Hi Minh,

Thanks for sending over the dataset.  Here are my responses to your questions:

When I filter the table (c2=='Unmapped'), it returns an empty table. 

It's normal behavior for the filter tool to skip lines that are incomplete. This, as you pointed out, is the reason why filtering with condition c2=='Unmapped' returns an empty dataset. You can however achieve the same by using "Select" tool under "Filter and sort" section, with the condition NOT matching the pattern Unmapped.

When I sort the table (c2) , it returns a table without sorting it. 

I'm still unable to reproduce this issue. It definitely seems like the sort command on your machine might be treating certain options differently. May be if you could send us the tool options chosen by you(or the generated command line), we could try debugging it further.

Thanks,
Guru
Galaxy team.
 

On Aug 6, 2010, at 9:41 AM, Minh Bui wrote:

Hi Guru, 
I attached the original 454 GS Mapper in the email. 
Thank you for helping me. 


On Thu, Aug 5, 2010 at 2:01 PM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
Hi Minh,

I'm unable to reproduce this behavior with the small dataset pasted in one of your earlier emails. Would you mind sending me your large dataset with 30008 lines, so that I can take a look at what might be going wrong?

Thanks,
Guru
Galaxy team.


On Aug 5, 2010, at 1:32 PM, Minh Bui wrote:

Hi Jacob, Guru

I tried both of your methods and Galaxy didn't give me error $'\t anymore but somehow it didn't sort (or filter) the data. 
When I sort the table (c2) , it returns a table without sorting it. 
When I filter the table (c2=='Unmapped'), it returns an empty table. 

My data after convertion looks like this: 
GIQPZ7U01A1A82-W3_11_11	Partial	99	95	chr3	17443613	17443685	-
GIQPZ7U01BM124-W3_11_11	Partial	99	89	chr3	17443521	17443685	-
GIQPZ7U01CG1P0-S3_11_11	Partial	98	65	chr2	162180459	162180499	-
GIQPZ7U01B6DQ9-S3_11_11	Chimeric
GIQPZ7U01ASQA4-NL3_10_21	Partial	99	67	chr3	17443511	17443685	-
GIQPZ7U01CB92X-W3_10_21	Partial	99	88	chr3	17443608	17443685	-
GIQPZ7U01AW16P-S3_10_23	Unmapped
GIQPZ7U01B1FV1-S3_10_21	Partial	98	75	chr16	367117	367155	-
GIQPZ7U01B2PUV-S3_11_11	Chimeric
GIQPZ7U01CC7BN-S3_10_23	Partial	97	84	chr19	18614552	18614649	-
GIQPZ7U01BOQUL-NL3_10_21	Partial	96	95	chr3	17443615	17443685	-
GIQPZ7U01CHEFR-W3_11_11	Partial	99	95	chr3	17443611	17443685	-
GIQPZ7U01B2QVH-NL3_10_21	Partial	100	67	chr16	367117	367155	-
GIQPZ7U01BH73U-S3_11_11	Unmapped
GIQPZ7U01A2OJ8-NL3_10_23	Partial	99	64	chr3	17443511	17443685	-
GIQPZ7U01B96JR-S3_10_21	Unmapped
GIQPZ7U01BSF3A-W3_10_21	Partial	99	87	chr3	17443523	17443685	-
GIQPZ7U01AY7DH-S3_10_21	Partial	99	90	chr4	38640070	38640237	+
GIQPZ7U01B3I06-S3_10_23	Full	98	100	chr19	18614567	18614647	-
GIQPZ7U01AMR6X-S3_10_23	Partial	99	85	chr19	18614551	18614649	-
GIQPZ7U01ALYU8-W3_10_21	Partial	99	78	chr3	17443625	17443685	-
GIQPZ7U01BXRZ1-W3_10_21	Partial	95	91	chr3	17443509	17443685	-
GIQPZ7U01CGAG5-W3_10_21	Partial	99	88	chr3	17443521	17443685	-
GIQPZ7U01CBIX7-S3_10_23	Partial	96	85	chr19	18614551	18614649	-
GIQPZ7U01A1RCP-S3_10_23	Partial	99	85	chr19	18614551	18614649	-
GIQPZ7U01BYXFR-W3_10_21	Partial	98	79	chr3	17443608	17443685	-
GIQPZ7U01B275Q-S3_10_21	Partial	97	67	chr16	367117	367155	-
GIQPZ7U01AXBIJ-S3_11_11	Chimeric
GIQPZ7U01BXW15-S3_10_23	Full	95	100	chr19	18614579	18614649	-
GIQPZ7U01BV1GN-W3_10_21	Partial	98	78	chr3	17443608	17443685	-
GIQPZ7U01BIYVC-S3_10_23	Partial	98	88	chr19	18614551	18614649	-
GIQPZ7U01BS3VK-S3_10_23	Unmapped
GIQPZ7U01BOGIN-NL3_10_21	Partial	99	61	chr3	17443519	17443685
.....

