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Python: URI decoding: added metabaR output

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This commit is contained in:
mercierc
2021-11-02 11:16:29 +13:00
parent fedacfafe7
commit 405e6ef420
1 changed files with 28 additions and 5 deletions
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33
python/obitools3/uri/decode.pyx
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@ -277,7 +277,12 @@ def open_uri(uri,
iseq = urib iseq = urib
objclass = bytes objclass = bytes
else: # TODO update uopen to be able to write? else: # TODO update uopen to be able to write?
if not urip.path or urip.path == b'-': if config['obi']['outputformat'] == b'metabaR':
if 'metabarprefix' not in config['obi']:
raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
else:
file = open(config['obi']['metabarprefix']+'.tab', 'wb')
elif not urip.path or urip.path == b'-':
file = sys.stdout.buffer file = sys.stdout.buffer
else: else:
file = open(urip.path, 'wb') file = open(urip.path, 'wb')
@ -299,11 +304,11 @@ def open_uri(uri,
format=config["obi"][formatkey] format=config["obi"][formatkey]
except KeyError: except KeyError:
format=None format=None
if b'seqtype' in qualifiers: if b'seqtype' in qualifiers:
seqtype=qualifiers[b'seqtype'][0] seqtype=qualifiers[b'seqtype'][0]
else: else:
if format == b"ngsfilter" or format == b"tabular": # TODO discuss if format == b"ngsfilter" or format == b"tabular" or format == b"metabaR": # TODO discuss
seqtype=None seqtype=None
else: else:
try: try:
@ -437,7 +442,7 @@ def open_uri(uri,
try: try:
na_int_to_0=config["obi"]["na_int_to_0"] na_int_to_0=config["obi"]["na_int_to_0"]
except KeyError: except KeyError:
if format==b"tabular": if format==b"tabular" or format==b"metabaR":
na_int_to_0=True na_int_to_0=True
else: else:
na_int_to_0=False na_int_to_0=False
@ -487,6 +492,13 @@ def open_uri(uri,
except KeyError: except KeyError:
only_keys=[] only_keys=[]
if b"metabaR_prefix" in qualifiers:
metabaR_prefix = tobytes(qualifiers[b"metabaR_prefix"][0][0])
else:
try:
metabaR_prefix = tobytes(config["obi"]["metabarprefix"])
except KeyError:
metabaR_prefix=None
if format is not None: if format is not None:
if seqtype==b"nuc": if seqtype==b"nuc":
@ -552,6 +564,17 @@ def open_uri(uri,
skip=skip, skip=skip,
only=only, only=only,
header=header) header=header)
elif format==b"metabaR":
print(file)
objclass = dict
if input:
raise NotImplementedError('Input data file format not implemented')
else:
iseq = TabWriter(TabFormat(tags=only_keys, header=header, NAString=nastring, sep=sep, NAIntTo0=na_int_to_0, metabaR=True),
file,
skip=skip,
only=only,
header=header)
elif format==b"ngsfilter": elif format==b"ngsfilter":
objclass = dict objclass = dict
if input: if input:
@ -565,7 +588,7 @@ def open_uri(uri,
skip = skip, skip = skip,
only = only) only = only)
else: else:
raise NotImplementedError('Output sequence file format not implemented') raise NotImplementedError('Output data file format not implemented')
else: else:
if input: if input:
iseq, objclass, format = entryIteratorFactory(file, iseq, objclass, format = entryIteratorFactory(file,