Commit df700863 by Celine Mercier

New command: obi export

parent 32d8396e
# from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
# from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
# from obitools3.utils cimport bytes2str
#
# import time
# import re
#
#
# __title__="Export a NUC_SEQS view to a fasta or fastq file"
#
#
# default_config = { 'inputview' : None,
# }
#
# def addOptions(parser):
#
# # TODO put this common group somewhere else but I don't know where
# group=parser.add_argument_group('DMS and view options')
#
# group.add_argument('--default-dms','-d',
# action="store", dest="obi:defaultdms",
# metavar='<DMS NAME>',
# default=None,
# type=str,
# help="Name of the default DMS for reading and writing data.")
#
# group.add_argument('--input-view','-i',
# action="store", dest="obi:inputview",
# metavar='<INPUT VIEW NAME>',
# default=None,
# type=str,
# help="Name of the input view, either raw if the view is in the default DMS,"
# " or in the form 'dms:view' if it is in another DMS.")
#
# group=parser.add_argument_group('obi export specific options')
#
# group.add_argument('--format','-f',
# action="store", dest="export:format",
# metavar='<FORMAT>',
# default="fasta",
# type=str,
# help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.") # TODO export in csv
#
#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.apps.optiongroups import addMinimalInputOption, \
addExportOutputOption
__title__="Export a view to a different file format"
def addOptions(parser):
addMinimalInputOption(parser)
addExportOutputOption(parser)
def run(config):
pass
#
# # TODO import doesn't work
# NUC_SEQUENCE_COLUMN = "NUC_SEQ"
# ID_COLUMN = "ID"
# DEFINITION_COLUMN = "DEFINITION"
# QUALITY_COLUMN = "QUALITY"
#
# special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
#
# # Open DMS
# d = OBIDMS(config['obi']['defaultdms'])
#
# # Open input view
# iview = d.open_view(config['obi']['inputview'])
#
# print(iview.type)
#
# # TODO check that the view has the type NUC_SEQS
# if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") : # TODO find a way to import those macros
# raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
#
# # Initialize the progress bar
# pb = ProgressBar(len(iview), config, seconde=5)
#
# i=0
# for seq in iview :
# pb(i)
#
# toprint = ">"+seq.id+" "
#
# for col_name in seq :
# if col_name not in special_columns :
# toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
#
# if DEFINITION_COLUMN in seq :
# toprint = toprint + seq.definition
#
# nucseq = bytes2str(seq.nuc_seq)
#
# if config['export']['format'] == "fasta" :
# nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
#
# toprint = toprint + "\n" + nucseq
#
# if config['export']['format'] == "fastq" :
# toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
#
# print(toprint)
# i+=1
#
# iview.close()
# d.close()
#
# print("Done.")
#
#
#
#
#
#
#
#
\ No newline at end of file
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]
# 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")
# Initialize the progress bar
pb = ProgressBar(len(iview), config, seconde=5)
i=0
for seq in iview :
pb(i)
try:
writer(seq)
except StopIteration:
break
i+=1
# TODO save command in input dms?
output_object.close()
iview.close()
input[0].close()
logger("info", "obi export: Done")
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