fixing usearch upgrade

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2190 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/uclust_seq b/bp_bin/uclust_seq
index f155bdf53f06328bfe5d0c62232a667d3ee45d2c..5a6d0ef901a1f9cb298b324106c568c721a50b1d 100755 (executable)
--- a/bp_bin/uclust_seq
+++ b/bp_bin/uclust_seq
@@ -33,9 +33,10 @@ require 'maasha/fasta'
 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}
+casts << {long: 'cpus',     short: 'C', type: 'uint',  mandatory: false, default: 1,   allowed: nil, disallowed: "0"}
 
 options = Biopieces.options_parse(ARGV, casts)
 

diff --git a/bp_bin/usearch_seq b/bp_bin/usearch_seq
index c390708a46fc8535a43b1b7f2b76d538334a01b8..d139957f1929fdd40ff46b038d924580260df0c8 100755 (executable)
--- a/bp_bin/usearch_seq
+++ b/bp_bin/usearch_seq
@@ -33,13 +33,22 @@ require 'maasha/fasta'
 require 'maasha/usearch'
 
 casts = []
-casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'e_val',    :short=>'e', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {long: 'program',    short: 'p', type: 'string', mandatory: false, default: 'global', allowed: "local,global", disallowed: nil}
+casts << {long: 'database',   short: 'd', type: 'file!',  mandatory: true,  default: nil,      allowed: nil,            disallowed: nil}
+casts << {long: 'identity',   short: 'i', type: 'float',  mandatory: false, default: nil,      allowed: nil,            disallowed: nil}
+casts << {long: 'e_val',      short: 'e', type: 'float',  mandatory: false, default: nil,      allowed: nil,            disallowed: nil}
+casts << {long: 'cpus',       short: 'c', type: 'uint',   mandatory: false, default: 1,        allowed: nil,            disallowed: "0"}
+casts << {long: 'maxaccepts', short: 'm', type: 'uint',   mandatory: false, default: 0,        allowed: nil,            disallowed: nil}
 
 options = Biopieces.options_parse(ARGV, casts)
 
-raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
+if options[:program] == 'global'
+  raise ArgumentError, "--identity be specified for global search" unless options[:identity]
+  raise ArgumentError, "--e_val is invalid for global search" if options[:e_val]
+else
+  raise ArgumentError, "--identity or --e_val must be specified" unless options[:identity] or options[:e_val]
+end
+
 
 tmpdir  = Biopieces.mktmpdir
 infile  = File.join(tmpdir, "in.fna")
@@ -58,7 +67,11 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
   us = Usearch.new(infile, outfile, options)
 
-  us.usearch
+  case options[:program]
+  when "local"  then us.usearch_local
+  when "global" then us.usearch_global
+  else raise "no such program #{options[:program]}"
+  end
 
   us.each_hit do |record|
     output.puts record

diff --git a/bp_test/in/usearch_seq.in b/bp_test/in/usearch_seq.in
new file mode 100644 (file)
index 0000000..b53c0ae
--- /dev/null
+++ b/bp_test/in/usearch_seq.in
@@ -0,0 +1,28 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---

diff --git a/bp_test/in/usearch_seq.in.db b/bp_test/in/usearch_seq.in.db
new file mode 100644 (file)
index 0000000..fc369b2
--- /dev/null
+++ b/bp_test/in/usearch_seq.in.db
@@ -0,0 +1,14 @@
+>test1
+tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+>test1_100
+tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+>test1_2
+tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+>test2
+ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+>test2_100
+ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+>test2_1
+ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+>test1_rc
+cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca

diff --git a/bp_test/lib/test.sh b/bp_test/lib/test.sh
index f560e2042266a236d4e6dfc810c41a5a1ebcd802..7ce41900d12068649fdf92320f6110f779c17398 100755 (executable)
--- a/bp_test/lib/test.sh
+++ b/bp_test/lib/test.sh
@@ -14,6 +14,7 @@ function run
 
     msg="${command/$BP_DIR/\$BP_DIR}"
     msg="${msg//$BP_TMP/\$BP_TMP}"
+    msg="${msg/$BP_DIR/\$BP_DIR}"
 
     echo -n "Testing $msg ... "
     eval $command > /dev/null 2>&1

diff --git a/bp_test/out/uclust_seq.out.2 b/bp_test/out/uclust_seq.out.2
index 5c1b6e47af0d74f85dbe2cb3c764e90506b550e5..43691ea56df1d97f358001ab9ed64dfc9ee65dc4 100644 (file)
--- a/bp_test/out/uclust_seq.out.2
+++ b/bp_test/out/uclust_seq.out.2
@@ -1,20 +1,20 @@
 SEQ_NAME: test1
 SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 3
+CLUSTER: 2
 IDENT: *
 ---
 SEQ_NAME: test1_100
 SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 3
+CLUSTER: 2
 IDENT: 100
 ---
 SEQ_NAME: test1_2
 SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 4
-IDENT: *
+CLUSTER: 2
+IDENT: 96
 ---
 SEQ_NAME: test2
 SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
@@ -31,12 +31,12 @@ IDENT: *
 SEQ_NAME: test2_1
 SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
 SEQ_LEN: 59
-CLUSTER: 1
-IDENT: *
+CLUSTER: 0
+IDENT: 96
 ---
 SEQ_NAME: test1_rc
 SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
 SEQ_LEN: 59
-CLUSTER: 2
+CLUSTER: 1
 IDENT: *
 ---

