Comments (9)
I find a biopython=1.69 version and then install vcfkit. Still not work.
Error:
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
Specifications:
- vcfkit -> python[version='3.4.|3.5.|3.6.*|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
Your python: python=2.7
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.
from vcf-kit.
I have solved the problem and it seems working well.
The solution:
conda create -n vcf-kit python=2.7
conda install matplotlib=2.2.5
conda install yahmm=1.1.2
pip install numpy==1.16.0
pip install VCF-kit
After this, find the "anaconda3/envs/vcf-kit/lib/python2.7/site-packages/vcfkit/utils/vcf.py"
change line 11 "np.set_printoptions(threshold=np.nan)" to "np.set_printoptions(threshold=10000000000000)"
And it works.
Because i cannot install vcfkit with conda(I don't know why.), I create a env of python2.7 with conda and then install the package which vcfkit need as the auther says.
Maybe the numpy version or some other package version is different from the auther use, I have to change the code slightly. I believe it is a numpy version issue.
from vcf-kit.
@Haoyuan17 I recommend installing vcf-kit in it's own environment.
I think you can simply do:
condo create -n vcf-kit vcf-kit
from vcf-kit.
@danielecook
At first I have used conda to install with the code:
conda config --add channels bioconda
conda create -n vcf-kit python=2.7 vcfkit
But there is a error as following:
from vcf-kit.
@Haoyuan17 what tools are you looking to use within vcf-kit? I am working on a new version that is compiled here: https://www.github.com/danielecook/seq-collection
Do you have docker installed? Python2 is being deprecated it looks like, so getting vcf-kit to work with Python3 will take some time.
One nice alternative you can try is running your analysis in a docker container.
docker pull ezequieljsosa/vcfkit
from vcf-kit.
@danielecook
Thanks a lot.
My python version is 2.7 and I don't why I could not install vcf-kit easily. My friend could install in a few minutes, so it is the problem with my pc.
Actually I could use the vcf-kit now with a complicated process. I need the newick file and vcf-kit help me convert vcf to newick. The "vk phylo" command is good enough except for the large vcf file(I have a 50GB vcf file).
Do you have any advice on this issue: using "vk phylo" for large file?
I noticed that "seq-collection" could convert VCF to JSON. I am not familiar with JSON. Could I use JSON to get a newick file? How the JSON works with large file?
from vcf-kit.
@danielecook
I am writing to say the vcf-kit is really good.
I mentioned about the large vcf file issue. It is not an issue. At first, I believe that I cannot run large file with my pc with a normal size RAM. I am wrong. The "vk phylo" command works well with the 50GB vcf.
When I use MEGA, online tools or other software, it is hard to get a fasta from vcf. I have to align the fasta and then make a phylo-tree. These takes a really long time more than vcf-kit. And my pc usually breakdown at the alignment step.
Thanks for your work and I would like to introduce the vcf-kit to my lab colleagues.
from vcf-kit.
Thanks!
from vcf-kit.
I noticed that "seq-collection" could convert VCF to JSON. I am not familiar with JSON. Could I use JSON to get a newick file? How the JSON works with large file?
JSON format is not really useful from a genetics perspective; It is designed for sending data and might be useful if you wanted to send VCF data to a web browser.
from vcf-kit.
Related Issues (20)
- vcf2tsv error HOT 1
- calculate Tajima'D on haploid HOT 2
- TypeError Python 3 HOT 2
- error loading tabix index for building a region specific tree HOT 2
- ImportError: No module named vcfkit HOT 4
- got an KeyError with the tajima.py HOT 1
- cannot get this to work HOT 5
- vk primer bio.alphabet error HOT 3
- KeyError: b'AC' in Tajima'sD calculation HOT 1
- Warning --sample option not given
- error while using docker image (andersenlab/vcf-kit:20200822175018b7b60d: TypeError: a bytes-like object is required, not 'str' HOT 1
- TypeError: '<' not supported between instances of 'int' and 'NoneType'
- Custom genome assembly?
- Memory Issues when running tajima module
- Muscle 5.1 no longer has "-maketree" command, breaking vk phylo
- Cannot find thermo path '/primer3_config/
- Running Docker version: "ModuleNotFoundError: No module named 'pomegranate'"
- problem with primer3 in both conda and docker
- vcf2tsv cna't print header
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from vcf-kit.