added tests for uclust_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1668 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/uclust_seq.in b/bp_test/in/uclust_seq.in
new file mode 100644 (file)
index 0000000..b53c0ae
--- /dev/null
+++ b/bp_test/in/uclust_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/out/uclust_seq.out.1 b/bp_test/out/uclust_seq.out.1
new file mode 100644 (file)
index 0000000..6a64040
--- /dev/null
+++ b/bp_test/out/uclust_seq.out.1
@@ -0,0 +1,42 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: *
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 100
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 96
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: *
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: 100
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: 96
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: *
+---

diff --git a/bp_test/out/uclust_seq.out.2 b/bp_test/out/uclust_seq.out.2
new file mode 100644 (file)
index 0000000..92997a0
--- /dev/null
+++ b/bp_test/out/uclust_seq.out.2
@@ -0,0 +1,42 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: *
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 100
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: *
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: *
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: 100
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 3
+IDENT: *
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+CLUSTER: 4
+IDENT: *
+---

diff --git a/bp_test/out/uclust_seq.out.3 b/bp_test/out/uclust_seq.out.3
new file mode 100644 (file)
index 0000000..d4b8e23
--- /dev/null
+++ b/bp_test/out/uclust_seq.out.3
@@ -0,0 +1,42 @@
+SEQ_NAME: test1
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: *
+---
+SEQ_NAME: test1_100
+SEQ: tgtacgtagctagctagctagctagctagctagctagctagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 100
+---
+SEQ_NAME: test1_2
+SEQ: tgtacgtagctagctagctagctagcGagctagctagcAagctgactatcgtgatcgtg
+SEQ_LEN: 59
+CLUSTER: 1
+IDENT: *
+---
+SEQ_NAME: test2
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: *
+---
+SEQ_NAME: test2_100
+SEQ: ggttgtgtgtgtgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 2
+IDENT: 100
+---
+SEQ_NAME: test2_1
+SEQ: ggtAgtgtgtgAgtatcgatgtagtctacatcgtctatctgtactgacttactgactac
+SEQ_LEN: 59
+CLUSTER: 3
+IDENT: *
+---
+SEQ_NAME: test1_rc
+SEQ: cacgatcacgatagtcagctagctagctagctagctagctagctagctagctacgtaca
+SEQ_LEN: 59
+CLUSTER: 0
+IDENT: 100
+---

diff --git a/bp_test/test/test_uclust_seq b/bp_test/test/test_uclust_seq
new file mode 100755 (executable)
index 0000000..583737b
--- /dev/null
+++ b/bp_test/test/test_uclust_seq
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in -i 1 -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -I $in -i 1 -c -O $tmp"
+assert_no_diff $tmp $out.3
+clean

diff --git a/code_ruby/lib/maasha/backtrack.rb b/code_ruby/lib/maasha/backtrack.rb
index f5e581b802df1da0d63b28f3e1c5703476fe7e90..c47f97ebbf84562b38af7bd15125eac36c811ad7 100644 (file)
--- a/code_ruby/lib/maasha/backtrack.rb
+++ b/code_ruby/lib/maasha/backtrack.rb
@@ -32,7 +32,8 @@ class BackTrackError < StandardError; end
 # pattern match engine is based on a backtrack algorithm.
 # Insertions are nucleotides found in the pattern but not in the sequence.
 # Deletions are nucleotides found in the sequence but not in the pattern.
-# Algorithm based on code kindly provided by j_random_hacker @ Stackoverflow.
+# Algorithm based on code kindly provided by j_random_hacker @ Stackoverflow:
+# http://stackoverflow.com/questions/7557017/approximate-string-matching-using-backtracking/
 module BackTrack
   OK_PATTERN = Regexp.new('^[flsycwphqrimtnkvadegu]+$')
   MAX_MIS    = 5 # Maximum number of mismatches allowed