Re: [galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hi Robert,
It's probably fine, although you lose the benefit of datatype sniffing. The
binary detection is there to prevent abuse on our public site. This error
should really only occur if there's a non-ASCII character in your bed file, so
you may want to check it programatically, e.g. (slowly):
for lineno, line in enumerate(open('foo.txt')):
... for charno, char in enumerate(line):
... try:
... assert ord(char) 128
... except:
... print 'Non-ASCII character at line %i position %i: %s' %
(lineno, charno, char)
...
--nate
On Jul 12, 2012, at 5:24 PM, Robert Chase wrote:
Hi Nate,
I don't think that it does. We get the bed files from our GWAS pipelines. We
were able to upload the file by adding 'bed' to the list of
unsniffable_binary_formats in binary.py and manually specifying the format.
Do you think this could cause problems later?
-Rob
On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jul 5, 2012, at 4:15 PM, Robert Chase wrote:
Hello,
We tried to upload a directory of files to our local data library and all
uploads were successful except for one. The .bed file did not upload and
gave an error message; The uploaded binary file contains inappropriate
content. We would like to be able to share our data set with other
researchers using galaxy but we need to be able to upload this bed file.
Hi Rob,
Is there any chance that the file contains Unicode?
--nate
-Rob
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Re: [galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hi Nate, I don't think that it does. We get the bed files from our GWAS pipelines. We were able to upload the file by adding 'bed' to the list of unsniffable_binary_formats in binary.py and manually specifying the format. Do you think this could cause problems later? -Rob On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 5, 2012, at 4:15 PM, Robert Chase wrote: Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. Hi Rob, Is there any chance that the file contains Unicode? --nate -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hi Rob, The 'bed' datatype in Galaxy refers to UCSC's Browser Extensible Data format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). Is this a binary PLINK .bed file (http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)? If so, you may want to consider looking at/using the 'pbed' datatype in Galaxy (for Rgenetics tools; datatype is galaxy_root/lib/galaxy/datatypes/genetics.py). It is a composite datatype that holds the .bim, .bed, and .fam files all together as a single Galaxy item. If you have a use for keeping the .bed file separate from the other two files, or if this is a different .bed file, then this doesn't apply. Thanks for using Galaxy, Dan On Jul 12, 2012, at 5:24 PM, Robert Chase wrote: Hi Nate, I don't think that it does. We get the bed files from our GWAS pipelines. We were able to upload the file by adding 'bed' to the list of unsniffable_binary_formats in binary.py and manually specifying the format. Do you think this could cause problems later? -Rob On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 5, 2012, at 4:15 PM, Robert Chase wrote: Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. Hi Rob, Is there any chance that the file contains Unicode? --nate -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] bed files - The uploaded binary file contains inappropriate content
Hello, We tried to upload a directory of files to our local data library and all uploads were successful except for one. The .bed file did not upload and gave an error message; The uploaded binary file contains inappropriate content. We would like to be able to share our data set with other researchers using galaxy but we need to be able to upload this bed file. -Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