diff --git a/bp_test/out/uclust_seq.out.3 b/bp_test/out/uclust_seq.out.3
index 8052dfc9d1c074c7e445fd8b7bd85df85f14a2c6..5c1b6e47af0d74f85dbe2cb3c764e90506b550e5 100644 (file)
--- a/bp_test/out/uclust_seq.out.3
+++ b/bp_test/out/uclust_seq.out.3
@@ -1,19 +1,19 @@
 SEQ_NAME: test1
 SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 2
-IDENT: 100
+CLUSTER: 3
+IDENT: *
 ---
 SEQ_NAME: test1_100
 SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 2
+CLUSTER: 3
 IDENT: 100
 ---
 SEQ_NAME: test1_2
 SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
 SEQ_LEN: 59
-CLUSTER: 3
+CLUSTER: 4
 IDENT: *
 ---
 SEQ_NAME: test2

diff --git a/bp_test/out/uclust_seq.out.4 b/bp_test/out/uclust_seq.out.4
new file mode 100644 (file)
index 0000000..8052dfc
--- /dev/null
+++ b/bp_test/out/uclust_seq.out.4
@@ -0,0 +1,42 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: 100
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: 100
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 3
+IDENT: *
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 100
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: *
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: *
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: *
+---

diff --git a/bp_test/out/usearch_seq.out.1 b/bp_test/out/usearch_seq.out.1
new file mode 100644 (file)
index 0000000..75e33c7
--- /dev/null
+++ b/bp_test/out/usearch_seq.out.1
@@ -0,0 +1,253 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_2
+S_ID: test1_2
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2
+S_ID: test2
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2
+S_ID: test2_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2_100
+S_ID: test2
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2_100
+S_ID: test2_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2_1
+S_ID: test2_1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_rc
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1_rc
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1_rc
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---

diff --git a/bp_test/out/usearch_seq.out.2 b/bp_test/out/usearch_seq.out.2
new file mode 100644 (file)
index 0000000..3739ccc
--- /dev/null
+++ b/bp_test/out/usearch_seq.out.2
@@ -0,0 +1,403 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 36
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 7
+Q_END: 42
+S_BEG: 16
+S_END: 51
+E_VAL: 1.1e-16
+SCORE: 67.6
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 6
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 2
+Q_END: 7
+S_BEG: 51
+S_END: 56
+E_VAL: 5.2
+SCORE: 12.2
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 36
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 7
+Q_END: 42
+S_BEG: 16
+S_END: 51
+E_VAL: 1.1e-16
+SCORE: 67.6
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 6
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 2
+Q_END: 7
+S_BEG: 51
+S_END: 56
+E_VAL: 5.2
+SCORE: 12.2
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_100
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_2
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 6
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 2
+Q_END: 7
+S_BEG: 2
+S_END: 7
+E_VAL: 5.2
+SCORE: 12.2
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1_2
+S_ID: test1_100
+IDENT: 100.0
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+---
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+---

diff --git a/bp_test/out/usearch_seq.out.3 b/bp_test/out/usearch_seq.out.3
new file mode 100644 (file)
index 0000000..dac569e
--- /dev/null
+++ b/bp_test/out/usearch_seq.out.3
@@ -0,0 +1,253 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
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+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
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+Q_BEG: 0
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+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
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+S_ID: test1_100
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+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
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+S_ID: test1_rc
+IDENT: 100.0
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+Q_BEG: 0
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+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: -
+---
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+IDENT: 100.0
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+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
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+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
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+Q_ID: test1_2
+S_ID: test1_2
+IDENT: 100.0
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+MISMATCHES: 0
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+S_BEG: 0
+S_END: 58
+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: +
+---
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+Q_ID: test2
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+---
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+---
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+---
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+---
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+E_VAL: 1.1e-26
+SCORE: 100.8
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+---
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+SCORE: 110.1
+STRAND: -
+---
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+E_VAL: 1.8e-29
+SCORE: 110.1
+STRAND: -
+---
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+IDENT: 100.0
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+STRAND: +
+---

