Nucleotide frequency workflow

Created: 2010-05-13 01:51:22 Last updated: 2010-11-12 10:30:15

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ALDH2 gene encodes enzyme which transform from acetaldehyde to acetic acid. It is known that variation of one DNA weakens the function. It is said that there are a lot of people who have the gene of such a type in Asia including Japan. However there are few people of such type of the gene in Europe or America. Therefore this workflow verifies that how type of the gene is distributed among Asian and Europe or America by using DDBJ and dbSNP data.

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Titles (1)

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Inputs (3)

Name	Description
gene_name
function
email

Processors (28)

Name	Type	Description
Make_query_for_searching_DDBJ	beanshell	Script String url = "http://xml.nig.ac.jp/rest/Invoke?"; String queryPath = "/ENTRY/DDBJ/organism=='Homo sapiens' AND "; queryPath += "(/ENTRY/DDBJ/feature-table/feature{/f_key=='variation' AND /f_quals/qualifier{/q_name=='gene' AND /q_value=='" + gene + "'}})"; queryPath = URLEncoder.encode(queryPath); String returnPath = "/ENTRY/DDBJ/primary-accession,/ENTRY/DDBJ/definition"; returnPath = URLEncoder.encode(returnPath); String query = "service=ARSA&method=searchByXMLPath&queryPath=" + queryPath + "&returnPath=" + returnPath + "&offset=1&count=100"; url += query;
Get_DDBJ_list_by_ARSA_searchByXMLPath	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Split_string_DDBJ_list_by_enter	localworker	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]); } }
Split_string_enter	stringconstant	Value \n
Skip_first_two_lines	beanshell	Script List ddbjList = new ArrayList(); for(int i=0; i
Split_string_tab	stringconstant	Value \t
Split_string_DDBJ_list_lines_by_tab	localworker	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]); } }
Make_query_for_searching_DDBJ_to_get_feature_info	beanshell	Script List urlList = new ArrayList(); String baseUrl = "http://xml.nig.ac.jp/rest/Invoke?"; for(int i=0; i
Get_variation_information_by_DDBJ_getFeatureInfo	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Split_string_variation_information_by_enter	localworker	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]); } }
Summarize_variation_information	beanshell	Script StringBuffer variation = new StringBuffer(); for(int i=0; i 0) { variationAnnotation = variationAnnotation.substring(0, variationAnnotation.length() - 1); } else { variationAnnotation = ""; }
Split_string_variation_information_lines_by_tab	localworker	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]); } }
Make_output_for_DDBJ	beanshell	Script String output = ""; for(int i=0; i
Make_query_for_searching_dbsnp_by_esearch	beanshell	Script if( function == null \|\| function.equals("null")) { function = ""; } String baseUrl = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"; String db ="snp"; String term="@@gene@@[GENE] AND human[ORGN] AND \"by cluster\"[Validation] AND \"by frequency\"[Validation] AND \"@@function@@\"[Function_Class]"; String retmax="100"; String encode = "UTF8"; term = term.replaceAll("@@gene@@", gene); if(function != null && !function.equals("")) { term = term.replaceAll("@@function@@", function); } else { term = term.replaceAll(" AND \\\\\"@@function@@\\\\\"\\[Function_Class\\]", ""); } String url = baseUrl + "db="+db +"&term=" + URLEncoder.encode(term,encode) +"&retmax=" + retmax +"&email=" + email;
