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|
#cython: language_level=3
import sys
import os
import re
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms.view.view cimport View
from obitools3.dms.view import RollbackException
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.column.column cimport Column
from obitools3.dms.obiseq cimport Nuc_Seq
from obitools3.dms import DMS
from obitools3.dms.taxo.taxo cimport Taxonomy
from obitools3.files.uncompress cimport CompressedFile
from obitools3.utils cimport tobytes, \
tostr, \
get_obitype, \
update_obitype
from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN, \
COUNT_COLUMN, \
TAXID_COLUMN, \
MERGED_PREFIX, \
SCIENTIFIC_NAME_COLUMN
from obitools3.dms.capi.obidms cimport obi_import_view
from obitools3.dms.capi.obitypes cimport obitype_t, \
OBI_VOID, \
OBI_QUAL, \
OBI_STR, \
OBI_INT
from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.apps.optiongroups import addImportInputOption, \
addTabularInputOption, \
addTaxdumpInputOption, \
addMinimalOutputOption, \
addNoProgressBarOption, \
addTaxonomyOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
from cpython.exc cimport PyErr_CheckSignals
from io import BufferedWriter
import ast
__title__="Import sequences from different formats into a DMS"
default_config = { 'destview' : None,
'skip' : 0,
'only' : None,
'skiperror' : False,
'seqinformat' : None,
'moltype' : 'nuc',
'source' : None
}
def addOptions(parser):
addImportInputOption(parser)
addTabularInputOption(parser)
addTaxdumpInputOption(parser)
addTaxonomyOption(parser)
addMinimalOutputOption(parser)
addNoProgressBarOption(parser)
group = parser.add_argument_group('obi import specific options')
group.add_argument('--preread',
action="store_true", dest="import:preread",
default=False,
help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
"a much faster import. This option is not recommended and will slow down the import in any other case.")
group.add_argument('--space-priority',
action="store_true", dest="import:space_priority",
default=False,
help="If importing a view into another DMS, do it by importing each line, saving disk space if the original view "
"has a line selection associated.")
# group.add_argument('--only-id',
# action="store", dest="import:onlyid",
# help="only id")
def run(config):
cdef tuple input
cdef tuple output
cdef int i
cdef type value_type
cdef obitype_t value_obitype
cdef obitype_t old_type
cdef obitype_t new_type
cdef bint get_quality
cdef bint NUC_SEQS_view
cdef bint silva
cdef bint rdp
cdef bint unite
cdef bint sintax
cdef int nb_elts
cdef object d
cdef View view
cdef object entries
cdef object entry
cdef Column id_col
cdef Column def_col
cdef Column seq_col
cdef Column qual_col
cdef Column old_column
cdef Column sci_name_col
cdef bytes sci_name
cdef bint rewrite
cdef dict dcols
cdef int skipping
cdef bytes tag
cdef object value
cdef list elt_names
cdef int old_nb_elements_per_line
cdef int new_nb_elements_per_line
cdef list old_elements_names
cdef list new_elements_names
cdef ProgressBar pb
global obi_errno
DMS.obi_atexit()
logger("info", "obi import: imports an object (file(s), obiview, taxonomy...) into a DMS")
entry_count = -1
pb = None
if not config['obi']['taxdump']:
input = open_uri(config['obi']['inputURI'])
if input is None: # TODO check for bytes instead now?
raise Exception("Could not open input URI")
if config['obi']['only'] is not None:
entry_count = min(input[4], config['obi']['only'])
else:
entry_count = input[4]
if entry_count > 0:
logger("info", "Importing %d entries", entry_count)
else:
logger("info", "Importing an unknown number of entries")
# TODO a bit dirty?
if input[2]==Nuc_Seq or input[2]==View_NUC_SEQS:
v = View_NUC_SEQS
else:
v = View
else:
v = None
if config['obi']['taxdump'] or (isinstance(input[1], View) and not config['import']['space_priority']):
dms_only=True
else:
dms_only=False
output = open_uri(config['obi']['outputURI'],
input=False,
newviewtype=v,
dms_only=dms_only)
if output is None:
raise Exception("Could not open output")
o_dms = output[0]
# Read taxdump
if config['obi']['taxdump']: # The input is a taxdump to import in a DMS
# Check if taxonomy name isn't already taken
taxo_name = output[1].split(b'/')[1]
if Taxonomy.exists(o_dms, taxo_name):
raise Exception("Taxonomy name already exists in this DMS")
taxo = Taxonomy.open_taxdump(o_dms, config['obi']['inputURI'])
taxo.write(taxo_name)
taxo.close()
o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close(force=True)
logger("info", "Done.")
return
# Open taxonomy if there is one
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
taxo_uri = open_uri(config['obi']['taxoURI'])
if taxo_uri is None or taxo_uri[2] == bytes:
raise Exception("Couldn't open taxonomy")
taxo = taxo_uri[1]
else :
taxo = None
# If importing a view between two DMS and not wanting to save space if line selection in original view, use C API
if isinstance(input[1], View) and not config['import']['space_priority']:
if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 :
input[0].close(force=True)
output[0].close(force=True)
raise Exception("Error importing a view in a DMS")
o_dms.record_command_line(" ".join(sys.argv[1:]))
input[0].close(force=True)
output[0].close(force=True)
logger("info", "Done.")
