maxaccepts #{@options[:maxaccepts]}"
+ @command << "-threads #{@options[:cpus]}"
+
+ execute
+ end
+
+ # Method to execute uchime chimera detection.
+ def uchime
+ @command << "usearch --uchime #{@infile} --db #{@options[:database]} --uchimeout #{@outfile}"
+
+ execute
+ end
+
+ # Method to execute ustar alignment.
+ def ustar
+ command = %Q{grep "^[SH]" #{@outfile} > #{@outfile}.sub}
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ File.rename "#{@outfile}.sub", @outfile
+
+ @command << "usearch --uc2fastax #{@outfile} --input #{@infile} --output #{@infile}.sub"
+
+ execute
+
+ @command << "usearch --staralign #{@infile}.sub --output #{@outfile}"
+
+ execute
+
+ File.delete "#{@infile}.sub"
end
# Method to parse a Uclust .uc file and for each line of data
def each_cluster
record = {}
- File.open(@outfile, mode="r") do |ios|
+ File.open(@outfile, "r") do |ios|
ios.each_line do |line|
if line !~ /^#/
fields = line.chomp.split("\t")
def each_hit
record = {}
- File.open(@outfile, mode="r") do |ios|
- ios.gets # skip comment line
+ File.open(@outfile, "r") do |ios|
ios.each_line do |line|
fields = line.chomp.split("\t")
-
- record[:REC_TYPE] = "USEARCH"
- record[:S_ID] = fields[0]
- record[:S_BEG] = fields[1].to_i
- record[:S_END] = fields[2].to_i
- record[:Q_ID] = fields[3]
- record[:SCORE] = fields[4].to_f
- record[:STRAND] = fields[5]
+ record[:REC_TYPE] = "USEARCH"
+ record[:Q_ID] = fields[0]
+ record[:S_ID] = fields[1]
+ record[:IDENT] = fields[2].to_f
+ record[:ALIGN_LEN] = fields[3].to_i
+ record[:MISMATCHES] = fields[4].to_i
+ record[:GAPS] = fields[5].to_i
+ record[:Q_BEG] = fields[6].to_i - 1
+ record[:Q_END] = fields[7].to_i - 1
+ record[:S_BEG] = fields[8].to_i - 1
+ record[:S_END] = fields[9].to_i - 1
+ record[:E_VAL] = fields[10] == '*' ? '*' : fields[10].to_f
+ record[:SCORE] = fields[11] == '*' ? '*' : fields[11].to_f
+ record[:STRAND] = record[:S_BEG].to_i < record[:S_END].to_i ? '+' : '-'
+
+ record[:S_BEG], record[:S_END] = record[:S_END], record[:S_BEG] if record[:STRAND] == '-'
yield record
end
self # conventionally
end
+ # Method to parse a FASTA file with Ustar alignments and for each alignment
+ # yield an Align object.
+ def each_alignment
+ old_cluster = 0
+ entries = []
+
+ Fasta.open(@outfile, "r") do |ios|
+ ios.each do |entry|
+ entry.seq.tr!('.', '-') # Replace . with - in Ustar alignments.
+ cluster, identity, name = entry.seq_name.split('|')
+ cluster = cluster.to_i
+
+ if cluster == old_cluster
+ entries << entry
+ else
+ fix_alignment(entries)
+
+ yield Align.new(entries)
+
+ old_cluster = cluster
+ entries = []
+ entries << entry
+ end
+ end
+
+ yield Align.new(entries) unless entries.empty?
+ end
+
+ self # conventionally
+ end
+
private
+ # Method that fixed Ustar bug resulting in alignments with uneven
+ # sequence length.
+ def fix_alignment(entries)
+ if entries.size > 1
+ min, max = entries.minmax { |a, b| a.length <=> b.length }
+
+ if min.length != max.length
+ entries.each do |entry|
+ entry.seq << '-' * (max.length - entry.length)
+ end
+ end
+ end
+ end
+
# Method to execute a command using a system() call.
# The command is composed of bits from the @command variable.
def execute
- @command.unshift "nice -n 19"
- @command << "--rev" if @options[:comp]
- @command << "> /dev/null 2>&1" unless @options[:verbose]
+ @command << "--quiet" unless @options[:verbose]
command = @command.join(" ")
+ $stderr.puts "Running command: #{command}" if @options[:verbose]
system(command)
raise "Command failed: #{command}" unless $?.success?
projects / biopieces.git / blobdiff