Homology workflow
Created: 2010-05-12 07:31:32
Last updated: 2010-05-12 07:33:11
Download WorkflowThere are many kinds of DNA data derived from many species in DDBJ. It makes possible to carry out the comparative study of genes of multiple species. The workflow provides a list of species and their genes that are similar to a human gene in response to a name of the human gene.
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Workflow Components
Authors (0)
None
Titles (1)
| Homology workflow |
Descriptions (0)
None
Dependencies (0)
None
Inputs (1)
| Name | Description |
|---|---|
| human_gene_name | Specify name of a human gene |
Processors (17)
| Name | Type | Description |
|---|---|---|
| Make_query_for_searching_against_DDBJ_by_human_gene_name | beanshell |
ScriptString baseUrl = "http://xml.nig.ac.jp/rest/Invoke";
String service = "ARSA";
String method = "searchByXMLPath";
String count = "100";
String offset = "1";
String encode = "UTF8";
String queryPath = "/ENTRY/DDBJ/division=='HUM' AND (/ENTRY/DDBJ/length>=300 AND /ENTRY/DDBJ/length<=1000) "
+ "AND (/ENTRY/DDBJ/feature-table/feature{/f_key = 'CDS' AND "
+ "/f_quals/qualifier{/q_name = 'gene' AND /q_value=='"
+ geneName
+ "'}})";
String returnPath = "/ENTRY/DDBJ/primary-accession";
//make url
String url = baseUrl + "?" + "queryPath=" + URLEncoder.encode(queryPath, encode)
+ "&returnPath=" + URLEncoder.encode(returnPath, encode)
+ "&service=" + URLEncoder.encode(service, encode)
+ "&method=" + URLEncoder.encode(method, encode)
+ "&count=" + URLEncoder.encode(count, encode)
+ "&offset="+ URLEncoder.encode(offset, encode);
|
| Get_DDBJ_list_by_ARSA_searchByXMLPath | localworker |
ScriptURL 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 |
ScriptList 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 |
| Get_representative_accession | beanshell |
ScriptString repAccession = (String)arsaResultLines.get(2); |
| Make_query_for_retrieving_sequence | beanshell |
ScriptString baseUrl = "http://xml.nig.ac.jp/rest/Invoke"; String service = "GetEntry"; String method = "getFASTA_DDBJEntry"; String url = baseUrl +"?service=" + service +"&method=" + method +"&accession=" + accession; |
| Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry | localworker |
ScriptURL 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_BLAST | beanshell |
ScriptString service = "Blast"; String method = "searchParam"; String program = "blastn"; String encode = "UTF8"; String query = "service=" + service +"&method=" + method +"&program=" + program +"&database=" + URLEncoder.encode(database,encode) +"&query=" + URLEncoder.encode(dnaSeq,encode) +"¶m=" + URLEncoder.encode(param,encode); |
| Execute_BLAST | beanshell |
ScriptURL url = new URL("http://xml.nig.ac.jp/rest/Invoke");
URLConnection urlc = url.openConnection();
urlc.setDoOutput(true);
urlc.setAllowUserInteraction(false);
PrintStream ps = new PrintStream(urlc.getOutputStream());
ps.print(query);
ps.close();
BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream()));
StringBuffer sb = new StringBuffer();
String line = null;
while ((line = br.readLine()) != null) {
sb.append(line + "\n");
}
String contents = sb.toString();
br.close(); |
| Split_string_BLAST_result_by_enter | localworker |
ScriptList 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_accession_and_similarity_score_form_BLAST_result | beanshell |
Script//extract accession number and similariy from blast result.
