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python: genbank parser: better handling of white spaces

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This commit is contained in:
mercierc
2021-09-13 11:44:38 +12:00
parent f43856b712
commit 2d66e0e965
1 changed files with 7 additions and 7 deletions
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10
python/obitools3/parsers/genbank.pyx
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@ -22,11 +22,11 @@ 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(\s*))',re.DOTALL + re.M)
_headerMatcher = re.compile(b'^LOCUS.+(?=\nFEATURES)', re.DOTALL + re.M)
_seqMatcher = re.compile(b'^ORIGIN .+(?=//\n)', re.DOTALL + re.M)
_cleanSeq1 = re.compile(b'ORIGIN.+\n')
_seqMatcher = re.compile(b'^ORIGIN.+(?=//\n)', re.DOTALL + re.M)
_cleanSeq1 = re.compile(b'ORIGIN(\s*)\n')
_cleanSeq2 = re.compile(b'[ \n0-9]+')
_acMatcher = re.compile(b'(?<=^ACCESSION ).+',re.M)
_deMatcher = re.compile(b'(?<=^DEFINITION ).+\n( .+\n)*',re.M)
@ -155,9 +155,9 @@ def genbankIterator_file(lineiterator,
yield seq
read+=1
# Last sequence
# Last sequence if not empty lines
if entry.strip():
seq = genbankParser(entry)
yield seq
free(entry)