Merge branch 'dev' into feature/evalue-d

algo/tests/should-get-tests/example_mouse.should-get

+!LAUNCH: $VIDJIL_DIR/vidjil $VIDJIL_DEFAULT_OPTIONS -c segment -g $VIDJIL_DIR/germline/mus-musculus.g $VIDJIL_DIR/data/example_mouse.fa
+
+$ Segment sequence on IGK
+1:segIGK.*IGKV.*IGKJ
+
+$ Segment sequence on IGH
+1:segIGH.*IGHV.*IGHD.*IGHJ
+
+$ Segment sequence on IGL
+1:segIGL.*IGLV.*IGLJ

algo/tests/should-vdj-to-tap.py

@@ -217,8 +217,8 @@ def should_result_to_tap(should_pattern, result, tap_id):
         should_regex = should_pattern_to_regex(should_pattern)
         # match = should_regex.search(result)
         match = os.system("echo '%s' | grep -E '%s' > /dev/null 2>&1" \
-                          % (result.replace("'", "\\'"),
-                             should_regex.pattern.replace("'", "\\'")))
+                          % (result.replace("'", "'\\''"),
+                             should_regex.pattern.replace("'", "'\\''")))
         found = (match == 0)
 
     globals()['global_stats'][locus] += 1

data/example_mouse.fa

+>segIGK
+GGGAGTCATTCTTGGTCAGGAGACGTTGTAGAAATGAGACCGTCTATTCAGTTCCTGGGG
+CTCTTGTTGTTCTGGCTTCATGGTGCTCAGTGTGACATCCAGATGACACAGTCTCCATCC
+TCACTGTCTGCATCTCTGGGAGGCAAAGTCACCATCACTTGCAAGGCAAGCCAAGACATT
+AACAAGTATATAGCTTGGTACCAACACAAGCCTGGAAAAGGTCCTAGGCTGCTCATACAT
+TACACATCTACATTACAGCCAGGCATCCCATCAAGGTTCAGTGGAAGTGGGTCTGGGAGA
+GATTATTCCTTCAGCATCAGCAACCTGGAGCCTGAAGATATTGCAACTTATTATTGTCTA
+CAGTATGATAATCTGTGGACGTTCGGTGGAGGCACCAAGCTGGAAATCAAACGGGCTGAT
+GCTGCACCAACTGTATCCATCTTCCCACCATCCAGTG
+>segIGH
+GGGAAGACATTTGGGAAGGACTGACTCTCTGAGGAGACTGTGAGAGTGGTGCCTTGGCCCCAGTAGTCAAAGTAGCTACTACCGTAGTAATCGTATCTTGCACAATAATAGACCGCAGAGTCCTCAGATGTCAGGCTGCTGAGCTGCATGTAGGCTGTGCTGGAGGGTTTGTCTACAGTCAGTGTGGCCTTGCTCTTGAACTTCTCATTGTACTTAGTACCACCACTATTAGGATCAATCCTTCCAATCCACTCAAGGCCTCGTCCAGGCCTCTGCTTCACCCAGTGCATCCAGTAGCTGGTGAAGGTGTAGCCAGAAGCCTTGCAGGACAGCTTCACTGAAGCCCCAGGCTTCACAAGCTCAGCCCCAGGCTGCTGCAGTTGGACCTGGGAGTGGACACCTGTAGCTGTTGCTACCAAGAAGAGGATGATACAGCTCCATCCCATAGTGAGGTCCTGTGTGCTCAGTAACTGTAAAGAGAACAGTGATCTCAACCCGTATTTATGAAGTGAAGTATT
+>segIGL
+GAGAGTGGGAGTGGACTTGGGCTGACCTAGGACAGTGACCTTGGTTCCACTGCCGAAAATAAATGGTTGCTGTACCATAGAGCACAGAAATATATTGCCTCATCCTCAGTCTGTGCCCCTGTGATGGTGAGGGCAGCCTTGTCTCCAATCAGGGAGCCTGAGAATCTGGCAGGAACACCTGGAGCTCGGTTGTTGGTACCACCTATTAGACCAGTGAATAAATGATCTGGTTTTTCTTGGACCCAGTTGGCATAGTTACTAGTTGTAACAGCCCCAGTACTTGAGCGACAAGTGAGTGTGACTGTTTCACCAGGTGATGTGGTGAGTGCAGATTCGTGAGTCACAACAGCCTGGGAAATGGCCCCTGAGCTGAGAGCCAGGAGAGAGAGTATAAGTGAAATCCAGGCCATAATTCACAAACCAGGTCTATTCTTTTCAATATTGGTCCCCCGTAGATCGGTGTATTCACATTGTC
\ No newline at end of file

germline/germline_id

-40
+46