Get_dbsnp_list_by_ncbieutils_esearch	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Make_query_for_searching_dbsnp_by_efetch	beanshell	Script List idList = new ArrayList(); List urlList = new ArrayList(); String baseUrl = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"; String report="FLT"; String db="snp"; for(int i=0; i") > -1 && l.indexOf("") > -1) { String id = l.substring(l.indexOf("") + 4); id = id.substring(0, id.indexOf("<")); idList.add(id); String url = baseUrl + "report=" + report + "&db=" + db + "&id=" + id + "&email=" + email; urlList.add(url); } }
Split_string_dbsnp_list_by_enter	localworker	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]); } }
Get_dbsnp_summary_by_ncbieutils_efetch	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Extract_not_merged_rsid	beanshell	Script List notMergedRsidList = new ArrayList(); for(int i = 0; i < dbsnpEfetchResultList.size(); i++) { List oneResultList = (List)dbsnpEfetchResultList.get(i); if(oneResultList.size() < 4) { continue; } String idLine = (String)oneResultList.get(3); String id = idLine.substring(3); id = id.substring(0, id.indexOf(" ")); String nextLine = (String)oneResultList.get(4); if(nextLine.startsWith(id)) { notMergedRsidList.add(id); } else { continue; } }
Make_query_for_retrieving_genotype	beanshell	Script String baseUrl = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"; String report="GENXML"; String db="snp"; String mode="text"; String url = baseUrl + "report=" + report + "&db=" + db + "&mode=" + mode + "&id=" + rsId.substring(2) + "&email=" + email;
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Extraction_of_genotype_and_frequency_of_each_population	beanshell	Script List output = new ArrayList(); org.xml.sax.helpers.DefaultHandler handler = new org.xml.sax.helpers.DefaultHandler() { public String output = ""; public Stack elements = new Stack(); public HashMap popGroup = new HashMap(); public HashMap popDiversity = new HashMap(); public String ssId = ""; public String popId = ""; public void printNCBI(String id) { StringBuffer rsBuffer = new StringBuffer(); rsBuffer.append("Reference SNP ID:" + id + "\n"); for(Iterator it = popDiversity.keySet().iterator(); it.hasNext();) { boolean hasDiversity = false; String ssId = (String)it.next(); StringBuffer ssBuffer = new StringBuffer("\tSubmitter SNP ID:" + ssId + "\n"); HashMap popIdMap = (HashMap)popDiversity.get(ssId); HashMap genotypeFreq = new HashMap(); for(Iterator it2 = popIdMap.keySet().iterator(); it2.hasNext();) { String popId = (String)it2.next(); HashMap genotypeMap = (HashMap)popIdMap.get(popId); String popLabel = getPopLabel(popId); ssBuffer.append("\t\t" + popLabel + ":"); StringBuffer sb = new StringBuffer(); for(Iterator it3 = genotypeMap.keySet().iterator(); it3.hasNext();) { String genotype = (String)it3.next(); String freq = (String)genotypeMap.get(genotype); ArrayList freqList = new ArrayList(); if(genotypeFreq.containsKey(genotype)) { freqList = (ArrayList)genotypeFreq.get(genotype); if(checkDiversity(freqList, freq)) { hasDiversity = true; } } freqList.add(freq); genotypeFreq.put(genotype, freqList); sb.append(genotype + ":" + freq + ","); } // delete last character ',' sb.deleteCharAt(sb.length() - 1); ssBuffer.append(sb.toString()+"\n"); } if(hasDiversity) { rsBuffer.append(ssBuffer.toString()); } } if(rsBuffer.length() > 20) { output += rsBuffer.toString().trim() + "\n"; } } public boolean checkDiversity(ArrayList freqList, String freq) { float freqFloat = Float.parseFloat(freq); for(int i = 0; i < freqList.size(); i++) { String f = (String)freqList.get(i); float ff = Float.parseFloat(f); if(Math.abs(ff - freqFloat) > 0.3) { return true; } } return false; } public String getPopLabel(String