return
# Reinitialize the progress bar
if entry_count >= 0 and config['obi']['noprogressbar'] == False:
pb = ProgressBar(entry_count, config)
else:
pb = None
NUC_SEQS_view = False
if isinstance(output[1], View) :
view = output[1]
if output[2] == View_NUC_SEQS :
NUC_SEQS_view = True
else:
raise NotImplementedError()
# Save basic columns in variables for optimization
if NUC_SEQS_view :
id_col = view[ID_COLUMN]
def_col = view[DEFINITION_COLUMN]
seq_col = view[NUC_SEQUENCE_COLUMN]
# Prepare taxon scientific name and taxid refs if RDP/SILVA/UNITE/SINTAX formats
silva = False
rdp = False
unite = False
sintax=False
if 'inputformat' in config['obi'] and (config['obi']['inputformat'] == b"silva" or \
config['obi']['inputformat'] == b"rdp" or \
config['obi']['inputformat'] == b"unite" or \
config['obi']['inputformat'] == b"sintax"):
#if taxo is None:
# raise Exception("A taxonomy (as built by 'obi import --taxdump') must be provided for SILVA and RDP files")
if config['obi']['inputformat'] == b"silva":
silva = True
elif config['obi']['inputformat'] == b"rdp":
rdp = True
elif config['obi']['inputformat'] == b"unite":
unite = True
elif config['obi']['inputformat'] == b"sintax":
sintax = True
sci_name_col = Column.new_column(view, SCIENTIFIC_NAME_COLUMN, OBI_STR)
if taxo is not None:
taxid_col = Column.new_column(view, TAXID_COLUMN, OBI_INT)
dcols = {}
# First read through the entries to prepare columns with dictionaries as they are very time-expensive to rewrite
if config['import']['preread']:
logger("info", "First readthrough...")
entries = input[1]
i = 0
dict_dict = {}
for entry in entries:
PyErr_CheckSignals()
if entry is None: # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
if config['obi']['skiperror']:
i-=1
continue
else:
raise Exception("obi import error in first readthrough")
if pb is not None:
pb(i)
elif not i%50000:
logger("info", "Read %d entries", i)
for tag in entry :
newtag = tag
if tag[:7] == b"merged_":
newtag = MERGED_PREFIX+tag[7:]
if type(entry[tag]) == dict :
if tag in dict_dict:
dict_dict[newtag][0].update(entry[tag].keys())
else:
dict_dict[newtag] = [set(entry[tag].keys()), get_obitype(entry[tag])]
i+=1
if pb is not None:
pb(i, force=True)
print("", file=sys.stderr)
for tag in dict_dict:
dcols[tag] = (Column.new_column(view, tag, dict_dict[tag][1], \
nb_elements_per_line=len(dict_dict[tag][0]), \
elements_names=list(dict_dict[tag][0]), \
dict_column=True), \
dict_dict[tag][1])
# Reinitialize the input
if isinstance(input[0], CompressedFile):
input_is_file = True
# Reinitialize the progress bar
if entry_count >= 0 and config['obi']['noprogressbar'] == False:
pb = ProgressBar(entry_count, config)
else:
pb = None
try:
input[0].close()
except AttributeError:
pass
input = open_uri(config['obi']['inputURI'], force_file=input_is_file)
if input is None:
raise Exception("Could not open input URI")
# if 'onlyid' in config['import']:
# onlyid = tobytes(config['import']['onlyid'])
# else:
# onlyid = None
entries = input[1]
i = 0
for entry in entries :
PyErr_CheckSignals()
if entry is None: # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
if config['obi']['skiperror']:
continue
else:
raise RollbackException("obi import error, rollbacking view", view)
if pb is not None:
pb(i)
elif not i%50000:
logger("info", "Imported %d entries", i)
# if onlyid is not None and entry.id != onlyid:
# continue
try:
if NUC_SEQS_view:
id_col[i] = entry.id
def_col[i] = entry.definition
seq_col[i] = entry.seq
# Check if there is a sequencing quality associated by checking the first entry # TODO haven't found a more robust solution yet
if i == 0:
get_quality = QUALITY_COLUMN in entry
if get_quality:
Column.new_column(view, QUALITY_COLUMN, OBI_QUAL)
qual_col = view[QUALITY_COLUMN]
if get_quality:
qual_col[i] = entry.quality
# Parse taxon scientific name if RDP or Silva or Unite file
if (rdp or silva or unite or sintax):
if rdp or silva:
sci_names = entry.definition.split(b";")
sci_name_col[i] = sci_names[-1]
elif unite:
sci_names = entry.id.split(b'|')[-1].split(b';')
sci_name_col[i] = re.sub(b'[a-zA-Z]__', b'', sci_names[-1])
elif sintax:
reconstructed_line = entry.id+b' '+entry.definition[:-1]
splitted_reconstructed_line = reconstructed_line.split(b';')
taxa = splitted_reconstructed_line[1].split(b'=')[1]
taxa = splitted_reconstructed_line[1].split(b',')
sci_names = []
