tests/should-vdj-to-tap.py, curly braces { } patterns

Will be used to test CDR3/JUNCTION detection.

tests/should-vdj-to-tap.py, curly braces { } patterns
Will be used to test CDR3/JUNCTION detection.
b323bbc0 · Mathieu Giraud · f16dcf0a · b323bbc0
Commit b323bbc0 authored Feb 28, 2016 by Mathieu Giraud
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algo/tests/should-vdj-to-tap.py algo/tests/should-vdj-to-tap.py +7 -0

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--- a/algo/tests/should-vdj-to-tap.py
+++ b/algo/tests/should-vdj-to-tap.py
@@ -99,6 +99,13 @@ def should_pattern_to_regex(p):
        if term.startswith('#'):
            continue

+        # (such as CDR3 / junction)
+        if term.startswith('{'):
+            term = term.replace('*','[*]').replace('!','#')
+            term = term.replace('{', '.*[{].*').replace('}', '.*[}]')
+            r += [term]
+            continue
+
        # deletion/insertion/deletion
        # Note that '/' may be also in gene name, such as in IGKV1/OR-3*01
        if term.count('/') == 2: