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Cython: added possibility to output in tabular format

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This commit is contained in:
Celine Mercier
2019-03-31 15:39:38 +02:00
parent e39c1a7fbf
commit 2b8c066f8e
2 changed files with 35 additions and 7 deletions
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27
python/obitools3/apps/optiongroups/__init__.py
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@ -115,9 +115,9 @@ def __addImportInputOption(optionManager):
type=str,
help="String associated with Non Available (NA) values in the input")
def __addTabularInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for tabular files")
def __addTabularOption(optionManager):
group = optionManager.add_argument_group("Input and output format options for tabular files")
group.add_argument('--header',
action="store_true", dest="obi:header",
@ -126,9 +126,15 @@ def __addTabularInputOption(optionManager):
group.add_argument('--sep',
action="store", dest="obi:sep",
default=None,
default="\t",
type=str,
help="Column separator")
def __addTabularInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for tabular files")
__addTabularOption(optionManager)
group.add_argument('--dec',
action="store", dest="obi:dec",
@ -244,6 +250,12 @@ def __addExportOutputOption(optionManager):
const=b'fastq',
help="Output file is in fastq format")
group.add_argument('--tab-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'tabular',
help="Output file is in tabular format")
group.add_argument('--print-na',
action="store_true", dest="obi:printna",
default=False,
@ -260,13 +272,20 @@ def addMinimalOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
def addTabularOutputOption(optionManager):
__addTabularOption(optionManager)
def addExportOutputOption(optionManager):
__addOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)
def addAllOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)

15
python/obitools3/uri/decode.pyx
View File

@ -15,14 +15,18 @@ from obitools3.parsers.universal import entryIteratorFactory
from obitools3.writers.fasta import FastaNucWriter
from obitools3.writers.fastq import FastqWriter
from obitools3.writers.tab import TabWriter
from obitools3.format.fasta import FastaFormat
from obitools3.format.fastq import FastqFormat
from obitools3.format.tab import TabFormat
from obitools3.dms.obiseq import Nuc_Seq
from obitools3.apps.config import getConfiguration,logger
from obitools3.apps.temp import get_temp_dms
from obitools3.utils cimport tobytes, count_entries # TODO tobytes because can't read options as bytes
from obitools3.files.universalopener cimport uopen
from obitools3.dms.capi.obierrno cimport obi_errno, \
OBIVIEW_ALREADY_EXISTS_ERROR
@ -283,17 +287,18 @@ def open_uri(uri,
format=config["obi"][formatkey]
except KeyError:
format=None
if b'seqtype' in qualifiers:
seqtype=qualifiers[b'seqtype'][0]
else:
if format == b"ngsfilter": # TODO discuss
if format == b"ngsfilter" or format == b"tabular": # TODO discuss
seqtype=None
else:
try:
seqtype=config["obi"]["seqtype"]
except KeyError:
seqtype=b"nuc"
config["obi"]["seqtype"] = seqtype
if b'skip' in qualifiers:
skip=int(qualifiers[b"skip"][0])
@ -504,7 +509,11 @@ def open_uri(uri,
skip = skip,
only = only)
else:
raise NotImplementedError('Output sequence file format not implemented')
iseq = TabWriter(TabFormat(header=header, NAString=nastring, sep=sep),
file,
skip=skip,
only=only,
header=header)
elif format==b"ngsfilter":
objclass = dict
if input: