dipper | Data Ingestion Pipeline for Monarch | Genomics library
kandi X-RAY | dipper Summary
kandi X-RAY | dipper Summary
The Dipper data pipeline was born out of the need for a uniform representation of human and model organism genotype-to-phenotype data, and an Extract-Transform-Load (ETL) pipeline to process it all. It became too cumbersome to first get all of these data into a relational schema; so, we decided to go straight from each source into triples that are semantically captured, using standard modeling patterns. We are currently working on tooling around defining, documenting, and constraining our schema as biolink models.
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Top functions reviewed by kandi - BETA
- Parse command line arguments
- Create a spo representation of a subject
- Generate a unique id
- Construct a Biolink category
- Transform an NCBI entry
- Adds a triples
- Add an individual to the ontology
- Add association to the graph
- Parse the drugbank output file
- Process gene interaction associations
- Parses the G2p_clean output file
- Fetch the most recent files from the system
- Process a single phene phenotype row
- Make a property graph from the given properties
- Add triples
- Write the graph to a file
- Add property axioms to the graph
- Return a mapping of uniprot IDs to Entrez IDs
- Process a breeding phene row
- Convert KEGG disease to Gene object
- Populate the OMIM type
- Process a disease2gene
- Process pheno envirom
- Fetch data from udp
- Parse the genotype files
- Process OMIM to KEGG gene
dipper Key Features
dipper Examples and Code Snippets
pip3 install -r requirements.txt
pip3 install -r requirements/mgi.txt
pip3 install -r requirements.txt
pip3 install -r requirements/all-sources.txt
def reverse_list(lst):
new = []
for name in lst:
temp = name.split(" ")
new += [temp[1]+" "+temp[0]]
Community Discussions
Trending Discussions on dipper
QUESTION
I need to get all Storage Accounts which last modified date is 6 months ago with PS script. I didn't found any cmdlet or function which could provide such information. I thought it would be enough to sort by 'LastModifiedTime' but then I dig dipper, I saw that I have a lot of new files inside containers with the parameter "Modified". Question is how can I access these files with Powershell? Any cmdlet, function, etc?
Here is what I used to get SA before:
...ANSWER
Answered 2020-Mar-16 at 02:44Not sure if you just want to get the blobs which LastModifiedTime (aka: LMT) is in 180 days. If so, you don't need to check the container LMT, since it is not related with blob last modify time. (container LMT is for container properties modification).
Following script works with pipeline. If you don't need to check container LMT, just remove the check:
QUESTION
I already have a CSS/HTML mockup that makes it look like WhatsApp messaging, but only for conversations between 2 people. I want to add the group-chat feature, which means the names.
It's based on a
- list, so the HTML looks like this:
...
ANSWER
Answered 2020-Feb-04 at 04:26From what I understand,
You need the full name + text to come in one bubble. For that you can give background and styling to the .in and .out divs. Same goes for the pointing arrow.
You need to have some width, so the bubble has some width. For this remove the float left/right given to dd.
Rest you can fix using margin and padding.
QUESTION
I am developing a menu kiosk app right now, and I have some problems loading the images on my app, I made sure to specify each image in my pubspec.yaml but the images still does not show. The error i'm getting is this:
════════ Exception caught by image resource service ════════════════════════════
Unable to load asset: assets/images/sideDesserts/Dippers with Choco Dip.png
════════════════════════════════════════════════════════════════════════════════
Here is what my pubspec.yaml contains
...ANSWER
Answered 2020-Jan-30 at 13:14Rename your image. Your image name has space. In android image not load with space name. so Refactor your image name Dippers with Choco Dip to Dippers_with_Choco_Dip
QUESTION
I am trying to fetch JSON from external API and parse it so that I can access JSON object values in order to avoid values(fields) that I do not need.
I have studied JSONOBject library a little and parsed the objects, however, it feels that I am doing too much hard coding and not doing it correctly at all, feedback is much appreciated.
Output result after user input :
Sending 'GET' request to URL: https://api.coindesk.com/v1/bpi/currentprice/(user input currency)
Data fetched at UTC time/date : Sep 17, 2019 22:51:00 UTC Description: Ukrainian Hryvnia Rate float: 253737.6633
...ANSWER
Answered 2019-Sep-18 at 01:55I wrote a sample code to demonstrate what I said in comment by using ObjectMapper
to transform response json string into POJO.
