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  • #114

Closed
Open
Opened Aug 04, 2021 by Frédéric Boyer@fboyerOwner

obi ls not managing properly views with complicated names

See the following sequences of two commands:

$obi grep -p 'sequence["error"]=="No reverse primer match"' WCH-80.3tag2/NOTFILTERED WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:26:57,551 [grep : INFO ]  obi grep
 100.0 % |##################################################|] remain : 00:00:00
2021-08-04 10:27:07,277 [grep : INFO ]  Grepped 1297012 entries
2021-08-04 10:27:29,126 [grep : INFO ]  Done.

$ obi ls WCH-80.3tag2
2021-08-04 10:27:40,664 [ls : INFO ]  obi ls
# DMS name: WCH-80.3tag2
# Views:
  # AMPLICON: Date created: Tue Jul 20 02:06:02 2021 ; Line count: 6230849
  # FILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 1695966
  # FORWARD: Date created: Tue Jul 20 01:45:54 2021 ; Line count: 6230849
  # NGSFILTER: Date created: Tue Jul 20 02:25:52 2021 ; Line count: 38400
  # NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
  # NOTFILTERED: Date created: Tue Jul 20 02:25:53 2021 ; Line count: 4534883
  # REVERSE: Date created: Tue Jul 20 01:56:00 2021 ; Line count: 6230849
# Taxonomies:

the View NOTFILTERED is listed twice whereas the view NOTFILTERED.NOREVERSEPRIMERMATCH is not listed.

Nevertheless, the view NOTFILTERED.NOREVERSEPRIMERMATCH can be individually checked with obi ls

$obi ls WCH-80.3tag2/NOTFILTERED.NOREVERSEPRIMERMATCH
2021-08-04 10:31:42,608 [ls : INFO ]  obi ls
# View name:
NOTFILTERED.NOREVERSEPRIMERMATCH
# Date created:
Wed Aug  4 10:27:07 2021
# Line count:
1297012
# Columns:
NUC_SEQ, data type: OBI_SEQ
ID, data type: OBI_STR
DEFINITION, data type: OBI_STR
QUALITY, data type: OBI_QUAL
seq_length, data type: OBI_INT
overlap_length, data type: OBI_INT
score_norm, data type: OBI_FLOAT
shift, data type: OBI_INT
ali_direction, data type: OBI_STR
score, data type: OBI_FLOAT
mode, data type: OBI_STR
COUNT, data type: OBI_INT
avg_quality, data type: OBI_FLOAT
head_quality, data type: OBI_FLOAT
mid_quality, data type: OBI_FLOAT
tail_quality, data type: OBI_FLOAT
seq_length_ori, data type: OBI_INT
direction, data type: OBI_STR
reverse_errors, data type: OBI_INT
reverse_primer, data type: OBI_SEQ
reverse_match, data type: OBI_SEQ
error, data type: OBI_STR
forward_errors, data type: OBI_INT
forward_primer, data type: OBI_SEQ
forward_match, data type: OBI_SEQ
status, data type: OBI_STR
forward_tag, data type: OBI_SEQ
reverse_tag, data type: OBI_SEQ
reversed, data type: OBI_BOOL
pairedend_limit, data type: OBI_INT
Edited Aug 04, 2021 by Frédéric Boyer
To upload designs, you'll need to enable LFS and have an admin enable hashed storage. More information
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Reference: obitools/obitools3#114