corna's People
Forkers
ankur09011corna's Issues
Auto-detect indistinguishable isotopes are being detected but not corrected for correctly
Try running this file
auto_detect_indistinguish_dual_label copy.txt
For Glutathione the expected output is:
40% unlabeled and 60% 13C-3 15N-1 which I get if I give the indistinguishable isotopes manually i.e. {'C': ['H','O'], 'N':['S']}
But not with auto-detect. The reason being this function:
def make_correction_matrix(trac_atom, formuladict, na_dict, indist_elems):
"""create matrix M such that Mx=y where y is the observed isotopic distribution
and x is the expected distribution of input labels
atom_bag: dict of element:number of atoms in molecule (e.g. {'C':2,'O':1,'H':6})
label_elem: element with input labeling
indist_elems: elements with identical mass shift
na_dict: dict of element:expected isotopic distribution
:TODO This function relates to issue NCT-247. Need to change the function
in more appropriate way.
"""
M = make_expected_na_matrix(formuladict.get(trac_atom, 0), na_dict[trac_atom])
for e in indist_elems:
if e in formuladict:
e1 = ISOTOPE_NA_MASS[KEY_ELE][e]
M = add_indistinguishable_element(M, formuladict[e1], na_dict[e])
return pinv(M)
So, the if statement would reject indistinguishable isotopes like 'O17','O18' and 'S33' because these won't be in the formula. And I tested it is giving the same result as what you would get if manual input was 'C':['H'] because 'H' remains the same in both cases.
Create a GCMS demo
- Ipython notebook
- Use a publicly available dataset for correction
Make validation consistent across the package
Currently, one workflow is using olmonk and other some inbuilt validation. If olmonk is to be used across everything, it should be made optional such that if the user doesn't have olmonk, it doesn't stop the workflow only stops the validation.
Create a working LCMS demo for the package, remove existing one
This demo should have the following:
- Be an Ipython notebook
- Use publicly available raw files like used for Polly IsoCorrect demo.
- Include demo for - one label, two label, indistinguishible isotopes, auto-indistinguishible isotopes
corna package depends on some internal packages which are not opensource
Such dependencies should be optional
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ 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. ๐๐๐
-
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 โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.