sorsaffari’s gists

sorsaffari / clouds.py

Last active March 7, 2019 00:50

	def win(clouds):
	print(clouds)
	now_on = -1
	jumps = 0

	if clouds[-1] == 1:
	print("invalid game! ends with a thunderhead.")
	return None

	while True:

sorsaffari / example-working-with-tweets-pom.xml

Created January 16, 2019 12:10

example-working-with-tweets/pom.xml

	<?xml version="1.0" encoding="UTF-8"?>
	<project xmlns="http://maven.apache.org/POM/4.0.0"
	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
	<modelVersion>4.0.0</modelVersion>

	<groupId>ai.grakn</groupId>
	<artifactId>twitterexample</artifactId>
	<version>1.0-SNAPSHOT</version>

sorsaffari / movies-schema.gql

Created January 7, 2019 14:38

sample-datasets > movies > schema.gql

	insert
	"production" sub entity
	is-abstract
	## Filming details
	plays production-with-crew
	plays production-with-cast
	plays production-with-company

	plays production-with-location

sorsaffari / protein_structure_prediction_rule.gql

Created November 2, 2018 16:49

Protein Structure Prediction: Implied sequence-function-mapping rule

	sequence-function-mapping sub relationship,
	relates mapping-sequence,
	relates mapped-function;

	implied-sequence-function-mapping sub rule,
	when {
	$seq isa sequence;
	$struct isa structure;
	$func isa function;
	(mapping-sequence: $seq, mapped-structure: $struct) isa sequence-structure-mapping;

sorsaffari / protein_structure_prediction_query_5.gql

Created November 2, 2018 15:37

Protein Structure Prediction: Get all functions that relate directly or indirectly (via a similar sequence) to a particular sequence

	match
	$target-sequence isa sequence "MNVGTAHSEVNPNTRVMNSRGIWLSYVLAIGLLHIVLLSIPFVSVPVVWTLTNLIHNMGMYIFLHTVKGTPFETPDQGKARLLTHWEQMDYGVQFTASRKFLTITPIVLYFLTSFYTKYDQIHFVLNTVSLMSVLIPKLPQLHGVRIFGINKY";
	$direct-function isa function;
	(mapping-sequence: $target-sequence, mapped-function: $direct-function) isa sequence-function-mapping;
	$similar-sequence isa sequence;
	$alignment (target-sequence: $target-sequence, matched-sequence: $similar-sequence) isa sequence-sequence-alignment;
	$alignment has identicality > 0.8;
	$indirect-function isa function;
	(mapping-sequence: $similar-sequence, mapped-function: $indirect-function) isa sequence-function-mapping;
	get $direct-function, $indirect-function;

sorsaffari / protein_structure_prediction_query_4.gql

Created November 2, 2018 15:34

Protein Structure Prediction: Get all sequences that have a particular function

	match
	$target-function isa function "enzyme";
	$sequence isa sequence;
	(mapping-sequence: $sequence, mapped-function: $target-function) isa sequence-function-mapping;
	get $sequence;

sorsaffari / protein_structure_prediction_query_3.gql

Last active November 2, 2018 15:29

Protein Structure Prediction: Get all structures of the sequences that have an alignment with a particular sequence (with unknown structure), given that the alignment has an identicality above 80%

	match
	$target-sequence isa sequence "MNVGTAHSEVNPNTRVMNSRGIWLSYVLAIGLLHIVLLSIPFVSVPVVWTLTNLIHNMGMYIFLHTVKGTPFETPDQGKARLLTHWEQMDYGVQFTASRKFLTITPIVLYFLTSFYTKYDQIHFVLNTVSLMSVLIPKLPQLHGVRIFGINKY";
	$similar-sequence isa sequence;
	$alignment (target-sequence: $target-sequence, matched-sequence: $similar-sequence) isa sequence-sequence-alignment;
	$alignment has identicality > 0.8;
	$structure isa structure;
	(mapping-sequence: $similar-sequence, mapped-structure: $structure) isa sequence-structure-mapping;
	get $structure;

sorsaffari / protein_structure_prediction_query_2.gql

Created November 2, 2018 15:25

Protein Structure Prediction: Get all sequences that have a particular structure

	match
	$target-structure isa strucuture has pdb-id "2RHC";
	$sequence isa sequence;
	(mapping-sequence: $sequence, mapped-structure: $target-structure) isa sequence-structure-mapping;
	get $sequence;

sorsaffari / protein_structure_prediction_query_1.gql

Created November 2, 2018 15:19

Protein Structure Prediction: Get all structures of a particular sequence

	match
	$target-sequence isa sequence "MNVGTAHSEVNPNTRVMNSRGIWLSYVLAIGLLHIVLLSIPFVSVPVVWTLTNLIHNMGMYIFLHTVKGTPFETPDQGKARLLTHWEQMDYGVQFTASRKFLTITPIVLYFLTSFYTKYDQIHFVLNTVSLMSVLIPKLPQLHGVRIFGINKY";
	$structure isa structure;
	(mapping-sequence: $target-sequence, mapped-structure: $structure) isa sequence-structure-mapping;
	get $structure;

sorsaffari / XmlMigration.java

Created October 23, 2018 16:39

Migrating XML data into Grakn using the Java client

	package ai.grakn.examples;

	import ai.grakn.GraknTxType;
	import ai.grakn.Keyspace;
	import ai.grakn.client.Grakn;
	import ai.grakn.util.SimpleURI;

	/**
	* a lean JSON Library for Java,
	* @see <a href="https://bolerio.github.io/mjson/">mjson</a>

Soroush Saffari sorsaffari