import: improved genbank parser and switch to version 3.0.0b42

python/obitools3/commands/test.pyx

@@ -442,7 +442,7 @@ def addOptions(parser):
                        default=20,
                        type=int,
                        help="Maximum length of tuples. "
-                            "Default: 50")
+                            "Default: 20")
   
     group.add_argument('--max_ini_col_count','-o',
                        action="store", dest="test:maxinicolcount",
@@ -455,7 +455,7 @@ def addOptions(parser):
     group.add_argument('--max_line_nb','-l',
                        action="store", dest="test:maxlinenb",
                        metavar='<MAX_LINE_NB>',
-                       default=10000,
+                       default=1000,
                        type=int,
                        help="Maximum number of lines in a column. "
                             "Default: 1000")

python/obitools3/dms/view/view.pyx

@@ -805,7 +805,7 @@ cdef class Line :
 
 
     def __repr__(self):
-        return bytes2str(self).repr_bytes()
+        return bytes2str(self.repr_bytes())
 
 
     cpdef repr_bytes(self):

python/obitools3/parsers/genbank.pyx

@@ -22,10 +22,10 @@ from libc.stdlib  cimport free, malloc, realloc
 from libc.string cimport strcpy, strlen
 
 
-_featureMatcher = re.compile(b'^FEATURES.+\n(?=ORIGIN)',re.DOTALL + re.M)
+_featureMatcher = re.compile(b'^FEATURES.+\n(?=ORIGIN )',re.DOTALL + re.M)
 
 _headerMatcher = re.compile(b'^LOCUS.+(?=\nFEATURES)', re.DOTALL + re.M)
-_seqMatcher    = re.compile(b'ORIGIN.+(?=//\n)', re.DOTALL + re.M)
+_seqMatcher    = re.compile(b'ORIGIN .+(?=//\n)', re.DOTALL + re.M)
 _cleanSeq1     = re.compile(b'ORIGIN.+\n')
 _cleanSeq2     = re.compile(b'[ \n0-9]+')
 _acMatcher     = re.compile(b'(?<=^ACCESSION   ).+',re.M)

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0b40'
+serial= '0b42'
 
 version ="%d.%d.%s" % (major,minor,serial)