Nucleotide frequency workflow

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

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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_get	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_get:url
Get_variation_information_by_DDBJ_get: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
Summarize_variation_information	Make_output_for_DDBJ
Skip_first_two_lines	Make_output_for_DDBJ
Extract_pubmed_id	Summarize_cited_snp
Split_string_dbsnp_summary_by_enter	Extract_not_merged_rsid
Extraction_of_genotype_and_frequency_of_each_population	Merge_output
Summarize_cited_snp	Merge_output
Get_dbsnp_genotype_frequency_by_ncbieutils_efetch	Extraction_of_genotype_and_frequency_of_each_population
Make_output_for_DDBJ	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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