Extract unique proteins from blast results
Created: 2011-03-24 19:49:43
Last updated: 2011-04-01 12:26:27
The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similarity to the source genome. Using these unique protein ids, and the original target protein fasta file, a list unique proteins is created.
Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome
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Workflow Components
Authors (2)
Titles (2)
| fetchEnsemblSeqsAndBlast |
| Extract unique proteins from blast results |
Descriptions (4)
| 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. |
| 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. |
|
| Workflow outputs a list of proteins encoded by the target genomes that do not have sequences similarity to those encoded by the source genome |
Dependencies (0)
Inputs (2)
| Name |
Description |
| blastFile |
The URL or file path location of the tab-delimited format of the Blast results.
The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not a file location).
inputs the xml format of the blast results
The URL or file path location of the tab-delimited format of the Blast results. Type the path as a string (not
|
| tfasta |
Fasta file of the target proteins to extract the sequences.
Fasta file of the target proteins to extract the sequences. Add as file location.
fasta file of the target proteins to extract the sequences
|
Processors (3)
| 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_blast_ids |
beanshell |
Script//import tab-delimited blast results
//split the input on new lines
String[] input = xml_result.split(System.getProperty("line.separator"));
ArrayList gi_lines = new ArrayList();
//for each line in the BLAST file
for (int i=0; i |
| find_unique_proteins |
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
// each value is set to false initially
for(int i = 0; i |
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| extract_blast_ids |
|
xml_result
|
gi_lines_val
|
| find_unique_proteins |
|
gi_val
tfasta_in
|
cfasta_out
|
Outputs (2)
| Name |
Description |
| unique_identifiers |
Unique identifiers that appear in the FASTA file but not in the BLAST file. Identifiers are separated by new lines.
|
| blasted_identifiers |
Identifiers of the target genome from the BLAST results. These identifiers are those that are similar to the source proteome.
|
Datalinks (6)
| Source |
Sink |
| blastFile |
Read_Text_File:fileurl |
| Read_Text_File:filecontents |
extract_blast_ids:xml_result |
| extract_blast_ids:gi_lines_val |
find_unique_proteins:gi_val |
| tfasta |
find_unique_proteins:tfasta_in |
| find_unique_proteins:cfasta_out |
unique_identifiers |
| extract_blast_ids:gi_lines_val |
blasted_identifiers |
Coordinations (1)
| Controller |
Target |
| Read_Text_File |
extract_blast_ids |
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License
All versions of this Workflow are
licensed under:
Version 2
(of 4)
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