BlastandParse2

Created: 2010-03-19 12:20:29

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Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.

Shortcomings:

The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.

The results of the blastall are parsed to give those that are above the max e-value and minimum percent identity as indicated by the user and an output of uniprot accession numbers is created that can be searched against KEGG.

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Workflow Components

Authors (2)

Titles (2)

Descriptions (2)

This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.Shortcomings:The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.The results of the blastall are parsed to give those that are above the max e-value and minimum percent identity as indicated by the user and an output of uniprot accession numbers is created that can be searched against KEGG.

This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "create_blastall_cmdArgs" and "create_formatdb_cmdArgs" are what you need to edit if the default locations are not appropriate for you.Shortcomings:The names of all the files created and used is hard coded in this workflow. This means that if you run this workflow more than once without editing anything, you will overwrite files you have previously created.All files created in the working directory are not yet coded to be deleted via the workflow. Ideally there would be an option that a user could choose that would set the files to be kept or deleted after use.

Dependencies (0)

Inputs (5)

Name	Description
sequenceFileName	Provide the name, and if not in your working directory, the location of the file of fasta sequence(s) that you wish to use to search the blast database created in this workflow.
database_input	the fasta filepath to be used to format a database to blastall against
evalue	evalue to be used for blastall
minP	minimum percent identity to parse the blast results. minimum percent identity to parse the blast results.
maxE	maximum expectation value to parse the blast results with

Processors (8)

Name	Type	Description
runBlastSearch	localworker	Script if (command == void \|\| command.equals("")) { throw new RuntimeException("The 'command' port cannot be null.");}Process proc = null;Runtime rt = Runtime.getRuntime();String osName = System.getProperty("os.name");String[] cmdArray = null;String qry = "";if (osName.equals("Windows NT") \|\| osName.equals("Windows XP") \|\| osName.equals("Windows Vista")) { cmdArray = new String[] { "cmd.exe", "/c", command };} else if (osName.equals("Windows 95")) { cmdArray = new String[] { "command.exe", "/c", command };} else {// TODO: investigate if this will work in Linux and OSX cmdArray = new String[] { command };}qry += command + " ";// concatenate the arraysif ((args == void) \|\| (args == null)) { args = new ArrayList();}int argSize = cmdArray.length + args.size();ArrayList appArray = new ArrayList(argSize);for (int i = 0; i < cmdArray.length; i++) { appArray.add(cmdArray[i]);}for (int i = 0; i < args.size(); i++) { appArray.add(args.get(i)); qry += args.get(i); qry += " ";}String[] applist = new String[argSize];appArray.toArray(applist);proc = rt.exec(applist);// Get the input stream and read from itInputStream in = proc.getInputStream();int c;StringBuffer sb = new StringBuffer();while ((c = in.read()) != -1) { sb.append((char) c);}in.close();result = sb.toString();theQuery = qry;
local_create_blastdb	localworker	Script if (command == void \|\| command.equals("")) { throw new RuntimeException("The 'command' port cannot be null.");}Process proc = null;Runtime rt = Runtime.getRuntime();String osName = System.getProperty("os.name");String[] cmdArray = null;if (osName.equals("Windows NT") \|\| osName.equals("Windows XP")) { cmdArray = new String[] { "cmd.exe", "/c", command };} else if (osName.equals("Windows 95")) { cmdArray = new String[] { "command.exe", "/c", command };} else {// TODO: investigate if this will work in Linux and OSX cmdArray = new String[] { command };}// concatenate the arraysif ((args == void) \|\| (args == null)) { args = new ArrayList();}int argSize = cmdArray.length + args.size();ArrayList appArray = new ArrayList(argSize);for (int i = 0; i < cmdArray.length; i++) { appArray.add(cmdArray[i]);}for (int i = 0; i < args.size(); i++) { appArray.add(args.get(i));}String[] applist = new String[argSize];appArray.toArray(applist);proc = rt.exec(applist);// Get the input stream and read from itInputStream in = proc.getInputStream();int c;StringBuffer sb = new StringBuffer();while ((c = in.read()) != -1) { sb.append((char) c);}in.close();result = sb.toString();
create_blastall_cmdArgs	beanshell	Script List cmdArgsList = new ArrayList();cmdArgsList.add("-p");cmdArgsList.add("blastp");cmdArgsList.add("-d");cmdArgsList.add("./BlastDB");cmdArgsList.add("-i");cmdArgsList.add(sequenceFileName);cmdArgsList.add("-e");cmdArgsList.add(evalue);cmdArgsList.add("-m");cmdArgsList.add("8");
create_formatdb_cmdArgs	beanshell	Script List cmdArgsList = new ArrayList();cmdArgsList.add("-i");cmdArgsList.add(dbsequences);cmdArgsList.add("-p");cmdArgsList.add("T");cmdArgsList.add("-n");cmdArgsList.add("BlastDB");
runBlastSearch_command_defaultValue	stringconstant	Value D:\BLAST\bin\blastall
local_create_blastdb_command_defaultValue	stringconstant	Value D:\BLAST\bin\formatdb
parse_blast_results	beanshell	Script // "uniprot:P02745 "// takes a string of \t separated results and \n //String minP = "30.0";//String maxE = "2.0";StringBuffer sb1 = new StringBuffer();StringBuffer sb2 = new StringBuffer(); double minPercent = Double.parseDouble(minP);double maxEvalue = Double.parseDouble(maxE);int count = 0;protein_list = new ArrayList();sb2.append("thresholds: minP=" + minP + ", maxE=" + maxE + "\n========================\n");String [] rows = blast_results.split("\n"); for(int i = 0; i < rows.length; ++i) { String [] cols = rows[i].split("\t"); if(cols != null && cols.length > 9) { String [] query = cols[0].split("[\|]"); String uniProtId = cols[1].replaceAll("[\|]","").trim(); String percent = cols[2].trim(); String e_val = cols[10].trim(); double max1 = 0; double max2 = 0; if( Double.parseDouble(percent) >= minPercent && Double.parseDouble(e_val) <= maxEvalue ) { //sb1.append("uniprot:" + uniProtId + " "); protein_list.add("uniprot:" + query[1]); sb2.append(">>> query id=" + query[1]); sb2.append(", name=" + query[2]); sb2.append(", hit uniProt id=" + uniProtId); sb2.append(", % identity=" + percent); sb2.append(", e value =" + e_val + "\n"); } } } HashSet h = new HashSet(protein_list); protein_list.clear(); protein_list.addAll(h);// "uniprot:P00734 uniprot:P00737"; // probably on works if both have same pathway id// sb1.toString(); records = sb2.toString();
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n";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();

