Retrieve Genome Seqn using gi nos
Created: 2010-03-19 15:17:53
Retrieves the genome seqn for both the target and source strains using gi nos
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Authors (2)
Titles (2)
| Retrieve Genome Seqn using gi nos |
| Retrieve Genome Seqn using gi ids |
Descriptions (1)
| Retrieves the genome seqn for both the target and source strains using gi nos |
Dependencies (0)
Inputs (2)
| Name |
Description |
| TargetId |
This is the gi input of a pathogen genome
This is the gi input of a non-pathogen genome
|
| SourceId |
This is the gi input of a non-pathogen genome
|
Processors (2)
| Name |
Type |
Description |
| Get_Nucleotide_FASTA |
localworker |
Scriptif ((id == void) || (id == null) || id.equals("")) {
throw new RunTimeException("port id must have a non-empty value");
}
URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
StringWriter writer = new StringWriter();
char[] buffer = new char[1024];
while (true) {
int r = reader.read(buffer);
if (r <= 0) {
break;
}
writer.write(buffer, 0, r);
}
outputText = writer.toString();
|
| Get_Nucleotide_FASTA_2 |
localworker |
Scriptif ((id == void) || (id == null) || id.equals("")) {
throw new RunTimeException("port id must have a non-empty value");
}
URL url = new URL ("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=nucleotide&retmode=text&id=" + id);
BufferedReader reader = new BufferedReader (new InputStreamReader(url.openStream()));
StringWriter writer = new StringWriter();
char[] buffer = new char[1024];
while (true) {
int r = reader.read(buffer);
if (r <= 0) {
break;
}
writer.write(buffer, 0, r);
}
outputText = writer.toString();
|
Outputs (2)
| Name |
Description |
| TargetGenomeSeq |
Ouputs the nucleotide genome sequence of a pathogen
|
| SourceGenomeSeq |
Ouputs the nucleotide genome sequence of a pathogen
|
Datalinks (4)
| Source |
Sink |
| SourceId |
Get_Nucleotide_FASTA:id |
| TargetId |
Get_Nucleotide_FASTA_2:id |
| Get_Nucleotide_FASTA_2:outputText |
TargetGenomeSeq |
| Get_Nucleotide_FASTA:outputText |
SourceGenomeSeq |
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