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Cleaner handling of reverse quality columns

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This commit is contained in:
Celine Mercier
2020-01-18 19:28:12 +01:00
parent ced82c4242
commit b4b2e62195
8 changed files with 85 additions and 46 deletions
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34
python/obitools3/commands/cat.pyx
View File

@ -2,15 +2,18 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.dms import DMS
from obitools3.dms.view.view cimport View, Line_selection
from obitools3.dms.view.view cimport View
from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
from obitools3.apps.optiongroups import addMinimalOutputOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport str2bytes
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
from obitools3.commands.ngsfilter import REVERSE_QUALITY_COLUMN_NAME # TODO should be stored in C
from obitools3.dms.view.view cimport View
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, REVERSE_SEQUENCE_COLUMN, \
QUALITY_COLUMN, REVERSE_QUALITY_COLUMN
from obitools3.dms.capi.obitypes cimport OBI_SEQ, OBI_QUAL
from obitools3.dms.column.column cimport Column
import time
import sys
@ -47,6 +50,8 @@ def run(config):
iview_list = []
idms_list = []
total_len = 0
remove_qual = False
remove_rev_qual = False
v_type = View_NUC_SEQS
for v_uri in config["cat"]["views_to_cat"]:
input = open_uri(v_uri)
@ -56,6 +61,10 @@ def run(config):
i_view = input[1]
if input[2] != View_NUC_SEQS: # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
v_type = View
if QUALITY_COLUMN not in i_view: # Check if keep quality column in output view (if all input views have it)
remove_qual = True
if REVERSE_QUALITY_COLUMN not in i_view: # same as above for reverse quality
remove_rev_qual = True
total_len += len(i_view)
iview_list.append(i_view)
idms_list.append(i_dms)
@ -69,6 +78,15 @@ def run(config):
o_dms = output[0]
o_view = output[1]
# Initialize quality columns and their associated sequence columns if needed
if not remove_qual:
if NUC_SEQUENCE_COLUMN not in o_view:
Column.new_column(o_view, NUC_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, QUALITY_COLUMN, OBI_QUAL, associated_column_name=NUC_SEQUENCE_COLUMN, associated_column_version=o_view[NUC_SEQUENCE_COLUMN].version)
if not remove_rev_qual:
Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
# Initialize the progress bar
pb = ProgressBar(total_len, config, seconde=5)
@ -80,11 +98,11 @@ def run(config):
o_view[i] = l
i+=1
# Deletes quality columns if there are any
if QUALITY_COLUMN in o_view:
# Deletes quality columns if needed
if QUALITY_COLUMN in o_view and remove_qual :
o_view.delete_column(QUALITY_COLUMN)
if REVERSE_QUALITY_COLUMN_NAME in o_view:
o_view.delete_column(REVERSE_QUALITY_COLUMN_NAME)
if REVERSE_QUALITY_COLUMN in o_view and remove_rev_qual :
o_view.delete_column(REVERSE_QUALITY_COLUMN)
pb(i, force=True)
print("", file=sys.stderr)