prodigy | Repository containing various scripts to predict | Genomics library
kandi X-RAY | prodigy Summary
kandi X-RAY | prodigy Summary
The scripts rely on Biopython to validate the PDB structures and calculate interatomic distances. freesasa, with the parameter set used in NACCESS (Chothia, 1976), is also required for calculating the buried surface area. DISCLAIMER: given the different software to calculate solvent accessiblity, predicted values might differ (very slightly) from those published in the reference implementations. The correlation of the actual atomic accessibilities is over 0.99, so we expect these differences to be very minor. To install and use the scripts, just clone the git repository or download the tarball zip archive. Make sure freesasa and Biopython are accessible to the Python scripts through the appropriate environment variables ($PYTHONPATH).
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Top functions reviewed by kandi - BETA
- Predict the connectivity of the structure
- Redirect stdout to destination
- Calculate the coordination index for a structure
- Convert decimal degrees to Kelvin
- Calculates the NIS coefficient
- Analyse a list of contacts
- Execute a freesasa API
- Calculate the percentage of buried interface residues in a dictionary
- Execute freesasa
- Parse a FASTA output file
- Parse a structure file
- Validate a structure
- Write PYMOL script to outfile
- Print the prediction
- Print the contacts
- Check if the file exists
- Read file contents
prodigy Key Features
prodigy Examples and Code Snippets
Lines of Code : 5License : Permissive (Apache-2.0)
Copygit clone http://github.com/haddocking/prodigy
cd prodigy
pip install .
# Have fun!
prodigy [--selection ]
prodigy --help
Community Discussions
Trending Discussions on prodigy
QUESTION
very new to ML and Python and appreciate any help for this issue. I've trained an NER model using Prodigy (based on en_core_web_lg) and saved the model to my virtual environment:
I'm on Windows 10 with CONDA/VSCODE, SpaCy 2.x environment and I'm now trying to load a comma delimited CSV file that looks like this:
...ANSWER
Answered 2021-Aug-12 at 03:16nlp accepts strings as inputs, you are correct.
If you want to use it on one paragraph, you can do it like this:
doc=nlp(input['Text'].values[0])
Where 0 is a number of the paragraph.
QUESTION
This question is in the context of adding a language to the spaCy v2 library, but it may be a generic python packaging question.
In spaCy, languages are subclasses of a Language base class, and much of the tooling expects a given language to be placed in a normatively named package (e.g. spacy.lang.en for english).
There are various ways arount this requirement (for example, @spacy.registry.languages), but this usually entails a few tradeoffs (e.g. you have to import some code first to register your classes and then it's all fine, but when you have tooling like custom scripts, prodigy recipes, libraries, ... that do not allow you to "inject" custom imports or have their own way of doing so, this does not work - or is generally error prone). I'd be happy to hear about suggestions for easing this out if there is a way.
So I thought I'd just put my language where spaCy expects it, and I'd be fine. Creating a language subclass is documented enough.
So I bootstraped a library :
...ANSWER
Answered 2021-May-31 at 11:46Be sure to follow the v2 docs for spaCy v2 since there are a number of differences. (The registry decorators are new in v3).
spaCy v2 supports entry points for custom languages: https://v2.spacy.io/usage/saving-loading#entry-points
Your package will have its own name (not spacy) and you can add a custom language in spaCy v2 by adding an entry point under spacy_languages in setup.py:
QUESTION
I have used this code:
...ANSWER
Answered 2021-May-23 at 19:39Splitting each line by spaces and then creating a flatmap of all these values when you are primarily interested in a count of the domains may be giving additional work and definitely additional overhead and processing.
Based on the sample data provided, the domain is the first item on each line. I have also noted that some of your lines begin with an empty space and as such results in an additional string piece. You may considering using the strip function to trim the line before the process.
You may consider modifying process to return only the first bit of the string or creating another map operation which does.
QUESTION
I have RDD as below:
...ANSWER
Answered 2021-May-21 at 20:00split returns a python list which does not have map. You may use the following instead
QUESTION
I am using the following code
...ANSWER
Answered 2021-May-20 at 15:31Your code looks fine with sample data you provided (I reformat it as below). I suppose the problem could come from your data itself. Try to break down or limit your dataset?
