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#cython: language_level=3
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from obitools3.dms import DMS
from obitools3.dms.obiseq import Nuc_Seq
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
from obitools3.writers.tab import TabWriter
from obitools3.format.tab import TabFormat
from obitools3.utils cimport tobytes, tostr
from obitools3.apps.optiongroups import addMinimalInputOption, \
addExportOutputOption, \
addNoProgressBarOption
import sys
import io
from cpython.exc cimport PyErr_CheckSignals
__title__="Export a view to a different file format"
def addOptions(parser):
addMinimalInputOption(parser)
addExportOutputOption(parser)
addNoProgressBarOption(parser)
def run(config):
DMS.obi_atexit()
logger("info", "obi export : exports a view to a different file format")
# Open the input
input = open_uri(config['obi']['inputURI'])
if input is None:
raise Exception("Could not read input")
iview = input[1]
if 'outputformat' not in config['obi']:
if iview.type == b"NUC_SEQS_VIEW":
if QUALITY_COLUMN in iview:
config['obi']['outputformat'] = b'fastq'
else:
config['obi']['outputformat'] = b'fasta'
else:
config['obi']['outputformat'] = b'tabular'
# Open the output
output = open_uri(config['obi']['outputURI'],
input=False)
if output is None:
raise Exception("Could not open output URI")
output_object = output[0]
writer = output[1]
# Check that the input view has the type NUC_SEQS if needed # TODO discuss, maybe bool property
if (output[2] == Nuc_Seq) and (iview.type != b"NUC_SEQS_VIEW") : # Nuc_Seq_Stored? TODO
raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
if config['obi']['only'] is not None:
withoutskip = min(input[4], config['obi']['only'])
else:
withoutskip = input[4]
if config['obi']['skip'] is not None:
skip = min(input[4], config['obi']['skip'])
else:
skip = 0
# Initialize the progress bar
if config['obi']['noprogressbar']:
pb = None
else:
pb = ProgressBar(withoutskip - skip, config)
if config['obi']['outputformat'] == b'metabaR':
# Check prefix
if "metabarprefix" not in config["obi"]:
raise Exception("Prefix needed when exporting for metabaR (--metabaR-prefix option)")
else:
metabaRprefix = config["obi"]["metabarprefix"]
i=0
for seq in iview :
PyErr_CheckSignals()
if pb is not None:
pb(i)
try:
writer(seq)
except (StopIteration, BrokenPipeError, IOError):
break
i+=1
if pb is not None:
pb(i, force=True)
print("", file=sys.stderr)
if config['obi']['outputformat'] == b'metabaR':
# Export ngsfilter file if view provided
if 'metabarngsfilter' in config['obi']:
ngsfilter_input = open_uri(config['obi']['metabarngsfilter'])
if ngsfilter_input is None:
raise Exception("Could not read ngsfilter view for metabaR output")
ngsfilter_view = ngsfilter_input[1]
ngsfilter_output = open(config['obi']['metabarprefix']+'.ngsfilter', 'w')
for line in ngsfilter_view:
line_to_print = b""
line_to_print += line[b'experiment']
line_to_print += b"\t"
line_to_print += line[b'sample']
line_to_print += b"\t"
line_to_print += line[b'forward_tag']
line_to_print += b":"
line_to_print += line[b'reverse_tag']
line_to_print += b"\t"
line_to_print += line[b'forward_primer']
line_to_print += b"\t"
line_to_print += line[b'reverse_primer']
line_to_print += b"\t"
line_to_print += line[b'additional_info']
print(tostr(line_to_print), file=ngsfilter_output)
if ngsfilter_input[0] != input[0]:
ngsfilter_input[0].close()
ngsfilter_output.close()
# Export sample metadata
samples_output = open(config['obi']['metabarprefix']+'_samples.csv', 'w')
# Export sample metadata file if view provided
if 'metabarsamples' in config['obi']:
samples_input = open_uri(config['obi']['metabarsamples'])
if samples_input is None:
raise Exception("Could not read sample view for metabaR output")
samples_view = samples_input[1]
# Export with tab formatter
TabWriter(TabFormat(header=True, sep='\t',),
samples_output,
header=True)
if samples_input[0] != input[0]:
samples_input[0].close()
# Else export just sample names from main view
else:
sample_list = []
if 'MERGED_sample' in iview:
sample_list = iview['MERGED_sample'].keys()
elif 'sample' not in iview:
for seq in iview:
sample = seq['sample']
if sample not in sample_list:
sample_list.append(sample)
else:
logger("warning", "Can not read sample list from main view for metabaR sample list export")
print("sample_id", file=samples_output)
for sample in sample_list:
line_to_print = b""
line_to_print += sample
line_to_print += b"\t"
print(tostr(line_to_print), file=samples_output)
samples_output.close()
# TODO save command in input dms?
if not BrokenPipeError and not IOError:
output_object.close()
iview.close()
input[0].close(force=True)
logger("info", "Done.")
if BrokenPipeError or IOError:
sys.stderr.close()
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