mjsull / contiguity Goto Github PK
View Code? Open in Web Editor NEWTool for visualising assemblies.
License: GNU General Public License v3.0
Tool for visualising assemblies.
License: GNU General Public License v3.0
I saw the following error after File -> Create CAG file
Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/local/Cellar/python/2.7.9/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "/usr/local/bin/contiguity", line 2817, in edge_thread
abort = self.get_nmer_freq_khmer()
File "/usr/local/bin/contiguity", line 3445, in get_nmer_freq_khmer
self.ht = khmer.new_counting_hash(nmersize, ht_size, ht_n, n_threads) # HT_size, number ht, threads
TypeError: new_counting_hash() takes at most 3 arguments (4 given)
You have a remnant MS Word backup file in your repository:
~$ntiguity_manual_0.3.docx
If the core documentation is written in ReStructuredText we can easily generate DOC/PDF from this. The added bonus is we can push to ReadTheDoc.
Also, we can easily grab/chomp stuff into the tutorial on the GitHub site etc.
Hi Mitchell,
I tried to create CAG file and came to this error. I am lost. Do you have any idea what might be my problem? Is it the issue with the khmer? I installed it using easy_install khmer and it's version 2.0. Sorry if my issue is not relevant to be posted here.
Cheers,
Cheng
Exception in thread Thread-1:
Traceback (most recent call last):
File "/data/chengyee/bin/anaconda/lib/python2.7/threading.py", line 810, in __ bootstrap_inner
self.run()
File "/data/chengyee/bin/anaconda/lib/python2.7/threading.py", line 763, in run
self.__target(_self.__args, *_self.__kwargs)
File "Contiguity.py", line 2883, in edge_thread
abort = self.get_nmer_freq_khmer()
File "Contiguity.py", line 3510, in get_nmer_freq_khmer
self.ht = khmer.new_counting_hash(nmersize, ht_size, ht_n) # HT_size, number ht, threads
AttributeError: 'module' object has no attribute 'new_counting_hash'
Hi Mitch,
I pip installed the latest version of Contiguity but I'm still getting this error after running create CAG:
TypeError: new_counting_hash() takes at most 3 arguments (4 given).
I saw this has already been reported as a bug - has it been fixed?
Cheers,
Leah
It says "BLAST" but I think you mean the "BLAST+" package, because you use "blastn" and not the old wrapper "blastall -p blastn" ?
Hi Mitch,
I can't create a CAG file - it exits with "Killed 9". Do you know how I can fix this?
Thanks.
Leah
Hi Mitch,
I'm trying to create CAG and it's been running for hours. Is this normal? And if my de novo assembly is using both paired-end reads and single-end read, will it be sufficient to use only interleaved paired-end reads for the read file input? Thanks.
Regards,
Cheng
Fix zooming out with mouse wheel
In the README it makes the user track down the manual.
You can link directly to it by the "Raw" link for it:
https://github.com/mjsull/Contiguity/raw/master/Contiguity_manual_0.3.pdf
Allow user to import a ruler with distance markings
If contig added has a hit to the reference add the blast hit as well.
Via @tseemann = needs to have a "quick start" on the GitHub site.
Also via @tseemann -
It needs to be made clear what the inputs are -
Just Velvet graph file or FASTG or need to generate the CAG. Also needs to explain the CAG.
I personally think sending someone to the manual/tutorial (which is large and comprehensive) already could scare them off.
This is related to #11
This would allow the automatic duplication of repeat regions,
Also via @tseemann - make it into a package/brew recipe/docker image.
When dragging contigs sometimes contig goes off the page.
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