using sff_extract - Page 2

chayan · 04-24-2013, 06:51 AM

hii, sorry to say that i dont have much knowladge about linux and all this. What i understood from your previous reply, i install "libsasl2-dev" with the following command sudo apt-get install libsasl2-dev

still the same error msg it showing... sorry if i missed anything particular.

Jose Blanca · 04-25-2013, 01:07 AM

Which python version are you using? Are you using python 2.7? It's a strange problem because that missing module belongs to the standard library.
The newest sff_extract is now included in a package named seq_crumbs. To avoid these problems we are also distributing binary versions of these scripts. These binaries might work for you. You can download them from:

http://bioinf.comav.upv.es/seq_crumbs/download.html

maubp · 04-25-2013, 01:25 AM

You can get missing core library modules like this if your Python was compiled without the underlying dependencies and their C headers. Perhaps you (or your systems administrator) can check that.

[This would not explain things if you used a pre-compiled Python from python.org, like the Windows installers]

chayan · 04-25-2013, 05:02 AM

My python version is 2.7.1.. sadly it seems that both the source distribution and binary distribution of latest "seq_crumbs 0.1.7" is unavailable right now to download. Additionally can you please tell me wheather this newest sff_extract can give the output in traceinfo/.xml format which are not possible with the 0.1.6 version??

Jose Blanca · 04-29-2013, 12:01 AM

The newest sff_extract can not create the traceinfo xml file. We have to add it to the new sff_extract, we add it to the TODO. If you need that functionallity you can use the old sff_extract:
http://bioinf.comav.upv.es/sff_extract/download.html

The latest new one you can always get it at github, but sff_extract have not been changed for a while.

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04-24-2013, 06:51 AM	#21
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	hii, sorry to say that i dont have much knowladge about linux and all this. What i understood from your previous reply, i install "libsasl2-dev" with the following command sudo apt-get install libsasl2-dev still the same error msg it showing... sorry if i missed anything particular.

04-25-2013, 01:07 AM	#22
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	Which python version are you using? Are you using python 2.7? It's a strange problem because that missing module belongs to the standard library. The newest sff_extract is now included in a package named seq_crumbs. To avoid these problems we are also distributing binary versions of these scripts. These binaries might work for you. You can download them from: http://bioinf.comav.upv.es/seq_crumbs/download.html

04-25-2013, 01:25 AM	#23
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	You can get missing core library modules like this if your Python was compiled without the underlying dependencies and their C headers. Perhaps you (or your systems administrator) can check that. [This would not explain things if you used a pre-compiled Python from python.org, like the Windows installers]

04-25-2013, 05:02 AM	#24
chayan Member Location: USA Join Date: Nov 2012 Posts: 51	My python version is 2.7.1.. sadly it seems that both the source distribution and binary distribution of latest "seq_crumbs 0.1.7" is unavailable right now to download. Additionally can you please tell me wheather this newest sff_extract can give the output in traceinfo/.xml format which are not possible with the 0.1.6 version??

04-29-2013, 12:01 AM	#25
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	The newest sff_extract can not create the traceinfo xml file. We have to add it to the new sff_extract, we add it to the TODO. If you need that functionallity you can use the old sff_extract: http://bioinf.comav.upv.es/sff_extract/download.html The latest new one you can always get it at github, but sff_extract have not been changed for a while.