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Cython: added full handling of NA strings when importing files

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This commit is contained in:
Celine Mercier
2018-10-17 16:41:15 +02:00
parent da76f911db
commit da0e3d4043
11 changed files with 43 additions and 32 deletions
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8
python/obitools3/uri/decode.pyx
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@ -425,7 +425,8 @@ def open_uri(uri,
if input:
iseq = fastaNucIterator(file,
skip=skip,
only=only)
only=only,
nastring=nastring)
else:
iseq = FastaNucWriter(FastaFormat(printNAKeys=printna, NAString=nastring),
file,
@ -437,7 +438,8 @@ def open_uri(uri,
skip=skip,
only=only,
offset=offset,
noquality=noquality)
noquality=noquality,
nastring=nastring)
else:
iseq = FastqWriter(FastqFormat(printNAKeys=printna, NAString=nastring),
file,
@ -464,6 +466,7 @@ def open_uri(uri,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only)
else:
@ -477,6 +480,7 @@ def open_uri(uri,
stripwhite = stripwhite,
blanklineskip = blanklineskip,
commentchar = commentchar,
nastring=nastring,
skip = skip,
only = only)
else: