GBrowse 2.55 - Search by Name with brackets - failed

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GBrowse 2.55 - Search by Name with brackets - failed

EmanLee
We search a feature by Name, such as "XXX YYY", it works. But it failed(Not found) when searching features whose names containing brackets/braces, i.e. AAA (BBB).

Failed:
Chr.1    source    feature1    23    45    .    .    .    ID=111;Name=AAA (BBB);

Success:
Chr.1    source    feature1    56    78    .    .    .    ID=222;Name=XXX YYY;

Many thanks
Eman



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Re: GBrowse 2.55 - Search by Name with brackets - failed

Scott Cain
Hi Eman,

You shouldn't have to do this, and it probably won't work, but what if you replace the parentheses with their URI escape codes, like this: AAA %28BBB%29?  Also, if you're using a database backend, look the the name table to see how that feature's name is represented.  I'm just wondering where the problem is, ie, is it how the name was stored in the database or how the name is being looked up?

Scott



On Sun, Feb 16, 2014 at 12:12 AM, EmanLee <[hidden email]> wrote:
We search a feature by Name, such as "XXX YYY", it works. But it failed(Not found) when searching features whose names containing brackets/braces, i.e. AAA (BBB).

Failed:
Chr.1    source    feature1    23    45    .    .    .    ID=111;Name=AAA (BBB);

Success:
Chr.1    source    feature1    56    78    .    .    .    ID=222;Name=XXX YYY;

Many thanks
Eman



------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GBrowse 2.55 - Search by Name with brackets - failed

EmanLee
Hi, Scott
Thanks. We reviewed the related data and configurations as follows (also included in email attachment):
It seems that this kind of Names were not imported into mysql.

-------------
  STEP 1: gff3
-------------

X    Animal_QTLdb    Reproduction_QTL    7735326    12629028    .    .    .    ID=QTL0002713;Name=Dystocia (maternal);PubmedID=12613879;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=2713;Trait_ID=1280;
4    Animal_QTLdb    Reproduction_QTL    52116252    52320303    .    .    .    ID=QTL0011381;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11381;Trait_ID=1280;
5    Animal_QTLdb    Reproduction_Association    75479851    75480051    .    .    .    ID=QTL0014700;Name=Dystocia (maternal);PubmedID=19968646;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=14700;Trait_ID=1280;
5    Animal_QTLdb    Reproduction_Association    106491682    106491882    .    .    .    ID=QTL0014701;Name=Dystocia (maternal);PubmedID=19968646;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=14701;Trait_ID=1280;
6    Animal_QTLdb    Reproduction_QTL    44526237    64253742    .    .    .    ID=QTL0011382;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11382;Trait_ID=1280;
8    Animal_QTLdb    Reproduction_QTL    44393492    89588554    .    .    .    ID=QTL0011442;Name=Dystocia (maternal);PubmedID=12613879;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11442;Trait_ID=1280;
10    Animal_QTLdb    Reproduction_QTL    75917952    92494840    .    .    .    ID=QTL0002702;Name=Dystocia (maternal);PubmedID=12613879;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=2702;Trait_ID=1280;
10    Animal_QTLdb    Reproduction_QTL    75917952    93540445    .    .    .    ID=QTL0011353;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11353;Trait_ID=1280;
11    Animal_QTLdb    Reproduction_QTL    46591394    73178408    .    .    .    ID=QTL0011384;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11384;Trait_ID=1280;
12    Animal_QTLdb    Reproduction_Association    24740513    24740713    .    .    .    ID=QTL0014710;Name=Dystocia (maternal);PubmedID=19968646;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=14710;Trait_ID=1280;
13    Animal_QTLdb    Reproduction_QTL    29549346    84240350    .    .    .    ID=QTL0011385;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11385;Trait_ID=1280;
17    Animal_QTLdb    Reproduction_QTL    63026466    70369810    .    .    .    ID=QTL0011386;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11386;Trait_ID=1280;
18    Animal_QTLdb    Reproduction_QTL    6885675    39814434    .    .    .    ID=QTL0002707;Name=Dystocia (maternal);PubmedID=12613879;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=2707;Trait_ID=1280;
19    Animal_QTLdb    Reproduction_QTL    45248309    51113618    .    .    .    ID=QTL0011367;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11367;Trait_ID=1280;
19    Animal_QTLdb    Reproduction_QTL    51113618    58089400    .    .    .    ID=QTL0011368;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11368;Trait_ID=1280;
23    Animal_QTLdb    Reproduction_QTL    7633315    12487278    .    .    .    ID=QTL0011371;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11371;Trait_ID=1280;
23    Animal_QTLdb    Reproduction_QTL    1522506    39294063    .    .    .    ID=QTL0011390;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11390;Trait_ID=1280;
24    Animal_QTLdb    Reproduction_QTL    9263292    9425900    .    .    .    ID=QTL0011391;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11391;Trait_ID=1280;
25    Animal_QTLdb    Reproduction_QTL    6693657    12159194    .    .    .    ID=QTL0011377;Name=Dystocia (maternal);PubmedID=19912419;TraitID=TRAIT0001280;Trait=Dystocia (maternal);QTL_ID=11377;Trait_ID=1280;


