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Cython API: obi import can now import ngsfilter files and tabular files

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Celine Mercier
2018-03-12 18:10:43 +01:00
parent 8a0b95c1d6
commit 15e43bb9a1
9 changed files with 168 additions and 142 deletions
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46
python/obitools3/parsers/header.pyx
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@ -6,54 +6,12 @@ Created on 25 mars 2016
@author: coissac
'''
from obitools3.utils cimport __etag__
import re
__ret__ = re.compile('''(([^ ]+)=('[^']*'|"[^"]*"|[^;]+); *)+?''')
__re_int__ = re.compile("^[+-]?[0-9]+$")
__re_float__ = re.compile("^[+-]?[0-9]+(\.[0-9]*)?([eE][+-]?[0-9]+)?$")
__re_str__ = re.compile("""^"[^"]*"|'[^']*'$""")
__re_dict__ = re.compile("""^\{\ *
(
("[^"]*"|'[^']*')
\ *:\ *
([^,}]+|
"[^"]*"|
'[^']*'
)
)?
(\ *,\ *
("[^"]*"|'[^']*')
\ *:\ *
([^,}]+|
"[^"]*"|
'[^']*'
)
)*\ *\}$""", re.VERBOSE)
__re_val__ = re.compile("""(("[^"]*"|'[^']*') *: *([^,}]+|"[^"]*"|'[^']*') *[,}] *)""")
__ret__ = re.compile('''(([^ ]+)=('[^']*'|"[^"]*"|[^;]+); *)+?''')
cdef object __etag__(str x):
cdef list elements
cdef tuple i
if __re_int__.match(x):
v=int(x)
elif __re_float__.match(x):
v=float(x)
elif __re_str__.match(x):
v=x[1:-1]
elif x=='None':
v=None
elif x=='False':
v=False
elif x=='True':
v=True
elif __re_dict__.match(x):
elements=__re_val__.findall(x)
v=dict([(i[1][1:-1],__etag__(i[2])) for i in elements])
else:
v=x
return v
cpdef tuple parseHeader(str header):
cdef list m