Beanshells (3)

Name	Inputs	Outputs
create_blastall_cmdArgs	sequenceFileName evalue	cmdArgsList
create_formatdb_cmdArgs	dbsequences	cmdArgsList
parse_blast_results	blast_results minP maxE	protein_list records

Outputs (4)

Name	Description
Result	resulting blast report in tabular format
queryEntered	A List of blast results containing the usual information such as query id, hit id, percent identity etc
proteinList	list of uniprot accession numbers in a format that can be searched against KEGG
Blast_hits	A List of blast results containing the usual information such as query id, hit id, percent identity etc

Datalinks (15)

Source	Sink
create_blastall_cmdArgs:cmdArgsList	runBlastSearch:args
runBlastSearch_command_defaultValue:value	runBlastSearch:command
local_create_blastdb_command_defaultValue:value	local_create_blastdb:command
create_formatdb_cmdArgs:cmdArgsList	local_create_blastdb:args
sequenceFileName	create_blastall_cmdArgs:sequenceFileName
evalue	create_blastall_cmdArgs:evalue
database_input	create_formatdb_cmdArgs:dbsequences
runBlastSearch:result	parse_blast_results:blast_results
maxE	parse_blast_results:maxE
minP	parse_blast_results:minP
parse_blast_results:protein_list	Merge_String_List_to_a_String:stringlist
runBlastSearch:result	Result
runBlastSearch:theQuery	queryEntered
Merge_String_List_to_a_String:concatenated	proteinList
parse_blast_results:records	Blast_hits