QUESTION
I am trying to remove double quotes from text file like :
in24.inetnebr.com [01/Aug/1995:00:00:01] "GET /shuttle/missions/sts-68/news/sts-68-mcc-05.txt" 200 1839 uplherc.upl.com [01/Aug/1995:00:00:07] "GET /" 304 0 uplherc.upl.com [01/Aug/1995:00:00:08] "GET /images/ksclogo-medium.gif" 304 0 uplherc.upl.com [01/Aug/1995:00:00:08] "GET /images/MOSAIC-logosmall.gif" 304 0 uplherc.upl.com [01/Aug/1995:00:00:08] "GET /images/USA-logosmall.gif" 304 0 ix-esc-ca2-07.ix.netcom.com [01/Aug/1995:00:00:09] "GET /images/launch-logo.gif" 200 1713 uplherc.upl.com [01/Aug/1995:00:00:10] "GET /images/WORLD-logosmall.gif" 304 0 slppp6.intermind.net [01/Aug/1995:00:00:10] "GET /history/skylab/skylab.html" 200 1687 piweba4y.prodigy.com [01/Aug/1995:00:00:10] "GET /images/launchmedium.gif" 200 11853 slppp6.intermind.net [01/Aug/1995:00:00:11] "GET /history/skylab/skylab-small.gif" 200 9202
The code I am trying is :
...ANSWER
Answered 2021-May-19 at 15:54Two things.
You missed return statement and instead of double quotes, use single quotes in replace statement. Here is pure python code, you can convert to "call from map" in spark.
QUESTION
For a project working with Prodigy, I want to have a .jsonl file, in which each line is a json file.
To do so, I have the following code:
...ANSWER
Answered 2021-May-07 at 14:23You solved the hard part. You can write jsonl directly to a file:
QUESTION
I have a prodigy session set up to annotate certain numeric values in a document for age (ranges from 0 to 100). I am only annotating the number. My question is, suppose there is a corrupt value which crept in (age being 1000 or 22.7), will the model understand that even though it is close to the age text in the document, it should not be picked up?
In other words, can it learn the range of integer values, and if it does, will that work for date format as well? For instance a date in the format dd/mm/yyyy which is DOB (all the annotated ones are < 01/01/2000) and there is a date 31/12/2020, will that get picked up as well since all the annotated dates are nowhere close to this range?
Thank you
...ANSWER
Answered 2021-Mar-25 at 03:44Good question! spaCy does not internally represent numeric tokens as numbers, so it doesn't have an explicit concept of the values. In that sense it can't tell between valid and invalid values for age.
However, spaCy does use "shape" features when representing tokens that will help it recognize valid ages. There are different kinds of shape tokens, but the one spaCy uses will represent words by converting characters to a representation of the character type. It works like this:
- spaCy → xxxXx
- fish → xxxx
- Fish → Xxxx
- 23 → dd
- 1000 → dddd
- 22.7 → dd.d
Because of this you could expect that spaCy learns that two-digit numbers are likely to be ages, but numbers with decimals or four digits aren't likely. On the other hand, this doesn't help it differentiate between 100 and 999.
For dates this will not help with determining valid or invalid birthdates. Shape is just one of spaCy's features, but other features like prefix and suffix aren't really going to help with this either.
Since it's easy to verify numeric values in code, what I would suggest is matching broadly in spaCy and then using your own function to check whether dates or ages are valid by parsing them.
Outside of spaCy in particular, the question of how NLP models represent numeric values is actually an increasingly popular research topic - if you'd like to know more about it this is a recent article on the topic: Do Language Models Know How Heavy an Elephant Is?
QUESTION
im currently working for a webapp using nodejs . this is my first time using Node. I have an items in array(topsongs_s[]) that will be pass (one by one) as an arguments to modules function tht get a data from a musixmatch API .
modules : https://github.com/c0b41/musixmatch#artistsearch example given in the modules :
...ANSWER
Answered 2021-Feb-09 at 09:27Use async/await
I have added comments in the code snippet for the explanation, it pretty straightforward.
QUESTION
I try to download a image from a website but I get an error. Can somebody help me and explain what is going on and how could I make a work around?
Sorry I'm completely new to programming stuff with websites.
...ANSWER
Answered 2021-Jan-15 at 19:07Maybe it helps you::
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Install prodigy
You can use prodigy like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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