obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

obi import: better checking of whether to import quality

Browse Source
This commit is contained in:
Celine Mercier
2018-11-19 11:23:39 +01:00
parent e9c1d5e48d
commit 4d51f4f015
1 changed files with 8 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files

22
python/obitools3/commands/import.pyx
View File

@ -105,7 +105,6 @@ def run(config):
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
input=False, input=False,
newviewtype=v) newviewtype=v)
#quality=get_quality) # TODO
if output is None: if output is None:
raise Exception("Could not create output view") raise Exception("Could not create output view")
@ -129,33 +128,28 @@ def run(config):
NUC_SEQS_view = True NUC_SEQS_view = True
else: else:
raise NotImplementedError() raise NotImplementedError()
get_quality = config["obi"]["noquality"]
# Save basic columns in variables for optimization # Save basic columns in variables for optimization
if NUC_SEQS_view : if NUC_SEQS_view :
id_col = view[b"ID"] # TODO use macros or globals for column names id_col = view[b"ID"] # TODO use macros or globals for column names
def_col = view[b"DEFINITION"] def_col = view[b"DEFINITION"]
seq_col = view[b"NUC_SEQ"] seq_col = view[b"NUC_SEQ"]
if get_quality:
qual_col = view[b"QUALITY"]
dcols = {} dcols = {}
i = 0 i = 0
for entry in entries : for entry in entries :
pb(i) pb(i)
if NUC_SEQS_view : if NUC_SEQS_view:
# Check if there is a sequencing quality associated # TODO
if i == 0:
get_quality = b"QUALITY" in entry
if get_quality:
Column.new_column(view, b"QUALITY", OBI_QUAL)
qual_col = view[b"QUALITY"]
id_col[i] = entry.id id_col[i] = entry.id
def_col[i] = entry.definition def_col[i] = entry.definition
seq_col[i] = entry.seq seq_col[i] = entry.seq
if get_quality : if get_quality :
qual_col[i] = entry.quality qual_col[i] = entry.quality