args << "scan_for_matches"
args << "-c" if options[:comp]
args << "-p" if options[:seq_type] == :protein
args << "scan_for_matches"
args << "-c" if options[:comp]
args << "-p" if options[:seq_type] == :protein
- args << "-o" if options[:overlap]
+ args << "-o 1" if options[:overlap]
args << "-n #{options[:max_misses]}" if options[:max_misses]
args << "-m #{options[:max_hits]}" if options[:max_hits]
args << File.join(@tmp_dir, "#{i}.pat")
args << "-n #{options[:max_misses]}" if options[:max_misses]
args << "-m #{options[:max_hits]}" if options[:max_hits]
args << File.join(@tmp_dir, "#{i}.pat")
-SEQ_NAME: test1
-SEQ: LLRVDNIIRARPRTANRQHM
+SEQ_NAME: test
+SEQ: GGACTACNNGGGTATCTAATAGTC
SEQ_LEN: 20
---
REC_TYPE: PATSCAN
SEQ_LEN: 20
---
REC_TYPE: PATSCAN
-S_ID: test1
-Q_ID: RARP
-MATCH: RARP
-S_BEG: 8
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 0
+S_END: 1
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 9
+S_END: 10
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test
+Q_ID: GG
+MATCH: GG
+S_BEG: 10
S_END: 11
STRAND: +
SCORE: 100
S_END: 11
STRAND: +
SCORE: 100
-SEQ: NIIRARPRTAN
-SEQ_LEN: 11
+SEQ: GGACTACNNGGGTATCTAATGCATACG
+SEQ_LEN: 27
---
REC_TYPE: PATSCAN
S_ID: test2
---
REC_TYPE: PATSCAN
S_ID: test2
-Q_ID: RARP
-MATCH: RARP
-S_BEG: 3
-S_END: 6
+Q_ID: GG
+MATCH: GG
+S_BEG: 0
+S_END: 1
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: GG
+MATCH: GG
+S_BEG: 9
+S_END: 10
+STRAND: +
+SCORE: 100
+MATCH_LEN: 2
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: GG
+MATCH: GG
+S_BEG: 10
+S_END: 11
SEQ_NAME: test1
SEQ: LLRVDNIIRARPRTANRQHM
SEQ_LEN: 20
SEQ_NAME: test1
SEQ: LLRVDNIIRARPRTANRQHM
SEQ_LEN: 20
+---
+REC_TYPE: PATSCAN
+S_ID: test1
+Q_ID: RARP
MATCH: RARP
S_BEG: 8
S_END: 11
STRAND: +
MATCH: RARP
S_BEG: 8
S_END: 11
STRAND: +
MATCH_LEN: 4
---
SEQ_NAME: test2
SEQ: NIIRARPRTAN
SEQ_LEN: 11
MATCH_LEN: 4
---
SEQ_NAME: test2
SEQ: NIIRARPRTAN
SEQ_LEN: 11
+---
+REC_TYPE: PATSCAN
+S_ID: test2
+Q_ID: RARP
MATCH: RARP
S_BEG: 3
S_END: 6
STRAND: +
MATCH: RARP
S_BEG: 3
S_END: 6
STRAND: +
--- /dev/null
+KEY: VALUE
+---
+SEQ_NAME: test1
+SEQ: LLRVDNIIRARPRTANRQHM
+SEQ_LEN: 20
+PATTERN: RARP
+MATCH: RARP
+S_BEG: 8
+S_END: 11
+STRAND: +
+MATCH_LEN: 4
+---
+SEQ_NAME: test2
+SEQ: NIIRARPRTAN
+SEQ_LEN: 11
+PATTERN: RARP
+MATCH: RARP
+S_BEG: 3
+S_END: 6
+STRAND: +
+MATCH_LEN: 4
+---
assert_no_diff $tmp $out.3
clean
assert_no_diff $tmp $out.3
clean
-run "$bp -I $in.2 -p RARP -O $tmp"
+run "$bp -I $in.1 -o -p GG -O $tmp"
assert_no_diff $tmp $out.4
clean
assert_no_diff $tmp $out.4
clean
-run "$bp -I $in.2 -p RARP -i -O $tmp"
+run "$bp -I $in.2 -p RARP -O $tmp"
assert_no_diff $tmp $out.5
clean
assert_no_diff $tmp $out.5
clean
+
+run "$bp -I $in.2 -p RARP -i -O $tmp"
+assert_no_diff $tmp $out.6
+clean