SNP Workflow

None

report = chrom + "," + position + "," + geneID;
String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

String seperatorString = "\n";
if (seperator != void) {
	seperatorString = seperator;
}
StringBuffer sb = new StringBuffer();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	sb.append(item);
	if (i.hasNext()) {
		sb.append(seperatorString);
	}
}
concatenated = sb.toString();

List strippedlist = new ArrayList();
for (Iterator i = stringlist.iterator(); i.hasNext();) {
	String item = (String) i.next();
	if (strippedlist.contains(item) == false) {
		strippedlist.add(item);
	}
}

Name	Type	Description
hsapiens_snp	biomart
SNPSpreadsheetImport	spreadsheet
SNPReport	beanshell	Script report = chrom + "," + position + "," + geneID;
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Merge_String_List_to_a_String_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
Remove_String_Duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
hsapiens_snp_2	biomart

Name	Description
chr_name
SpreadsheetImport_A
Merge_String_List_to_a_String_concatenated
Flatten_List_outputlist
associated_gene
snpconsequence

Source	Sink
SNPSpreadsheetImport:A	hsapiens_snp:hsapiens_snp.snp_filter_filter
snps	SNPSpreadsheetImport:fileurl
hsapiens_snp:hsapiens_snp.chr_name	SNPReport:chrom
hsapiens_snp:hsapiens_snp.chrom_start	SNPReport:position
hsapiens_snp:hsapiens_snp.ensembl_gene_stable_id	SNPReport:geneID
Remove_String_Duplicates:strippedlist	Merge_String_List_to_a_String:stringlist
Merge_String_List_to_a_String:concatenated	Merge_String_List_to_a_String_2:stringlist
SNPReport:report	Remove_String_Duplicates:stringlist
SNPSpreadsheetImport:A	hsapiens_snp_2:hsapiens_snp.distance_to_transcript_filter
SNPSpreadsheetImport:A	hsapiens_snp_2:hsapiens_snp.snp_filter_filter
SNPReport:report	chr_name
SNPSpreadsheetImport:A	SpreadsheetImport_A
Merge_String_List_to_a_String:concatenated	Merge_String_List_to_a_String_concatenated
Merge_String_List_to_a_String_2:concatenated	Flatten_List_outputlist
hsapiens_snp:hsapiens_snp.associated_gene	associated_gene
hsapiens_snp_2:hsapiens_snp.consequence_type_tv	snpconsequence

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