Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 
For your full 9-column GTF file, it is, as you have determined, tab-delimited
for the 9 columns.  In the ninth you can place any value tag pairs with
semi-colon ; delimiter.  Beware your excel produced file does not have
hidden characters that can upset the balance.  View your file in
an editor that can show the hidden characters, or on the command line:

cat -A yourFile.gtf | less

to see the hidden characters.  You should only see the 8 tab delimiters.

--Hiram

- Original Message -
From: "Noa Sher" 
To: "Hiram Clawson" 
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:54:54 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf 
fileissues



Hi Hiram, 

I managed to extract the columns in a different order (albeit I did it in excel 
and not using command line) but then the 9th column (attributes) of gtf is what 
I had problems with 

Thanks 

noa 
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Noa Sher 

  
  
Hi Hiram,
I managed to extract the columns in a different order (albeit I
  did it in excel and not using command line) but then the 9th
  column (attributes) of gtf is what I had problems with
Thanks
noa


On 04/12/2011 21:43, Hiram Clawson wrote:

  Pardon me, I see there is only one that says "tab-delimited" file.

That is a tough one to decode.  It almost looks like GTF already, but
not quite.  If we take it as a simple file of annotations on the genome,
without structure such as exons, introns, and merely rework the columns
to turn it into a bed file.  Extract columns in this order: 4,5,6,2,7
to get a bed file with the accession identities:

awk -F'\t' '{printf "%s\t%d\t%d\t%s\t%s\n", $4,$5,$6,$2,$7}' 59919.tab > 59919.bed

It would take some time to figure out how to convert this file
to something useful since I am not familiar with the format.
I can't see immediately how to use it properly.

--Hiram

- Original Message -
From: "Noa Sher" 
To: "Hiram Clawson" 
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf file	issues

Hi Hiram, 

I was trying to work with the tab delineated file (using the link under export genomic data). 
Thanks 
noa 

On 04/12/2011 20:29, Hiram Clawson wrote: 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher"  To: galaxy-user@lists.bx.psu.edu Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file	issues




The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 


  

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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 
Pardon me, I see there is only one that says "tab-delimited" file.

That is a tough one to decode.  It almost looks like GTF already, but
not quite.  If we take it as a simple file of annotations on the genome,
without structure such as exons, introns, and merely rework the columns
to turn it into a bed file.  Extract columns in this order: 4,5,6,2,7
to get a bed file with the accession identities:

awk -F'\t' '{printf "%s\t%d\t%d\t%s\t%s\n", $4,$5,$6,$2,$7}' 59919.tab > 
59919.bed

It would take some time to figure out how to convert this file
to something useful since I am not familiar with the format.
I can't see immediately how to use it properly.

--Hiram

- Original Message -
From: "Noa Sher" 
To: "Hiram Clawson" 
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf 
fileissues

Hi Hiram, 

I was trying to work with the tab delineated file (using the link under export 
genomic data). 
Thanks 
noa 

On 04/12/2011 20:29, Hiram Clawson wrote: 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher"  To: galaxy-user@lists.bx.psu.edu Sent: 
Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file
issues




The correct link: 
http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 
___
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 

Is this the genome you are working with:

http://archaea.ucsc.edu/cgi-bin/hgGateway?db=procMari_CCMP1375


- Original Message -
From: "Noa Sher" 
To: "Hiram Clawson" 
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf 
fileissues

Hi Hiram, 

I was trying to work with the tab delineated file (using the link under export 
genomic data). 
Thanks 
noa 

On 04/12/2011 20:29, Hiram Clawson wrote: 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher"  To: galaxy-user@lists.bx.psu.edu Sent: 
Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file
issues




The correct link: 
http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 
___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 

There are at least six of them there.  Which one ?

- Original Message -
From: "Noa Sher" 
To: "Hiram Clawson" 
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail - gtf 
fileissues

Hi Hiram, 

I was trying to work with the tab delineated file (using the link under export 
genomic data). 
Thanks 
noa 

On 04/12/2011 20:29, Hiram Clawson wrote: 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher"  To: galaxy-user@lists.bx.psu.edu Sent: 
Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file
issues




The correct link: 
http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Noa Sher 

  
  
Hi Hiram,

I was trying to work with the tab delineated file (using the link
under export genomic data).
Thanks
noa

On 04/12/2011 20:29, Hiram Clawson wrote:

  
Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher" 
To: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file	issues




The correct link: http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 


  

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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please use the interface at:

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Re: [galaxy-user] there was a wrong link in my previous mail - gtf file issues

2011-12-04 Thread Hiram Clawson 

Good Morning Noa:

Which one of the files at microbesonline are you trying to work with ?

--Hiram

- Original Message -
From: "Noa Sher" 
To: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 1:38:35 AM
Subject: [galaxy-user] there was a wrong link in my previous mail - gtf file
issues




The correct link: 
http://www.microbesonline.org/cgi-bin/genomeInfo.cgi?tId=59919 
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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use the Galaxy Development list:

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