popId) { StringBuffer label = new StringBuffer(); if(popGroup.containsKey(popId)) { HashSet set = (HashSet)popGroup.get(popId); if(set.size() > 3) { return "multiple(" + popId + ")"; } for(Iterator it = set.iterator(); it.hasNext();) { label.append((String)it.next() + ","); } } else { return "No description(" + popId + ")"; } String labelStr = label.toString(); return labelStr.substring(0, labelStr.length() - 1) + "(" + popId + ")"; } public void startElement(String uri, String localName, String qName, org.xml.sax.Attributes attributes) { elements.push(qName); String tree = getTree(); if(tree.equals("/GenoExchange/Individual/SubmitInfo")) { String popId = attributes.getValue("popId"); String subIndGroup = attributes.getValue("subIndGroup"); HashSet groupSet; if(popGroup.containsKey(popId)) { groupSet = (HashSet)popGroup.get(popId); } else { groupSet = new HashSet(); } groupSet.add(subIndGroup); popGroup.put(popId, groupSet); } else if(tree.equals("/GenoExchange/SnpInfo/SsInfo")) { ssId = attributes.getValue("ssId"); } else if(tree.equals("/GenoExchange/SnpInfo/SsInfo/ByPop")) { popId = attributes.getValue("popId"); } else if(tree.equals("/GenoExchange/SnpInfo/SsInfo/ByPop/GTypeFreq")) { String gtype = attributes.getValue("gtype"); String freq = attributes.getValue("freq"); HashMap popIdMap; if(popDiversity.containsKey(ssId)) { popIdMap = (HashMap)popDiversity.get(ssId); } else { popIdMap = new HashMap(); } setPopIdMap(popId, gtype, freq, popIdMap); popDiversity.put(ssId, popIdMap); } } public void setPopIdMap(String popId, String gtype, String freq, HashMap popIdMap) { HashMap genotypeMap; if(popIdMap.containsKey(popId)) { genotypeMap = (HashMap)popIdMap.get(popId); } else { genotypeMap = new HashMap(); } genotypeMap.put(gtype, freq); popIdMap.put(popId, genotypeMap); } public void endElement(String uri, String localName, String qName) { elements.pop(); } public String getTree() { StringBuffer tree = new StringBuffer(); for(int i = 0; i < elements.size(); i++) { String s = (String)elements.get(i); tree.append("/" + s); } return tree.toString(); } }; javax.xml.parsers.SAXParserFactory spfactory = javax.xml.parsers.SAXParserFactory.newInstance(); javax.xml.parsers.SAXParser parser = spfactory.newSAXParser(); for(int i=0; i
Make_query_for_searching_pubmed	beanshell	Script String baseUrl = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?"; String dbfrom="snp"; String db="pubmed"; String mode="text"; String url = baseUrl + "dbfrom=" + dbfrom + "&db=" + db + "&mode=" + mode + "&id="+ rsId.substring(2) + "&email=" + email; id = rsId;
Get_dbsnp_pubmed_cited_by_ncbieutils_elink	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Summarize_cited_snp	beanshell	Script List output = new ArrayList(); for(int i = 0; i < rsId.size(); i++) { List l = (List)pubmedIdList.get(i); String rs = (String)rsId.get(i); StringBuffer out = new StringBuffer(); for(int j=0; j
Merge_output	beanshell	Script StringBuffer sb = new StringBuffer(); sb.append(ddbj + "\n"); for(int i=0; i
Extract_pubmed_id	beanshell	Script boolean target = false; List pubmedIdList = new ArrayList(); BufferedReader br = new BufferedReader(new StringReader(elinkResult)); String l; while((l =br.readLine()) != null) { if(l.indexOf("snp_pubmed_cited") > -1) { target = true; continue; } if(target) { if(l.indexOf("") > -1) { l = l.substring(l.indexOf("") + 4); l = l.substring(0, l.indexOf("<")); pubmedIdList.add(l); } else if(l.indexOf("") > -1) { break; } } } br.close();
Split_string_dbsnp_summary_by_enter	localworker	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]); } }

