require 'maasha/usearch'
casts = []
-casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'comp', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.9, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'comp', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.9, :allowed=>nil, :disallowed=>nil}
options = Biopieces.options_parse(ARGV, casts)
file_uclust = File.join(tmpdir, "out.uc")
Biopieces.open(options[:stream_in], file_records) do |input, output|
- Fasta.open(file_fasta, mode="w") do |fasta_io|
+ Fasta.open(file_fasta, 'w') do |fasta_io|
input.each_record do |record|
output.puts record
end
us = Usearch.new(file_fasta, file_uclust, options)
-us.sort_length unless options[:no_sort]
-us.cluster
+
+us.sortbylength unless options[:no_sort]
+us.cluster_smallmem
hash = {}
-us.each_cluster do |record|
- hash[record[:Q_ID].to_sym] = record.dup
+us.each_cluster do |cluster|
+ hash[cluster[:Q_ID].to_sym] = cluster.dup
end
Biopieces.open(file_records, options[:stream_out]) do |input, output|
SEQ_NAME: test1
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 2
IDENT: *
---
SEQ_NAME: test1_100
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 2
IDENT: 100
---
SEQ_NAME: test1_2
SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 2
IDENT: 96
---
SEQ_NAME: test2
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 1
-IDENT: *
+CLUSTER: 0
+IDENT: 100
---
SEQ_NAME: test2_100
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 1
-IDENT: 100
+CLUSTER: 0
+IDENT: *
---
SEQ_NAME: test2_1
SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 1
+CLUSTER: 0
IDENT: 96
---
SEQ_NAME: test1_rc
SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
SEQ_LEN: 59
-CLUSTER: 2
+CLUSTER: 1
IDENT: *
---
SEQ_NAME: test1
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 3
IDENT: *
---
SEQ_NAME: test1_100
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 3
IDENT: 100
---
SEQ_NAME: test1_2
SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 1
+CLUSTER: 4
IDENT: *
---
SEQ_NAME: test2
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 2
-IDENT: *
+CLUSTER: 0
+IDENT: 100
---
SEQ_NAME: test2_100
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 2
-IDENT: 100
+CLUSTER: 0
+IDENT: *
---
SEQ_NAME: test2_1
SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 3
+CLUSTER: 1
IDENT: *
---
SEQ_NAME: test1_rc
SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
SEQ_LEN: 59
-CLUSTER: 4
+CLUSTER: 2
IDENT: *
---
SEQ_NAME: test1
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
-IDENT: *
+CLUSTER: 2
+IDENT: 100
---
SEQ_NAME: test1_100
SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 0
+CLUSTER: 2
IDENT: 100
---
SEQ_NAME: test1_2
SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
SEQ_LEN: 59
-CLUSTER: 1
+CLUSTER: 3
IDENT: *
---
SEQ_NAME: test2
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 2
-IDENT: *
+CLUSTER: 0
+IDENT: 100
---
SEQ_NAME: test2_100
SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 2
-IDENT: 100
+CLUSTER: 0
+IDENT: *
---
SEQ_NAME: test2_1
SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
SEQ_LEN: 59
-CLUSTER: 3
+CLUSTER: 1
IDENT: *
---
SEQ_NAME: test1_rc
SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
SEQ_LEN: 59
-CLUSTER: 0
-IDENT: 100
+CLUSTER: 2
+IDENT: *
---
# 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
# 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 -sortbylength #{@infile} -output #{@infile}.sort"
execute
# Method that calls Usearch sorting for sorting a FASTA file
# according to cluster size.
- def sort_size
- @command << "usearch --sortsize #{@infile} --output #{@infile}.sort"
+ def sortbysize
+ # usearch -sortbysize seqs.fasta -output seqs_sorted.fasta -minsize 4
+ @command << "usearch -sortbysize #{@infile} -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]}"
- @command << "--rev" if @options[:comp]
+ # Method to execute cluster_fast.
+ def cluster_fast
+ # usearch -cluster_fast query.fasta -id 0.9 -centroids nr.fasta -uc clusters.uc
+ @command << "usearch -cluster_fast #{@infile} -id #{@options[:identity]} -uc #{@outfile}"
- 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 -cluster_smallmem #{@infile} -id #{@options[:identity]} -uc #{@outfile}"
+ @command << "-strand both" if @options[:comp]
+
+ execute
end
# Method to execute database search.
yield Align.new(entries) unless entries.empty?
end
+
+ self # conventionally
end
private
# 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 << "--quiet" unless @options[:verbose]
command = @command.join(" ")
$stderr.puts "Running command: #{command}" if @options[:verbose]