for t in taxa:
tf = t.split(b':')[1]
sci_names.append(tf)
sci_name_col[i] = sci_names[-1]
id_col[i] = reconstructed_line.split(b';')[0]
def_col[i] = reconstructed_line
# Fond taxid if taxonomy provided
if taxo is not None :
for sci_name in reversed(sci_names):
if unite:
sci_name = re.sub(b'[a-zA-Z]__', b'', sci_name)
if sci_name.split()[0] != b'unidentified' and sci_name.split()[0] != b'uncultured' and sci_name.split()[0] != b'metagenome':
taxon = taxo.get_taxon_by_name(sci_name)
if taxon is not None:
sci_name_col[i] = taxon.name
taxid_col[i] = taxon.taxid
#print(taxid_col[i], sci_name_col[i])
break
for tag in entry :
if tag != ID_COLUMN and tag != DEFINITION_COLUMN and tag != NUC_SEQUENCE_COLUMN and tag != QUALITY_COLUMN : # TODO dirty
value = entry[tag]
if tag == b"taxid":
tag = TAXID_COLUMN
if tag == b"count":
tag = COUNT_COLUMN
if tag == b"scientific_name":
tag = SCIENTIFIC_NAME_COLUMN
if tag[:7] == b"merged_":
tag = MERGED_PREFIX+tag[7:]
if type(value) == bytes and value[:1]==b"[" :
try:
if type(eval(value)) == list:
value = eval(value)
#print(value)
except:
pass
if tag not in dcols :
value_type = type(value)
nb_elts = 1
value_obitype = OBI_VOID
dict_col = False
if value_type == dict :
nb_elts = len(value)
elt_names = list(value)
dict_col = True
else :
nb_elts = 1
elt_names = None
if value_type == list :
tuples = True
else:
tuples = False
value_obitype = get_obitype(value)
if value_obitype != OBI_VOID :
dcols[tag] = (Column.new_column(view, tag, value_obitype, nb_elements_per_line=nb_elts, elements_names=elt_names, dict_column=dict_col, tuples=tuples), value_obitype)
# Fill value
dcols[tag][0][i] = value
# TODO else log error?
else :
rewrite = False
# Check type adequation
old_type = dcols[tag][1]
new_type = OBI_VOID
new_type = update_obitype(old_type, value)
if old_type != new_type :
rewrite = True
try:
# Check that it's not the case where the first entry contained a dict of length 1 and now there is a new key
if type(value) == dict and \
dcols[tag][0].nb_elements_per_line == 1 \
and set(dcols[tag][0].elements_names) != set(value.keys()) :
raise IndexError # trigger column rewrite
# Fill value
dcols[tag][0][i] = value
except (IndexError, OverflowError):
value_type = type(value)
old_column = dcols[tag][0]
old_nb_elements_per_line = old_column.nb_elements_per_line
new_nb_elements_per_line = 0
old_elements_names = old_column.elements_names
new_elements_names = None
#####################################################################
# Check the length and keys of column lines if needed
if value_type == dict : # Check dictionary keys
for k in value :
if k not in old_elements_names :
new_elements_names = list(set(old_elements_names+[tobytes(k) for k in value]))
rewrite = True
break
elif value_type == list or value_type == tuple : # Check vector length
if old_nb_elements_per_line < len(value) :
new_nb_elements_per_line = len(value)
rewrite = True
#####################################################################
if rewrite :
if new_nb_elements_per_line == 0 and new_elements_names is not None :
new_nb_elements_per_line = len(new_elements_names)
# Reset obierrno
obi_errno = 0
dcols[tag] = (view.rewrite_column_with_diff_attributes(old_column.name,
new_data_type=new_type,
new_nb_elements_per_line=new_nb_elements_per_line,
new_elements_names=new_elements_names,
rewrite_last_line=False),
new_type)
# Update the dictionary:
for t in dcols :
dcols[t] = (view[t], dcols[t][1])
# Fill value
dcols[tag][0][i] = value
except Exception as e:
print("\nCould not import sequence:\n", repr(entry), "\nError raised:", e, "\n/!\ Check if '--input-na-string' option needs to be set")
if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
raise e
else:
pass
i-=1 # overwrite problematic entry
i+=1
if pb is not None:
pb(i, force=True)
print("", file=sys.stderr)
logger("info", "Imported %d entries", len(view))
# Save command config in View and DMS comments
command_line = " ".join(sys.argv[1:])
view.write_config(config, "import", command_line, input_str=[os.path.abspath(config['obi']['inputURI'])])
output[0].record_command_line(command_line)
#print("\n\nOutput view:\n````````````", file=sys.stderr)
#print(repr(view), file=sys.stderr)
try:
input[0].close()
except AttributeError:
pass
try:
output[0].close(force=True)
except AttributeError:
pass
logger("info", "Done.")
|
