jctoledo’s gists

jctoledo / gist:9002170

Created February 14, 2014 14:43

cycle size distribution of cycles that are in rna ligand neighbourhoods

	select STR(?size) as ?cycle_size COUNT(?a) as ?frequency
	from <http://bio2rdf.org/narf:rna_cycles>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?c.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?d.
	?d a <http://bio2rdf.org/narf_vocabulary:cycle_size>.
	?d <http://bio2rdf.org/narf_vocabulary:has_value> ?size.
	?c a <http://bio2rdf.org/narf_vocabulary:cycle_profile_level_2> .
	?c <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash .

jctoledo / gist:9002044

Created February 14, 2014 14:38

get the cycle size distribution of all rna cycles

	select STR(?size) as ?cycle_size COUNT(?a) as ?frequency
	from <http://bio2rdf.org/narf:rna_cycles>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?c.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?d.
	?d a <http://bio2rdf.org/narf_vocabulary:cycle_size>.
	?d <http://bio2rdf.org/narf_vocabulary:has_value> ?size.
	?c a <http://bio2rdf.org/narf_vocabulary:cycle_profile_level_2> .
	?c <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash .

jctoledo / gist:9001916

Last active August 29, 2015 13:56

query to get the counts of cycles in ligand neighbourhoods

	select STR(?ahash) AS ?level2profile COUNT(distinct ?a)
	from <http://bio2rdf.org/narf:rna_cycles>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?c.
	?c a <http://bio2rdf.org/narf_vocabulary:cycle_profile_level_2> .
	?c <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash .
	?a <http://bio2rdf.org/narf_vocabulary:has_part> ?ap.
	?lh <http://bio2rdf.org/lighood_vocabulary:has_member> ?ap.
	}

jctoledo / gist:8983325

Created February 13, 2014 20:37

get the counts of level 2 profiles in rna structures

	select distinct STR(?ahash) AS ?s COUNT(?s)
	from <http://bio2rdf.org/narf:rna_cycles>
	where{
	?a a <http://bio2rdf.org/narf_vocabulary:cycle>.
	?a <http://bio2rdf.org/narf_vocabulary:has_attribute> ?c.
	?c a <http://bio2rdf.org/narf_vocabulary:cycle_profile_level_2> .
	?c <http://bio2rdf.org/narf_vocabulary:has_md5hash> ?ahash .
	}

jctoledo / gist:8016481

Created December 18, 2013 02:40

Run RNAfold from Java. Based on this code: http://csbi.ltdk.helsinki.fi/meap/anduril/doc/components/RNAFold/RNAFold.java

	protected String execute(Sequence aSequence, String[] commands)
	throws InvalidSequenceException, IOException {
	String returnMe = "";
	if (aSequence.getLength() == 0) {
	throw new InvalidSequenceException(
	"The sequence provided to execute RNAFold was empty!");
	}

	String[] cmdArr = new String[commands.length + 1];
	System.arraycopy(new String[] { "RNAfold" }, 0, cmdArr, 0, 1);

jctoledo / gist:6717383

Created September 26, 2013 17:17

	<?php

	function write_predicate_object_counts($fh, $pred_obj_counts){
	GLOBAL $dataset_uri;
	GLOBAL $options;
	if($pred_obj_counts !== null){
	foreach($pred_obj_counts as $pred => $count){
	#create a resource for the property partition
	$partition_res = "http://bio2rdf.org/dataset_resource:".md5($options['url']).md5($options['url'].$pred.$count."predicate_object_count");
	#add the dataset type

jctoledo / gist:6715916

Created September 26, 2013 15:35

	<?php

	function write_predicate_object_counts($fh, $pred_obj_counts){
	GLOBAL $options;
	if($pred_obj_counts !== null){
	foreach($pred_obj_counts as $pred => $count){
	fwrite($fh, Quad("http://bio2rdf.org/dataset_resource:".md5($options['url']), "http://bio2rdf.org/dataset_vocabulary:has_predicate_object_count", "http://bio2rdf.org/dataset_resource:".md5($options['url'].$pred.$count."predicate_object_count")));
	fwrite($fh, Quad("http://bio2rdf.org/dataset_resource:".md5($options['url'].$pred.$count."predicate_object_count"), "http://bio2rdf.org/dataset_vocabulary:has_predicate", $pred));
	fwrite($fh, QuadLiteral("http://bio2rdf.org/dataset_resource:".md5($options['url'].$pred.$count."predicate_object_count"), "http://bio2rdf.org/dataset_vocabulary:has_count", $count));
	}

jctoledo / gist:6715600

Created September 26, 2013 15:14

	<?php
	function get_void_dataset_uri(){
	GLOBAL $cmd_pre;
	GLOBAL $cmd_post;
	$q = "select ?x where {?w <http://rdfs.org/ns/void#inDataset> ?x.}LIMIT 1";
	$cmd = $cmd_pre.$q.$cmd_post;
	$out = "";
	try{
	$out = execute_isql_command($cmd);
	}catch(Exception $e){

jctoledo / gist:6715580

Last active December 24, 2015 00:19

	<?php
	function write_type_counts($fh, $type_counts){
	GLOBAL $options;
	GLOBAL $dataset_uri;
	if($type_counts !== null){
	foreach($type_counts as $type => $count){
	#now create a resource for the class partition
	$partition_res = "http://bio2rdf.org/dataset_resource:".md5($options['url']).md5($options['url'].$type.$count."type_count");
	fwrite($fh, Quad($partition_res, "http://www.w3.org/1999/02/22-rdf-syntax-ns#type", "http://rdfs.org/ns/void#Dataset"));
	fwrite($fh, Quad($partition_res, "http://rdfs.org/ns/void#class", $type));

jctoledo / gist:6622850

Created September 19, 2013 12:40

Find details about a given ligand in a PDB structure using biopython

	from Bio.PDB import *
	import sys
	p = PDBParser(PERMISSIVE=1)
	ligand_id = "ADE"
	radius = 5.4
	pdbl = PDBList()
	structure_id = "1Y26"
	pdbl.retrieve_pdb_file(structure_id, pdir="/tmp")
	filename = "1y26.pdb"
	#see for more details: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc153

Jose Cruz-Toledo jctoledo