# HG changeset patch
# User bgruening
# Date 1426839342 14400
# Node ID e861182a8034a266ce8e3e95209a55790c804ec1
# Parent 1014a3941218557c9cc7e80743009e25c1c185d7
Uploaded
diff -r 1014a3941218 -r e861182a8034 find_subsequences.xml
--- a/find_subsequences.xml Thu Mar 19 19:02:21 2015 -0400
+++ b/find_subsequences.xml Fri Mar 20 04:15:42 2015 -0400
@@ -8,7 +8,7 @@
find_subsequences.py
--input $input
--output $output
- --pattern "$pattern"
+ --pattern "$pattern_conditional.pattern"
#if $input.ext == 'fasta':
--format 'fasta'
#else:
@@ -19,9 +19,240 @@
-
- ^[a-zA-Z]+$
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@@ -43,7 +282,7 @@
**What it does**
-Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamH1.
+Searches for a subsequence in a larger sequence. For example to get all restriction enzymes for BamHI.
If you are searching in a DNA sequence you can use ambiguous values using the standard
`nucleotide ambiguity code `_.
diff -r 1014a3941218 -r e861182a8034 test-data/find_subsequences_advanced_result1.bed
--- a/test-data/find_subsequences_advanced_result1.bed Thu Mar 19 19:02:21 2015 -0400
+++ b/test-data/find_subsequences_advanced_result1.bed Fri Mar 20 04:15:42 2015 -0400
@@ -1,2 +1,2 @@
-forward_advanced 9 15 +
-reverse_advanced 9 15 -
+forward_advanced 9 15 forward_advanced +
+reverse_advanced 9 15 reverse_advanced -
diff -r 1014a3941218 -r e861182a8034 test-data/find_subsequences_simple_result1.bed
--- a/test-data/find_subsequences_simple_result1.bed Thu Mar 19 19:02:21 2015 -0400
+++ b/test-data/find_subsequences_simple_result1.bed Fri Mar 20 04:15:42 2015 -0400
@@ -1,3 +1,3 @@
-forward_simple 9 13 +
-forward_simple 5 9 -
-reverse_simple 6 10 -
+forward_simple 9 13 forward_simple +
+forward_simple 5 9 forward_simple -
+reverse_simple 6 10 reverse_simple -
diff -r 1014a3941218 -r e861182a8034 test-data/find_subsequences_simple_result2.bed