SNP_ID2EntrezGene_ID

None

import java.util.*;

String [] line = string.split("\t");
out1=line[0].trim();
List split = new ArrayList();
if (!string.equals("")) {
	String regexString = ",";
	if (regex != void) {
		regexString = regex;
	}
	String[] result = string.split(regexString);
	for (int i = 0; i < result.length; i++) {
		split.add(result[i]);
	}
}

flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);
flatten(inputs, outputs, depth) {
	for (i = inputs.iterator(); i.hasNext();) {
	    element = i.next();
		if (element instanceof Collection && depth > 0) {
			flatten(element, outputs, depth - 1);
		} else {
			outputs.add(element);
		}
	}
}

outputlist = new ArrayList();

flatten(inputlist, outputlist, 1);
import java.util.*;

List tmp_end = new ArrayList();
List tmp_start = new ArrayList();
width =Integer.parseInt(in1.get(0));

int out_end=0;
int out_start=0;
for(int i=0; i < in2.size(); i++) {
           value_pos = Integer.parseInt(in2.get(i));
	   out_end = value_pos + width;
	   out_start = value_pos - width;	
	

		
    tmp_end.add(out_end);
    tmp_start.add(out_start);
 }

end_out = tmp_end;
start_out = tmp_start;
chr_out = chr_in;

Name	Description
SNP_ID	Use (a list of) Database of Single Nucleotide Polymorphisms (dbSNP) IDs as input, separated by the newline character (\n).
set_width	The allows the user to set the flanking width for the gene for determining SNPs.

Name	Type	Description
extract_snp_id	beanshell	This extracts the contents (snp_ids) from the input. Script import java.util.*; String [] line = string.split("\t"); out1=line[0].trim();
Split_string_into_string_list_by_regular_expression	localworker	This service splits the string value into a string list at every occurrence of the specified regular expression. The regular expression provided in this case is a new line: "\n" Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
regex_value	stringconstant	Value \n
hsapiens_snp	biomart	This is a Biomart service that takes the SNP ID as the input and returns chromosome name, and the position of the SNP.
Flatten_List	localworker	This service flattens the inputlist by one level. It returns the result of the flattening. Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_2	localworker	This service flattens the inputlist by one level. It returns the result of the flattening. Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
input_chr_position	beanshell	The purpose of this beanshell is to manipulate the start and end positions based on the flanking width provided by the user. Script import java.util.*; List tmp_end = new ArrayList(); List tmp_start = new ArrayList(); width =Integer.parseInt(in1.get(0)); int out_end=0; int out_start=0; for(int i=0; i < in2.size(); i++) { value_pos = Integer.parseInt(in2.get(i)); out_end = value_pos + width; out_start = value_pos - width; tmp_end.add(out_end); tmp_start.add(out_start); } end_out = tmp_end; start_out = tmp_start; chr_out = chr_in;
hsapiens_gene_ensembl	biomart	This is a Biomart service that takes the chromosome name and start and end positions and returns genes (entrez gene id) present in the region.

Name	Description	Inputs	Outputs
extract_snp_id	This extracts the contents (snp_ids) from the input.	string	out1
input_chr_position	The purpose of this beanshell is to manipulate the start and end positions based on the flanking width provided by the user.	chr_in in2 in1	chr_out end_out start_out

Source	Sink
Split_string_into_string_list_by_regular_expression:split	extract_snp_id:string
regex_value:value	Split_string_into_string_list_by_regular_expression:regex
SNP_ID	Split_string_into_string_list_by_regular_expression:string
extract_snp_id:out1	hsapiens_snp:hsapiens_snp.snp_filter_filter
hsapiens_snp:hsapiens_snp.chr_name	Flatten_List:inputlist
hsapiens_snp:hsapiens_snp.chrom_start	Flatten_List_2:inputlist
Flatten_List:outputlist	input_chr_position:chr_in
Flatten_List_2:outputlist	input_chr_position:in2
set_width	input_chr_position:in1
input_chr_position:chr_out	hsapiens_gene_ensembl:hsapiens_gene_ensembl.chromosome_name_filter
input_chr_position:end_out	hsapiens_gene_ensembl:hsapiens_gene_ensembl.end_filter
input_chr_position:start_out	hsapiens_gene_ensembl:hsapiens_gene_ensembl.start_filter
hsapiens_gene_ensembl:hsapiens_gene_ensembl.entrezgene	EntrezGene_ID

SNP_ID2EntrezGene_ID

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Magnus Palmblad	Monday 11 March 2013 13:57:43 (UTC)
	Works great and is well documented. Perhaps the output could also include a list with the gene names?