-------------
  STEP 2: configuration
-------------

[GENERAL]
search attributes  = load_id

[Animal_QTLdb]
feature       = Reproduction_QTL:Animal_QTLdb  Reproduction_Association:Animal_QTLdb
fgcolor       = orange
bgcolor          = orange
glyph         = generic
description   = 1
height        = 4
category      = QTL
key           = Animal QTLdb

-------------
  STEP 3: Test
-------------

Search by Name: "Dystocia (maternal)" in GBrowse, not found.
Search by ID: QTL0002713, success.



-------------
  STEP 4: MySQL
-------------


select * from attribute where attribute_value = 'Dystocia (maternal)'  ;
+--------+--------------+---------------------+
| id     | attribute_id | attribute_value     |
+--------+--------------+---------------------+
| 602728 |            3 | Dystocia (maternal) |
| 603885 |            3 | Dystocia (maternal) |
| 604592 |            3 | Dystocia (maternal) |
| 604690 |            3 | Dystocia (maternal) |
| 604741 |            3 | Dystocia (maternal) |
| 605723 |            3 | Dystocia (maternal) |
| 606269 |            3 | Dystocia (maternal) |
| 606297 |            3 | Dystocia (maternal) |
| 606314 |            3 | Dystocia (maternal) |
| 606609 |            3 | Dystocia (maternal) |
| 606809 |            3 | Dystocia (maternal) |
| 608183 |            3 | Dystocia (maternal) |
| 608230 |            3 | Dystocia (maternal) |
| 608492 |            3 | Dystocia (maternal) |
| 608493 |            3 | Dystocia (maternal) |
| 609840 |            3 | Dystocia (maternal) |
| 609967 |            3 | Dystocia (maternal) |
| 610025 |            3 | Dystocia (maternal) |
| 610185 |            3 | Dystocia (maternal) |
+--------+--------------+---------------------+
19 rows in set (0.21 sec)


select * from attributelist where id in (3);
+----+-------+
| id | tag   |
+----+-------+
|  3 | Trait |
+----+-------+
1 row in set (0.00 sec)


-------------
  STEP 5: Problem
-------------
It seemed that "Name=Dystocia (maternal);" was not imported into mysql, but , "Trait=Dystocia (maternal);" was imported.


--
Thanks
Eman

在2014-02-18,"Scott Cain" <[hidden email]> 写道:
-----原始邮件-----
发件人:"Scott Cain" <[hidden email]>
发送时间:2014年02月18日 星期二
收件人:"EmanLee" <[hidden email]>
抄送:"gmod-gbrowse" <[hidden email]>
主题:Re: [Gmod-gbrowse] GBrowse 2.55 - Search by Name with brackets - failed

Hi Eman,

You shouldn't have to do this, and it probably won't work, but what if you replace the parentheses with their URI escape codes, like this: AAA %28BBB%29?  Also, if you're using a database backend, look the the name table to see how that feature's name is represented.  I'm just wondering where the problem is, ie, is it how the name was stored in the database or how the name is being looked up?

Scott



On Sun, Feb 16, 2014 at 12:12 AM, EmanLee <[hidden email]> wrote:
We search a feature by Name, such as "XXX YYY", it works. But it failed(Not found) when searching features whose names containing brackets/braces, i.e. AAA (BBB).

Failed:
Chr.1    source    feature1    23    45    .    .    .    ID=111;Name=AAA (BBB);

Success:
Chr.1    source    feature1    56    78    .    .    .    ID=222;Name=XXX YYY;

Many thanks
Eman



------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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GBrowse 2.55 - Search by Name with brackets - failed (7K) Download Attachment