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obi import: removed old traces

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This commit is contained in:
Celine Mercier
2018-02-12 14:36:56 +01:00
parent 01ef85658c
commit c8097e14e1
1 changed files with 4 additions and 7 deletions
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11
python/obitools3/commands/import.pyx
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@ -87,11 +87,9 @@ def run(config):
DMS.obi_atexit() DMS.obi_atexit()
logger("info","obi import : imports file into an DMS") logger("info","obi import : imports file into an DMS")
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:
@ -105,8 +103,8 @@ def run(config):
if output is None: if output is None:
raise Exception("Could not create output view") raise Exception("Could not create output view")
print("input:", input) #print("input:", input)
print("output:", output) #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
@ -141,7 +139,6 @@ def run(config):
if i == 0: if i == 0:
get_quality = b"QUALITY" in seq get_quality = b"QUALITY" in seq
if get_quality: if get_quality:
print("yah")
Column.new_column(view, b"QUALITY", OBI_QUAL) Column.new_column(view, b"QUALITY", OBI_QUAL)
qual_col = view[b"QUALITY"] qual_col = view[b"QUALITY"]