P.S: I am using Ubuntu. 

On Wed, Aug 4, 2010 at 12:50 PM, Jacob Biesinger <jake.biesinger@uci.edu> wrote:
I just had this exact issue.  For me, the problem was caused by my
default shell (different than login shell) being set to dash instead
of bash.  Dash doesn't respect the $'\t' trick, and so fails.  The
sorter.py script performs a system call (os.system(...)) which uses
/bin/sh.  On Ubuntu (me) and perhaps other distro's, /bin/sh is a
symbolic link to dash.

To see if this is your issue, do:
$ ls -l /bin/sh

If it points to dash, then either do:
$ sudo dpkg-reconfigure dash      # for debian-based systems like ubuntu
then choose "No-- Don't install dash"
OR
$ sudo ln -s /bin/sh bash

--
Jake Biesinger
Graduate Student
Xie Lab, UC Irvine
(949) 231-7587



On Wed, Aug 4, 2010 at 8:58 AM, Guruprasad Ananda <gua110@bx.psu.edu> wrote:
> Hi Minh,
> Sorry for not getting back to you sooner. It looks like the sort command on
> your machine works differently from that on Galaxy, in that it doesn't
> recognize -t $'\t'as a valid option. Can you please make the following
> change and let me know if the tool ends in error state or not.
> galaxy_home_folder/tools/filters/sorter.py:
> line 42: replace
> cmd = "sort -f -t $'\t' %s %s %s" % (' '.join(cols), outputfile, inputfile)
> with
> cmd = 'TAB="\t"; sort -f -t "${TAB}" %s %s %s' % (' '.join(cols),
> outputfile, inputfile)
> Thanks,
> Guru.
> On Jul 29, 2010, at 4:22 PM, Minh Bui wrote:
>
> Hi Hans,
> This is interesting. I copied that table from Galaxy (I couldnt sort this
> table). If the big file have errors, it should give me some kind of errors
> when I Convert it.
>
> I don't know why but I still get the error. I'll run  more tests to see what
> happen.
> I also realize that when I filter C2=='Full' or 'Partial', Galaxy works fine
> and I don't get any error. But when I try to filter C2=='Chimeric' or
> 'Unmapped' ('Chimeric' and 'Unmapped' are incomplete data, they dont have
> chromosome, start-end position...), Galaxy can't filter them.
>
>
> On Thu, Jul 29, 2010 at 4:09 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
>>
>> Hi
>>
>> Does your small example really not work for you? It works fine for me
>> (after copy paste and sort on C2), see attachment.
>>
>> I suspect, there is an error in your big file?
>>
>> Hans
>>
>>
>>
>> On 07/28/2010 08:43 PM, Minh Bui wrote:
>>>
>>> And the table after I converted it to tabular format looks like this:
>>>
>>> GIQPZ7U01A1A82-W3_11_11 Full    90      100     chr3    17443613
>>>  17443686        -
>>> GIQPZ7U01BM124-W3_11_11 Partial 98      90      chr3    17443521
>>>  17443687        -
>>> GIQPZ7U01CG1P0-S3_11_11 Partial 98      65      chr2    162180459
>>> 162180499       -
>>> GIQPZ7U01B6DQ9-S3_11_11 Chimeric
>>> GIQPZ7U01ASQA4-NL3_10_21        Partial 98      67      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01CB92X-W3_10_21 Partial 98      89      chr3    17443608
>>>  17443686        -
>>> GIQPZ7U01AW16P-S3_10_23 Unmapped
>>> GIQPZ7U01B1FV1-S3_10_21 Partial 98      75      chr16   367117  367155  -
>>> GIQPZ7U01B2PUV-S3_11_11 Chimeric
>>> GIQPZ7U01CC7BN-S3_10_23 Partial 97      84      chr19   18614552
>>>  18614649        -
>>> GIQPZ7U01BOQUL-NL3_10_21        Full    86      100     chr3    17443615
>>>        17443686        -