ArrayList parsedBlastResult = new ArrayList();
for (int i = 0; i < lines.size(); i++) {
String[] cols = lines.get(i).toString().split("\t");
String accession = (String)cols[1].substring(0, cols[1].indexOf("|"));
String[] accessionAndSimilarity = { accession, cols[2] };
parsedBlastResult.add(accessionAndSimilarity);
}
result = parsedBlastResult.toArray(); |
| Make_query_for_retrieving_species_name | beanshell |
ScriptString baseUrl = "http://xml.nig.ac.jp/rest/Invoke"; String service = "ARSA"; String method = "searchByXMLPath"; String count = "100"; String offset = "1"; String encode = "UTF8"; String queryPath = "/ENTRY/DDBJ/primary-accession=='" + blastResult.get(0) + "'"; String returnPath = "/ENTRY/DDBJ/organism"; //make url String url = baseUrl + "?" + "queryPath=" + URLEncoder.encode(queryPath, encode) + "&returnPath=" + URLEncoder.encode(returnPath, encode) + "&service=" + URLEncoder.encode(service, encode) + "&method=" + URLEncoder.encode(method, encode) + "&count=" + URLEncoder.encode(count, encode) + "&offset="+ URLEncoder.encode(offset, encode); |
| Print_Result | beanshell |
ScriptHashtable organismAccession = new Hashtable();
for (int i = 0; i < organismNameResult.size(); i++) {
String[] organismLines = organismNameResult.get(i).split("\n");
String organism = organismLines[2];
if (!organismAccession.containsKey(organism)) {
organismAccession.put(organism, accessionAndSimilarity.get(i).get(0) + "\t" + accessionAndSimilarity.get(i).get(1));
}
}
String[] keys = new String[organismAccession.size()];
Enumeration enu = organismAccession.keys();
int count = 0;
while (enu.hasMoreElements()) {
keys[count] = (String) enu.nextElement();
count++;
}
Arrays.sort(keys);
StringBuffer sb = new StringBuffer();
sb.append("DDBJ entries:\t" + arsaResultNum + "\n");
sb.append("Representative accession:\t" + representiveAccession + "\n");
sb.append("Organism name\tDDBJ accession number\tSequence similarity \n");
for (int i = 0; i < keys.length; i++) {
sb.append(keys[i] + "\t" + (String)organismAccession.get(keys[i]) + "\n");
}
result = sb.toString(); |
| Get_species_name_by_ARSA_searchByXMLPath | localworker |
ScriptURL 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();
|
| database | stringconstant |
Valueddbjpri ddbjrod ddbjmam ddbjvrt ddbjinv |
| param | stringconstant |
Value-m 8 -b 50 -v 50 -e 0.0001 |
| Get_hit_count | beanshell |
ScripthitCount = (String)arsaResultLines.get(0).replaceAll("hitscount =", "").trim();
|
Beanshells (9)
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| Make_query_for_searching_against_DDBJ_by_human_gene_name | geneName | url | |
| Get_representative_accession | arsaResultLines | repAccession | |
| Make_query_for_retrieving_sequence | accession | url | |
| Make_query_for_BLAST |
database dnaSeq param |
query | |
| Execute_BLAST |
query baseUrl |
contents | |
| Get_accession_and_similarity_score_form_BLAST_result | lines | result | |
| Make_query_for_retrieving_species_name | blastResult | url | |
| Print_Result |
organismNameResult accessionAndSimilarity arsaResultNum representiveAccession |
result | |
| Get_hit_count | arsaResultLines | hitCount |
Outputs (1)
| Name | Description |
|---|---|
| Species_name_that_has_orthologue_gene_and_accession_number_and_degree_of_similarity |
Datalinks (22)
| Source | Sink |
|---|---|
| human_gene_name | Make_query_for_searching_against_DDBJ_by_human_gene_name:geneName |
| Make_query_for_searching_against_DDBJ_by_human_gene_name:url | Get_DDBJ_list_by_ARSA_searchByXMLPath:url |
| Split_string_enter:value | Split_string_DDBJ_list_by_enter:regex |
| Get_DDBJ_list_by_ARSA_searchByXMLPath:contents | Split_string_DDBJ_list_by_enter:string |
| Split_string_DDBJ_list_by_enter:split | Get_representative_accession:arsaResultLines |
| Get_representative_accession:repAccession | Make_query_for_retrieving_sequence:accession |
| Make_query_for_retrieving_sequence:url | Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry:url |
| Get_first_DNA_sequence_by_GetEntry_getFASTA_DDBJEntry:contents | Make_query_for_BLAST:dnaSeq |
| database:value | Make_query_for_BLAST:database |
| param:value | Make_query_for_BLAST:param |
| Make_query_for_BLAST:query | Execute_BLAST:query |
| Split_string_enter:value | Split_string_BLAST_result_by_enter:regex |
| Execute_BLAST:contents | Split_string_BLAST_result_by_enter:string |
| Split_string_BLAST_result_by_enter:split | Get_accession_and_similarity_score_form_BLAST_result:lines |
| Get_accession_and_similarity_score_form_BLAST_result:result | Make_query_for_retrieving_species_name:blastResult |
| Get_species_name_by_ARSA_searchByXMLPath:contents | Print_Result:organismNameResult |
| Get_hit_count:hitCount | Print_Result:arsaResultNum |
| Get_representative_accession:repAccession | Print_Result:representiveAccession |
| Get_accession_and_similarity_score_form_BLAST_result:result | Print_Result:accessionAndSimilarity |
| Make_query_for_retrieving_species_name:url | Get_species_name_by_ARSA_searchByXMLPath:url |
| Split_string_DDBJ_list_by_enter:split | Get_hit_count:arsaResultLines |
| Print_Result:result | Species_name_that_has_orthologue_gene_and_accession_number_and_degree_of_similarity |
Coordinations (1)
| Controller | Target |
|---|---|
| Get_species_name_by_ARSA_searchByXMLPath | Print_Result |
Workflow Type
Version 1
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