Parse unique proteins from Blast file
Created: 2010-03-19 14:07:24
Last updated: 2010-03-19 14:09:22
The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.
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Workflow Components
Authors (2)
Titles (2)
| fetchEnsemblSeqsAndBlast |
| Extract unique proteins from blast results |
Descriptions (4)
|
| Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome |
| 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. |
| The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created. |
Dependencies (0)
Inputs (3)
| Name |
Description |
| blastFile |
inputs the xml format of the blast results
|
| tfasta |
fasta file of the target proteins to extract the sequences
|
| cfasta_file_path |
Where the workflow will save the unique proteins to the specified filepath
|
Processors (4)
| Name |
Type |
Description |
| Read_Text_File |
localworker |
ScriptBufferedReader getReader (String fileUrl) throws IOException {
InputStreamReader reader;
try {
reader = new FileReader(fileUrl);
}
catch (FileNotFoundException e) {
// try a real URL instead
URL url = new URL(fileUrl);
reader = new InputStreamReader (url.openStream());
}
return new BufferedReader(reader);
}
StringBuffer sb = new StringBuffer(4000);
BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");
while ((str = in.readLine()) != null) {
sb.append(str);
sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
|
| Extract_unique_proteins |
beanshell |
Script//import xml blast results
String input = xml_result;
ArrayList gi_lines = new ArrayList();
while (input.contains("")){
//finds start and end of Iteration_query-def tag
int start_tag1 = input.indexOf("") + 20;
int end_tag1 = input.indexOf("");
//get the protein identifier
String output = input.substring(start_tag1, end_tag1);
//removes identifier
input = input.substring(end_tag1 + 22);
//finds the start of Iteration_message tag
int start_tag2 = input.indexOf("");
//finds next start of Iteration_query-def tag
start_tag1 = input.indexOf("") + 20;
if(start_tag1 == 19) {
start_tag1 = start_tag2 + 1;
}
//if there are no hits for that protein, then store the protein
if(start_tag2 |
| Tfasta_parser |
beanshell |
Script//import the target fasta
String input = tfasta_in;
String[] target_array = input.split("\n");
//import gi ids
String input2 = gi_val;
String[] gi_array = input2.split("\n");
String fastas = "";
String value = "";
boolean found = false;
//for each value in the gi_array, compare it to each value in the target_array
for(int i = 0; i")){
found = false;
}
if(target_array[n].contains(gi_array[i])) {
value = target_array[n] + "\n";
found = true;
}
if(!target_array[n].contains(">") && found)
{
value = value + target_array[n] + "\n";
}
}
fastas = fastas + value;
}//end for
//export proteins in fasta format
cfasta_out = fastas; |
| Write_Text_File |
localworker |
ScriptBufferedWriter out = new BufferedWriter(new FileWriter(outputFile));
out.write(filecontents);
out.close();
outputFile = filecontents;
|
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| Extract_unique_proteins |
|
xml_result
|
gi_lines_val
|
| Tfasta_parser |
|
gi_val
tfasta_in
|
cfasta_out
|
Datalinks (6)
| Source |
Sink |
| blastFile |
Read_Text_File:fileurl |
| Read_Text_File:filecontents |
Extract_unique_proteins:xml_result |
| Extract_unique_proteins:gi_lines_val |
Tfasta_parser:gi_val |
| tfasta |
Tfasta_parser:tfasta_in |
| cfasta_file_path |
Write_Text_File:outputFile |
| Tfasta_parser:cfasta_out |
Write_Text_File:filecontents |
Coordinations (1)
| Controller |
Target |
| Read_Text_File |
Extract_unique_proteins |
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