First, create a class, says CoinDeskResponse
to store the transformation result.
QUESTION
ANSWER
Answered 2019-Aug-29 at 08:30try this one :
QUESTION
I want to add extra field to lookup result but i need a condition here. Every user has a relationship status (local field) and it should be added to lookup result for each user, but It's adding every 'status' to every user.
...ANSWER
Answered 2019-Aug-01 at 04:48You need $unwind to get single document per relationship:
QUESTION
Its my 2nd day of trying to make my "receiving of partial delivery" for my app. I am trying my luck here with you masters.
I have these two tables, the first one is the order_items table,
This table holds the items from the purchase order. and the other table is warehouse1
which hold the partially receive items.
I get the logic, I have to group the warehouse1.order_item_id so that I could get the sum of the items from let say order_number_id=22 which is the id from order_items table. to show you, here's my code doing the GROUP
...ANSWER
Answered 2019-Mar-15 at 21:52If you are asking why the quantity on your quantity column is not giving you a form, or why the return from that input is not correct, you have a few problems that I can see. The first issue is that you are creating n+1 number of number input form items in the same space with the same ID. This will likely prevent them from showing up, and will never produce a usable form. This:
QUESTION
I'm trying to arrange my heatmap so that values with higher "Overall" will appear at the top and values with a lower "Overall" will appear at the bottom. The issue is that the data (mydata
) is already arranged like this, but this arrangement isn't being applied to the end.
Any idea how I can fix this?
Thanks.
...ANSWER
Answered 2019-Jan-21 at 19:52You need to get the order that you want track_name
to be in, and then use that order to create a factor.
QUESTION
I have a div tag with the class "dipper"
...ANSWER
Answered 2018-Apr-14 at 06:44I found the answer here
QUESTION
I have to set value to property by string name representation.
...ANSWER
Answered 2017-Nov-07 at 12:50Documentation
Swift without the Objective-C Runtime: Swift on Linux does not depend on the Objective-C runtime nor includes it. While Swift was designed to interoperate closely with Objective-C when it is present, it was also designed to work in environments where the Objective-C runtime does not exist.
https://swift.org/blog/swift-linux-port/
Which is clear, provided that it states:
value of type 'A' has no member 'setValue'
It basically tells that there is no KVC mechanism underneath. setValue
method comes from Objective-C runtime, which is absent on Linux. Thus, it's a no-go and what you're trying to accomplish is simply not possible.
Other than that, the following rule is applied on systems with Obj-C runtime environment:
Swift objects that inherit from NSObject or one of its subclasses are key-value coding compliant for their properties by default. Whereas in Objective-C, a property’s accessors and instance variables must follow certain patterns, a standard property declaration in Swift automatically guarantees this. On the other hand, many of the protocol’s features are either not relevant or are better handled using native Swift constructs or techniques that do not exist in Objective-C. For example, because all Swift properties are objects, you never exercise the default implementation’s special handling of non-object properties.
Also: Requiring Dynamic Dispatch
Swift APIs that are callable from Objective-C must be available through dynamic dispatch. However, the availability of dynamic dispatch doesn’t prevent the Swift compiler from selecting a more efficient dispatch approach when those APIs are called from Swift code.
You use the @objc attribute along with the dynamic modifier to require that access to members be dynamically dispatched through the Objective-C runtime. Requiring this kind of dynamic dispatch is rarely necessary. However, it is necessary when using APIs like key–value observing or the method_exchangeImplementations function in the Objective-C runtime, which dynamically replace the implementation of a method at runtime.
Declarations marked with the dynamic modifier must also be explicitly marked with the @objc attribute unless the @objc attribute is implicitly added by the declaration’s context. For information about when the @objc attribute is implicitly added, see Declaration Attributes in The Swift Programming Language (Swift 4).
Elements must also be declared dynamic in order to be KVO-compatible (for KVC, inheriting from NSObject
is enough):
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install dipper
You can use dipper 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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