Beanshells (14)

Name	Inputs	Outputs
Make_query_for_searching_DDBJ	gene	url
Skip_first_two_lines	list	ddbjList
Make_query_for_searching_DDBJ_to_get_feature_info	ddbjList	urlList
Summarize_variation_information	list	variationAnnotation
Make_output_for_DDBJ	ddbj variation	output
Make_query_for_searching_dbsnp_by_esearch	function gene email	url param
Make_query_for_searching_dbsnp_by_efetch	result email	urlList
Extract_not_merged_rsid	dbsnpEfetchResultList	notMergedRsidList
Make_query_for_retrieving_genotype	rsId email	url
Extraction_of_genotype_and_frequency_of_each_population	inputList rsIdList	output
Make_query_for_searching_pubmed	rsId email	url id
Summarize_cited_snp	pubmedIdList rsId	output
Merge_output	ddbj genotypeInfo citedPaper	output
Extract_pubmed_id	elinkResult	pubmedIdList

Outputs (1)

Name	Description
Nucleotide_frequency

Datalinks (43)

Source	Sink
gene_name	Make_query_for_searching_DDBJ:gene
Make_query_for_searching_DDBJ:url	Get_DDBJ_list_by_ARSA_searchByXMLPath:url
Get_DDBJ_list_by_ARSA_searchByXMLPath:contents	Split_string_DDBJ_list_by_enter:string
Split_string_enter:value	Split_string_DDBJ_list_by_enter:regex
Split_string_DDBJ_list_lines_by_tab:split	Skip_first_two_lines:list
Split_string_DDBJ_list_by_enter:split	Split_string_DDBJ_list_lines_by_tab:string
Split_string_tab:value	Split_string_DDBJ_list_lines_by_tab:regex
Skip_first_two_lines:ddbjList	Make_query_for_searching_DDBJ_to_get_feature_info:ddbjList
Make_query_for_searching_DDBJ_to_get_feature_info:urlList	Get_variation_information_by_DDBJ_getFeatureInfo:url
Get_variation_information_by_DDBJ_getFeatureInfo:contents	Split_string_variation_information_by_enter:string
Split_string_enter:value	Split_string_variation_information_by_enter:regex
Split_string_variation_information_lines_by_tab:split	Summarize_variation_information:list
Split_string_variation_information_by_enter:split	Split_string_variation_information_lines_by_tab:string
Split_string_tab:value	Split_string_variation_information_lines_by_tab:regex
Skip_first_two_lines:ddbjList	Make_output_for_DDBJ:ddbj
Summarize_variation_information:variationAnnotation	Make_output_for_DDBJ:variation
email	Make_query_for_searching_dbsnp_by_esearch:email
function	Make_query_for_searching_dbsnp_by_esearch:function
gene_name	Make_query_for_searching_dbsnp_by_esearch:gene
Make_query_for_searching_dbsnp_by_esearch:url	Get_dbsnp_list_by_ncbieutils_esearch:url
Split_string_dbsnp_list_by_enter:split	Make_query_for_searching_dbsnp_by_efetch:result
email	Make_query_for_searching_dbsnp_by_efetch:email
Get_dbsnp_list_by_ncbieutils_esearch:contents	Split_string_dbsnp_list_by_enter:string
Split_string_enter:value	Split_string_dbsnp_list_by_enter:regex
Make_query_for_searching_dbsnp_by_efetch:urlList	Get_dbsnp_summary_by_ncbieutils_efetch:url
Split_string_dbsnp_summary_by_enter:split	Extract_not_merged_rsid:dbsnpEfetchResultList
Extract_not_merged_rsid:notMergedRsidList	Make_query_for_retrieving_genotype:rsId
email	Make_query_for_retrieving_genotype:email
Make_query_for_retrieving_genotype:url	Get_dbsnp_genotype_frequency_by_ncbieutils_efetch:url
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch:contents	Extraction_of_genotype_and_frequency_of_each_population:inputList
Extract_not_merged_rsid:notMergedRsidList	Extraction_of_genotype_and_frequency_of_each_population:rsIdList
email	Make_query_for_searching_pubmed:email
Extract_not_merged_rsid:notMergedRsidList	Make_query_for_searching_pubmed:rsId
Make_query_for_searching_pubmed:url	Get_dbsnp_pubmed_cited_by_ncbieutils_elink:url
Extract_pubmed_id:pubmedIdList	Summarize_cited_snp:pubmedIdList
Make_query_for_searching_pubmed:id	Summarize_cited_snp:rsId
Summarize_cited_snp:output	Merge_output:citedPaper
Make_output_for_DDBJ:output	Merge_output:ddbj
Extraction_of_genotype_and_frequency_of_each_population:output	Merge_output:genotypeInfo
Get_dbsnp_pubmed_cited_by_ncbieutils_elink:contents	Extract_pubmed_id:elinkResult
Split_string_enter:value	Split_string_dbsnp_summary_by_enter:regex
Get_dbsnp_summary_by_ncbieutils_efetch:contents	Split_string_dbsnp_summary_by_enter:string
Merge_output:output	Nucleotide_frequency

Coordinations (8)

Controller	Target
Split_string_dbsnp_summary_by_enter	Extract_not_merged_rsid
Extraction_of_genotype_and_frequency_of_each_population	Merge_output
Summarize_variation_information	Make_output_for_DDBJ
Make_output_for_DDBJ	Merge_output
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch	Extraction_of_genotype_and_frequency_of_each_population
Skip_first_two_lines	Make_output_for_DDBJ
Extract_pubmed_id	Summarize_cited_snp
Summarize_cited_snp	Merge_output

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wabi

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Nucleotide frequency workflow

Created by wabi on Thursday 13 May 2010 01:51:24 (UTC)

Last edited by wabi on Thursday 13 May 2010 01:51:48 (UTC)
Nucleotide frequency workflow

Created by wabi on Friday 12 November 2010 10:30:12 (UTC)

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