Get top blastx hit of a list of contigs

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if ((url == void) || (url == null)) {
	throw new RuntimeException("The url must be specified");
}

URL inputURL = null;
if (base != void) {
  inputURL = new URL(new URL(base), url);
}
else {
  inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();

StringBuffer result = new StringBuffer();
BufferedReader reader;

String encoding = con.getContentEncoding();
if (encoding == null) {
  reader = new BufferedReader(new InputStreamReader(in));
} else {
  reader = new BufferedReader(new InputStreamReader(in, encoding));
}
String line = null;
String NEWLINE = System.getProperty("line.separator");
while ((line = reader.readLine()) != null) {
	result.append(line);
	result.append(NEWLINE);
}

reader.close();
contents = result.toString();

Name	Type	Description
Nucleotide_ORF_translation	workflow
EBI_NCBI_BLAST	workflow
MultipleBlastp	workflow
Table_Bacterial	stringconstant	Value 11
ORFlen	stringconstant	Value 200
Contigs_in_bucket	stringconstant	Value https://s3-eu-west-1.amazonaws.com/genomotator/sw/454LargeContigs.fna
Get_Web_Page_from_URL	localworker	Script if ((url == void) \|\| (url == null)) { throw new RuntimeException("The url must be specified"); } URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); StringBuffer result = new StringBuffer(); BufferedReader reader; String encoding = con.getContentEncoding(); if (encoding == null) { reader = new BufferedReader(new InputStreamReader(in)); } else { reader = new BufferedReader(new InputStreamReader(in, encoding)); } String line = null; String NEWLINE = System.getProperty("line.separator"); while ((line = reader.readLine()) != null) { result.append(line); result.append(NEWLINE); } reader.close(); contents = result.toString();

Name	Inputs	Outputs
get_gi	in1	out1
convert_GI_to_URL	id	url
Remove_first_character	input	fasta
Add_angle	stripped_fasta	full_fasta

Name	Description
GI
ORFS
fasta

Source	Sink
MultipleBlastp:Contigs_split	Nucleotide_ORF_translation:Sequences
Table_Bacterial:value	Nucleotide_ORF_translation:Translation_table
ORFlen:value	Nucleotide_ORF_translation:Minimum_ORF_length
Nucleotide_ORF_translation:ORF_list	EBI_NCBI_BLAST:Sequence
Get_Web_Page_from_URL:contents	MultipleBlastp:Contigs_Single
Contigs_in_bucket:value	Get_Web_Page_from_URL:url
EBI_NCBI_BLAST:GI_out	GI
Nucleotide_ORF_translation:ORF_list	ORFS
EBI_NCBI_BLAST:FirstHitFasta	fasta

Get top blastx hit of a list of contigs

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