GBSeq test

Created: 2009-07-03 14:48:38

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (10)

Name	Type	Description
protein_id	stringconstant	Value NP_000050
Get_Nucleotide_INSDSeq_XML	localworker	Script if ((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=gbc&db=nucleotide&retmode=xml&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_Protein_FASTA	localworker	Script if ((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=protein&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_Protein_INSDSeq_XML	localworker	Script if ((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=gbc&db=protein&retmode=xml&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_Protein_TinySeq_XML	localworker	Script if ((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=protein&retmode=xml&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();
nuc_id	stringconstant	Value NM_000059
Get_Nucleotide_FASTA	localworker	Script if ((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_GBSeq_XML	localworker	Script if ((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=gb&db=nucleotide&retmode=xml&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_Protein_GBSeq_XML	localworker	Script if ((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=gb&db=protein&retmode=xml&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_TinySeq_XML	localworker	Script if ((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=xml&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();

Beanshells (0)

Outputs (8)

Name	Description
protein_xml
nuc_xml
nuc_tiny
nuc_fasta
prot_fasta
prot_insd
nuc_insd
prot_tiny

Datalinks (16)

Source	Sink
nuc_id:value	Get_Nucleotide_INSDSeq_XML:id
protein_id:value	Get_Protein_FASTA:id
protein_id:value	Get_Protein_INSDSeq_XML:id
protein_id:value	Get_Protein_TinySeq_XML:id
nuc_id:value	Get_Nucleotide_FASTA:id
nuc_id:value	Get_Nucleotide_GBSeq_XML:id
protein_id:value	Get_Protein_GBSeq_XML:id
nuc_id:value	Get_Nucleotide_TinySeq_XML:id
Get_Protein_GBSeq_XML:outputText	protein_xml
Get_Nucleotide_GBSeq_XML:outputText	nuc_xml
Get_Nucleotide_TinySeq_XML:outputText	nuc_tiny
Get_Nucleotide_FASTA:outputText	nuc_fasta
Get_Protein_FASTA:outputText	prot_fasta
Get_Protein_INSDSeq_XML:outputText	prot_insd
Get_Nucleotide_INSDSeq_XML:outputText	nuc_insd
Get_Protein_TinySeq_XML:outputText	prot_tiny