mjsull/contiguity

Tool for visualising assemblies.

contiguity's Issues

new_counting_hash() takes at most 3 arguments (4 given)

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)

Remnant MS Word backup file in your repository

You have a remnant MS Word backup file in your repository:

~$ntiguity_manual_0.3.docx

Convert the .docx to RST (lowest priority)

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.

AttributeError: 'module' object has no attribute 'new_counting_hash'

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'

TypeError: new_counting_hash() takes at most 3 arguments (4 given) Again?

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

Clarify blast dependency - BLAST or BLAST+ ?

It says "BLAST" but I think you mean the "BLAST+" package, because you use "blastn" and not the old wrapper "blastall -p blastn" ?

"killed 9" error when making CAG file

Hi Mitch,
I can't create a CAG file - it exits with "Killed 9". Do you know how I can fix this?
Thanks.
Leah

Remove out of frame blast hits

Is slow process normal?

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

Zoom out off centre

Fix zooming out with mouse wheel

move sequence data etc. to a shelve

Provide direct link to PDF manual

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

Add ruler

Allow user to import a ruler with distance markings

Re-adding contig doesn't re-add blast hit

If contig added has a hit to the reference add the blast hit as well.

Quickstart is needed urgently.

Via @tseemann = needs to have a "quick start" on the GitHub site.

Undo/redo buttons

What are the minimum required inputs. (top priority)

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

create acyclic graph

This would allow the automatic duplication of repeat regions,

"Install-ability"

Also via @tseemann - make it into a package/brew recipe/docker image.

Display small contigs as circles.

Things moving too far

When dragging contigs sometimes contig goes off the page.