>>> GIQPZ7U01CHEFR-W3_11_11 Full    90      100     chr3    17443611
>>>  17443686        -
>>> GIQPZ7U01B2QVH-NL3_10_21        Partial 100     67      chr16   367117
>>>  367155  -
>>> GIQPZ7U01BH73U-S3_11_11 Unmapped
>>> GIQPZ7U01A2OJ8-NL3_10_23        Partial 98      65      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01B96JR-S3_10_21 Unmapped
>>> GIQPZ7U01BSF3A-W3_10_21 Partial 99      88      chr3    17443523
>>>  17443687        -
>>> GIQPZ7U01AY7DH-S3_10_21 Partial 99      90      chr4    38640070
>>>  38640237        +
>>> GIQPZ7U01B3I06-S3_10_23 Full    98      100     chr19   18614567
>>>  18614647        -
>>> GIQPZ7U01AMR6X-S3_10_23 Partial 99      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01ALYU8-W3_10_21 Partial 98      80      chr3    17443625
>>>  17443687        -
>>> GIQPZ7U01BXRZ1-W3_10_21 Partial 95      92      chr3    17443509
>>>  17443686        -
>>> GIQPZ7U01CGAG5-W3_10_21 Partial 98      89      chr3    17443521
>>>  17443687        -
>>> GIQPZ7U01CBIX7-S3_10_23 Partial 96      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01A1RCP-S3_10_23 Partial 99      85      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01BYXFR-W3_10_21 Partial 97      80      chr3    17443608
>>>  17443686        -
>>> GIQPZ7U01B275Q-S3_10_21 Partial 97      67      chr16   367117  367155  -
>>> GIQPZ7U01AXBIJ-S3_11_11 Chimeric
>>> GIQPZ7U01BXW15-S3_10_23 Full    95      100     chr19   18614579
>>>  18614649        -
>>> GIQPZ7U01BV1GN-W3_10_21 Partial 97      80      chr3    17443608
>>>  17443687        -
>>> GIQPZ7U01BIYVC-S3_10_23 Partial 98      88      chr19   18614551
>>>  18614649        -
>>> GIQPZ7U01BS3VK-S3_10_23 Unmapped
>>> GIQPZ7U01BOGIN-NL3_10_21        Partial 99      61      chr3    17443519
>>>        17443686        -
>>> GIQPZ7U01B313G-S3_11_11 Partial 98      68      chr2    162180459
>>> 162180501       -
>>> GIQPZ7U01BCMVY-W3_10_23 Partial 99      57      chr16   367117  367155  -
>>> GIQPZ7U01BL41A-W3_10_23 Partial 95      49      chr15   50814744
>>>  50814785        +
>>> GIQPZ7U01B8EWK-NL3_10_21        Partial 98      64      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01BY5AD-NL3_10_21        Partial 97      64      chr3    17443511
>>>        17443686        -
>>> GIQPZ7U01CA6RX-S3_10_21 Unmapped
>>> GIQPZ7U01BQOHG-W3_10_21 Partial 98      89      chr3    17443521
>>>  17443686        -
>>>
>>>
>>> On Wed, Jul 28, 2010 at 2:43 PM, Minh Bui<buiduyminh@gmail.com>  wrote:
>>>
>>>> And the table after I converted it to tabular format looks like this:
>>>>
>>>>
>>>>
>>>> On Wed, Jul 28, 2010 at 2:35 PM, Minh Bui<buiduyminh@gmail.com>  wrote:
>>>>
>>>>> Hi,
>>>>> I always get this error when I use Sort feature
>>>>> *"An error occurred running this job: sort: multi-character tab `$\t'"*
>>>>> Even I already use Text Manipulation->Convert to convert my table to
>>>>> Tabs
>>>>> format.
>>>>>
>>>>> Here is the screenshot of what happen (I want to sort C2 on job #12) :
>>>>> http://img408.imageshack.us/img408/7906/screenshotbu.png
>>>>>
>>>>>
>>>>> Could someone please show me how to fix this?
>>>>> Thank you.
>>>>>
>>>>
>>>>
>>>
>>>
>>>
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>>> galaxy-dev@lists.bx.psu.edu
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