diff --git a/bp_test/out/usearch_seq.out.4 b/bp_test/out/usearch_seq.out.4
new file mode 100644 (file)
index 0000000..75e33c7
--- /dev/null
+++ b/bp_test/out/usearch_seq.out.4
@@ -0,0 +1,253 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
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+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1
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+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
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+Q_ID: test1_100
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+IDENT: 100.0
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+Q_BEG: 0
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+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
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+---
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+E_VAL: *
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+---
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+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
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+---
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+---
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+---
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+---
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+---
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+E_VAL: *
+SCORE: *
+STRAND: -
+---
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+SCORE: *
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+---
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+S_ID: test1_rc
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+---

diff --git a/bp_test/out/usearch_seq.out.5 b/bp_test/out/usearch_seq.out.5
new file mode 100644 (file)
index 0000000..ab230fa
--- /dev/null
+++ b/bp_test/out/usearch_seq.out.5
@@ -0,0 +1,178 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
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+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
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+IDENT: 100.0
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+S_END: 58
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+SCORE: *
+STRAND: -
+---
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+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_2
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+IDENT: 100.0
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+SCORE: *
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+---
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+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
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+GAPS: 0
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+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test2_1
+S_ID: test2_1
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---
+REC_TYPE: USEARCH
+Q_ID: test1_rc
+S_ID: test1_100
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: -
+---
+REC_TYPE: USEARCH
+Q_ID: test1_rc
+S_ID: test1_rc
+IDENT: 100.0
+ALIGN_LEN: 59
+MISMATCHES: 0
+GAPS: 0
+Q_BEG: 0
+Q_END: 58
+S_BEG: 0
+S_END: 58
+E_VAL: *
+SCORE: *
+STRAND: +
+---

diff --git a/bp_test/test/test_uclust_seq b/bp_test/test/test_uclust_seq
index 583737b38abb7dafc6a95305c8e35663d7513184..d19ecfa1e4852a1d85cb06b28b5c6e70d21d5f4f 100755 (executable)
--- a/bp_test/test/test_uclust_seq
+++ b/bp_test/test/test_uclust_seq
@@ -6,10 +6,14 @@ run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
 clean
 
-run "$bp -I $in -i 1 -O $tmp"
+run "$bp -I $in -C 2 -O $tmp"
 assert_no_diff $tmp $out.2
 clean
 
-run "$bp -I $in -i 1 -c -O $tmp"
+run "$bp -I $in -i 1 -O $tmp"
 assert_no_diff $tmp $out.3
 clean
+
+run "$bp -I $in -i 1 -c -O $tmp"
+assert_no_diff $tmp $out.4
+clean

diff --git a/bp_test/test/test_usearch_seq b/bp_test/test/test_usearch_seq
new file mode 100755 (executable)
index 0000000..394a602
--- /dev/null
+++ b/bp_test/test/test_usearch_seq
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -d $in.db -i 1 -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -d $in.db -i 1 -p local -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -I $in -d $in.db -i 0.99 -e 0.1 -p local -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -I $in -d $in.db -i 0.99 -O $tmp"
+assert_no_diff $tmp $out.4
+clean
+
+run "$bp -I $in -d $in.db -i 1 -m 1 -O $tmp"
+assert_no_diff $tmp $out.5
+clean

diff --git a/code_ruby/lib/maasha/usearch.rb b/code_ruby/lib/maasha/usearch.rb
index 0bc72352d648c92d958a82aed390b3118518d4d2..63757911deebea8e62de71ea688e29311d5427b8 100644 (file)
--- a/code_ruby/lib/maasha/usearch.rb
+++ b/code_ruby/lib/maasha/usearch.rb
@@ -43,7 +43,9 @@ class Usearch
   # according to decending sequence length.
   def sortbylength
     # usearch -sortbylength seqs.fasta -output seqs_sorted.fasta -minseqlength 64
-    @command << "usearch -sortbylength #{@infile} -output #{@infile}.sort"
+    @command << "usearch"
+    @command << "-sortbylength #{@infile}"
+    @command << "-output #{@infile}.sort"
 
                execute
 
@@ -54,7 +56,9 @@ class Usearch
   # according to cluster size.
   def sortbysize
     # usearch -sortbysize seqs.fasta -output seqs_sorted.fasta -minsize 4
-    @command << "usearch -sortbysize #{@infile} -output #{@infile}.sort"
+    @command << "usearch"
+    @command << "-sortbysize #{@infile}"
+    @command << "-output #{@infile}.sort"
 
                execute
 
@@ -64,7 +68,11 @@ class Usearch
   # 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}"
+    @command << "usearch"
+    @command << "-cluster_fast #{@infile}"
+    @command << "-id #{@options[:identity]}"
+    @command << "-uc #{@outfile}"
+    @command << "-threads #{@options[:cpus]}"
 
     execute
   end
@@ -73,21 +81,49 @@ class Usearch
   # 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 << "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[:identity]
-    @command << "--evalue #{@options[:e_val]}" if @options[: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
+    execute
+  end
+
+  # 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.
@@ -147,17 +183,24 @@ class Usearch
     record = {}
 
     File.open(@outfile, "r") do |ios|
-      ios.gets   # skip comment line
       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