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
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:
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 <nate@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:
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 <nate@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:
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 <nate@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:
___________________________________________________________ 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:
Hi Dan, You're right; it is a binary PLINK .bed file. It would be helpful to bundle the bim bed and fam files together as a pbed item. I think the bed file is too large to upload from the file system so I tried to upload it within a directory of files. When I try to upload these files as a directory of files and select "pbed" as the file format, they are not bundled together but uploaded separately and then the bed file upload fails. -Rob On Fri, Jul 13, 2012 at 4:31 PM, Daniel Blankenberg <dan@bx.psu.edu> wrote:
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 <nate@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:
___________________________________________________________ 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:
participants (3)
-
Daniel Blankenberg -
Nate Coraor -
Robert Chase