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obi import: fixed creation of quality columns (to discuss)

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This commit is contained in:
Celine Mercier
2017-12-19 11:07:00 +01:00
parent 1a5b499b5c
commit 428c4eb5e6
1 changed files with 23 additions and 12 deletions
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35
python/obitools3/commands/import.pyx
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@ -19,7 +19,8 @@ from obitools3.utils cimport tobytes, \
update_obitype update_obitype
from obitools3.dms.capi.obitypes cimport obitype_t, \ from obitools3.dms.capi.obitypes cimport obitype_t, \
OBI_VOID OBI_VOID, \
OBI_QUAL
from obitools3.dms.capi.obierrno cimport obi_errno from obitools3.dms.capi.obierrno cimport obi_errno
@ -45,7 +46,7 @@ def addOptions(parser):
addSequenceInputOption(parser) addSequenceInputOption(parser)
addMinimalOutputOption(parser) addMinimalOutputOption(parser)
# addTaxdumpInputOption(parser)
def run(config): def run(config):
@ -89,17 +90,23 @@ def run(config):
input = open_uri(config['obi']['inputURI']) input = open_uri(config['obi']['inputURI'])
print(input)
if input[2]==Nuc_Seq: if input[2]==Nuc_Seq:
v = View_NUC_SEQS v = View_NUC_SEQS
else: else:
v = View v = View
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
input=False, input=False,
newviewtype=v) newviewtype=v)
#quality=get_quality) # TODO
#print(input)
#print(output) if output is None:
raise Exception("Could not create output view")
print("input:", input)
print("output:", output)
pb = ProgressBar(1000000, config, seconde=5) # TODO should be number of records in file pb = ProgressBar(1000000, config, seconde=5) # TODO should be number of records in file
@ -107,14 +114,11 @@ def run(config):
NA_value = config['obi']['nastring'] NA_value = config['obi']['nastring']
get_quality = False
NUC_SEQS_view = False NUC_SEQS_view = False
if isinstance(output[1], View) : if isinstance(output[1], View) :
view = output[1] view = output[1]
if output[2] == View_NUC_SEQS : if output[2] == View_NUC_SEQS :
NUC_SEQS_view = True NUC_SEQS_view = True
if "QUALITY" in view : # TODO
get_quality = True
else: else:
raise NotImplementedError() raise NotImplementedError()
@ -123,8 +127,6 @@ def run(config):
id_col = view[b"ID"] id_col = view[b"ID"]
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 = {}
@ -132,8 +134,17 @@ def run(config):
for seq in iseq : for seq in iseq :
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 seq
if get_quality:
print("yah")
Column.new_column(view, b"QUALITY", OBI_QUAL)
qual_col = view[b"QUALITY"]
id_col[i] = seq.id id_col[i] = seq.id
def_col[i] = seq.definition def_col[i] = seq.definition
seq_col[i] = seq.seq seq_col[i] = seq.seq