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Old 03-19-2012, 04:39 AM   #1
MikeT
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Default CAMERA Blast output - invalid XML?

Hi all,
I've ran some of my datasets on the tBLASTx program on the CAMERA portal. Since the hit number was quite big, the portal let me download the output as a .xml file.
Sadly, as I run blast_formatter on the .xml it appears to be an invalid file format: Galaxy tells me it's a simple .txt, instead of a .xml. How can I reformat it?

-MikeT
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Old 03-19-2012, 06:45 AM   #2
maubp
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Can you show us the first 10 lines or so using the [ code ] and [ /code ] forum tags to preserve the formatting? Try using the Unix command 'head' for this,

head -n 10 example.xml
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Old 03-19-2012, 07:13 AM   #3
MikeT
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Here's a screenshot of the first lines:
http://www.box.com/s/d9b5d73367bdb67e3617
Hope it helps!

-MikeT
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Old 03-19-2012, 07:48 AM   #4
maubp
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Quote:
Originally Posted by MikeT View Post
Here's a screenshot of the first lines:
http://www.box.com/s/d9b5d73367bdb67e3617
Hope it helps!
That does look like BLAST XML.

It is possible Galaxy failed to auto-detect the file type. You can set this explicitly when you upload a file to Galaxy. Or, after uploading from the history entry use the "pencil" icon ("edit attributes") to change the filetype.

Quote:
Originally Posted by MikeT View Post
Sadly, as I run blast_formatter on the .xml it appears to be an invalid file format
The NCBI tool blast_formatter does not expect an XML input, rather an ASN.1 file.
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Old 03-19-2012, 07:57 AM   #5
MikeT
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Quote:
Originally Posted by maubp View Post
That does look like BLAST XML.

It is possible Galaxy failed to auto-detect the file type. You can set this explicitly when you upload a file to Galaxy. Or, after uploading from the history entry use the "pencil" icon ("edit attributes") to change the filetype.
Already tried, but when I do it and then use the "Parse BLAST output" command it still doesn't recognize the file as a .xml BLAST output.


Quote:
Originally Posted by maubp View Post
The NCBI tool blast_formatter does not expect an XML input, rather an ASN.1 file.
Are you sure? Because the -help section for the tool explicitly says that it expects some ASN.1 files and .XMLs. Anyway, how can I reformat my output as an ASN.1 file?

-MikeT
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Old 03-19-2012, 08:05 AM   #6
maubp
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Quote:
Originally Posted by MikeT View Post
Already tried, but when I do it and then use the "Parse BLAST output" command it still doesn't recognize the file as a .xml BLAST output.
In that case (assuming you are using the public Galaxy), write to the galaxy-users mailing list and offer to share a history with the problematic XML file with them for diagnosis.
Quote:
Originally Posted by MikeT View Post
Are you sure? Because the -help section for the tool explicitly says that it expects some ASN.1 files and .XMLs. Anyway, how can I reformat my output as an ASN.1 file?
I only have BLAST 2.2.25+ installed on this machine (the latest is now 2.2.26), and it doesn't say that in the 'blast_formatter -help' text. I doesn't say much at all about the -archive argument, but the website is pretty clear it expects a BLAST archive format (ASN.1) file: http://www.ncbi.nlm.nih.gov/books/NBK1763/
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