Compare genome, extract proteins which are drug targets, apply to KEGG pathway

None

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();

Name	Description
TargetId	This is the gi input of a non-pathogen genome This is the gi input of a pathogen genome
SourceId	This is the gi input of a non-pathogen genome
source_fasta_filepath
target_fasta_filepath
cfasta_filepath
drugs_fasta_filepath
sourcedb_filepath_and_name
blast1_eval
blast1_filepath
drugsdb_filepath_and_name
blast2.eval
fg_colour
bg_colour
proteins_list_filepath
end_filepath
blast2_filepath

Name	Type	Description
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_FASTA_2	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();
target	workflow
source	workflow
blast1	workflow
cfasta	workflow
blast2	workflow
interesting	workflow
KEGG	workflow

Name	Inputs	Outputs
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
add_ncbi_to_string	input	output
Extract_unique_proteins	xml_result	gi_lines_val
Tfasta_parser	gi_val tfasta_in	cfasta_out
create_blastall_cmdArgs	inputFilePath eValue dbSave outputFilePath	cmdArgsList
create_formatdb_cmdArgs	seqFile1 dbSave	cmdArgsList
Extraction_of_info	xml_result	fastas_out
Extract_unique_proteins	xml_result	gi_lines_val
Tfasta_parser	gi_val tfasta_in	cfasta_out
extract_gis	gi_lines_in	gis
create_blastall_cmdArgs	inputFilePath eValue dbSave outputFilePath	cmdArgsList
create_formatdb_cmdArgs	seqFile1 dbSave	cmdArgsList

Name	Description
TargetGenomeSeq	Ouputs the nucleotide genome sequence of a pathogen
SourceGenomeSeq	Ouputs the nucleotide genome sequence of a pathogen
kegg_descriptions
kegg_id
ncbi_id
image
url
pathway_descriptions
pathway_by_genes
list_of_proteins

Source	Sink
SourceId	Get_Nucleotide_FASTA:id
TargetId	Get_Nucleotide_FASTA_2:id
TargetId	target:id
target_fasta_filepath	target:fasta_file_path
SourceId	source:id
source_fasta_filepath	source:fasta_file_path
sourcedb_filepath_and_name	blast1:dbSave
blast1_eval	blast1:eValue
blast1_filepath	blast1:blastFile
source_fasta_filepath	blast1:sourceProteins
target_fasta_filepath	blast1:targetProteins
target:file_output	cfasta:tfasta
cfasta_filepath	cfasta:cfasta_file_path
blast1_filepath	cfasta:blastFile
drugs_fasta_filepath	blast2:drugProteins
drugsdb_filepath_and_name	blast2:dbSave
blast2.eval	blast2:eValue
blast2_filepath	blast2:blastFile
cfasta_filepath	blast2:uniqueProteins
target:file_output	interesting:tfasta
proteins_list_filepath	interesting:list_of_proteins
end_filepath	interesting:end_file_path
blast2_filepath	interesting:blastFile
interesting:protein_gi_nos	KEGG:Gi_numbers
fg_colour	KEGG:fg_color
bg_colour	KEGG:bg_color
Get_Nucleotide_FASTA_2:outputText	TargetGenomeSeq
Get_Nucleotide_FASTA:outputText	SourceGenomeSeq
KEGG:kegg_descriptions	kegg_descriptions
KEGG:KEGGID	kegg_id
KEGG:ncbigiID	ncbi_id
KEGG:image	image
KEGG:URL	url
KEGG:pathway_descriptions	pathway_descriptions
KEGG:pathway_by_genes	pathway_by_genes
interesting:protein_gi_nos	list_of_proteins

Compare genome, extract proteins which are drug targets, apply to KEGG pathway

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Controller	Target
blast2	interesting
blast1	cfasta
cfasta	blast2
target	blast1
interesting	KEGG
source	blast1