yachielab/queen

QUEEN: a framework to generate quinable and efficiently editable nucleotide sequence resources

queen's Issues

visualizemap does not indicate overhangs

from queen import *
fragment = QUEEN(seq="CCGGTATGCG----/----ATACGCAGCT") 
fragment.printsequence(display=True)
fig = visualizemap(fragment, seq= True )
fig = visualizemap(fragment, seq=True, rcseq = True)

I'd expect overhang bases to be grayed/alphaed out instead.

Out tata

"AttributeError: 'ExactPosition' object has no attribute 'position' when using QUEEN(seq='...')" in Colab

When running the Example code 1 (Create a QUEEN class object (blunt-ends), dna = QUEEN(seq="CCGGTATGCGTCGA")) in Colab, I now get the "AttributeError". This error has probably occurred between 20-25.12 2023. I have tried with both versions in Colab (queen=1.1.0 and 1.2.0). Interestingly, it works locally in jupyter notebook.

flipdna() breaks visualizeflow()

Hi @ponnhide,
The flipdna() function against a QUEEN instance breaks visualizeflow(). Here's a minimal example.

This works without any errors (No flow map would be visualized though).

M13F = QUEEN("GTAAAACGACGGCCAGT")
visualizeflow(M13F)

However, this one fails with the error below.

M13F = QUEEN("GTAAAACGACGGCCAGT")
visualizeflow(flipdna(M13F))

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[83], line 1
----> 1 visualizeflow(flipdna(M13F))

File ~/micromamba/envs/general/lib/python3.11/site-packages/QUEEN/qgraph.py:845, in visualizeflow(search_function, grouping, inherited_process, process_description, split_input, sf, ip, pd, si, alias_dict, *dnas)
    843 sdgflag = 0 
    844 for productname in productnames:
--> 845     if "_load" in info_dict and "cutdna" not in funcname:
    846         if productname not in nodes:
    847             dg.node(productname, label=productname, margin="0.05", shape="oval", fontname="Arial") 

TypeError: argument of type 'NoneType' is not iterable

Here's my environment

% pip list | grep -i queen
python-queen                  1.2.0

unable to pip instal V1.2 from git

Looks like there is an invalid file path in the repository: see below for error message.

error: invalid path 'demo/sakata_et_al_2020/input/original/addg:Users:hideto:Dropbox (Yachie Lab):HIDETO_MORI.LAB:Experiments:Project:Dbrick:github:demo:sakata_et_al_2020:input:original:addgene_79620.gbkene_79620.gbk'
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'