Fetch Fasta and Genbank files
Created: 2010-03-19 13:32:07
Fetches fasta and genbank files for a given identifier.,
e.g., CP000256
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Workflow Components
Authors (1)
Titles (1)
| Fetch Fasta and GenBank files. |
Descriptions (1)
| Fetches fasta and genbank files for a given identifier.,e.g., CP000256 |
Dependencies (0)
Inputs (1)
| Name |
Description |
| sequence_id |
The id to get the Fasta format
The ID to get the Fasta format
|
Processors (4)
| Name |
Type |
Description |
| fetch_fasta_from_ncbi |
localworker |
ScriptString base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=";String arg1 = "fasta";String mid = "&db=nucleotide&retmode=text&id=";// http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gp&db=nucleotide&retmode=text&id=CP000257URL url = new URL( base + arg1 + mid + 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); }ext = "fasta";content = writer.toString(); |
| fetch_genbank_from_ncbi |
localworker |
ScriptString base = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=";String arg1 = "gp";String mid = "&db=nucleotide&retmode=text&id=";// http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?rettype=gp&db=nucleotide&retmode=text&id=CP000257URL url = new URL( base + arg1 + mid + 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); }ext = "gb";content = writer.toString(); |
| save_fasta_file |
beanshell |
ScriptStringBuffer sb = new StringBuffer();sb.append("D:/DATA/demo/");sb.append(id);sb.append("." + ext);File f = new File( sb.toString() );BufferedWriter writer = new BufferedWriter(new FileWriter(f));writer.write(content);writer.close();String file_location = f.getCanonicalPath(); |
| save_genbank_file |
beanshell |
ScriptStringBuffer sb = new StringBuffer();sb.append("D:/DATA/demo/");sb.append(id);sb.append("." + ext);File f = new File( sb.toString() );BufferedWriter writer = new BufferedWriter(new FileWriter(f));writer.write(content);writer.close();String filePath = f.getCanonicalPath(); |
Beanshells (2)
| Name |
Description |
Inputs |
Outputs |
| save_fasta_file |
|
id
ext
content
|
content
file_location
|
| save_genbank_file |
|
id
ext
content
|
content
|
Outputs (3)
| Name |
Description |
| genbank_nucleotide |
GenBank File
GenBank
|
| fasta_nucleotide |
Fasta File
Nucelot
Nucelotide
|
| file_location |
Location of the files generated
Location
|
Datalinks (11)
| Source |
Sink |
| sequence_id |
fetch_fasta_from_ncbi:id |
| sequence_id |
fetch_genbank_from_ncbi:id |
| fetch_fasta_from_ncbi:ext |
save_fasta_file:ext |
| fetch_fasta_from_ncbi:id |
save_fasta_file:id |
| fetch_fasta_from_ncbi:content |
save_fasta_file:content |
| fetch_genbank_from_ncbi:content |
save_genbank_file:content |
| fetch_genbank_from_ncbi:ext |
save_genbank_file:ext |
| fetch_genbank_from_ncbi:id |
save_genbank_file:id |
| save_genbank_file:content |
genbank_nucleotide |
| save_fasta_file:content |
fasta_nucleotide |
| save_fasta_file:file_location |
file_location |
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Version 1
(of 1)
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