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JAL-3641 allow protocol to be configured at top of script
features/JAL-3641_phredfromfastq
author
Jim Procter
<jprocter@issues.jalview.org>
Mon, 8 Jun 2020 10:22:36 +0000
(11:22 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Mon, 8 Jun 2020 10:22:36 +0000
(11:22 +0100)
examples/groovy/FastQParser.groovy
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diff --git
a/examples/groovy/FastQParser.groovy
b/examples/groovy/FastQParser.groovy
index
7658539
..
8414e54
100644
(file)
--- a/
examples/groovy/FastQParser.groovy
+++ b/
examples/groovy/FastQParser.groovy
@@
-18,9
+18,9
@@
import jalview.io.DataSourceType
/*
* EDIT THE FILE PATH BELOW TO IMPORT A FASTQ FILE
*/
/*
* EDIT THE FILE PATH BELOW TO IMPORT A FASTQ FILE
*/
-FASTQ_FILE = "/Users/jprocter/Downloads/small_normalised_illumina_adeno.fastq.gz"
-FASTQ_FILE = "/Users/jprocter/Downloads/test.fastq"
+FASTQ_FILE = "/Users/jprocter/Downloads/test.fastq"
+FASTQ_FILE_PROTOCOL = DataSourceType.FILE // could also be DataSourceType.URL
/*
* A parser class to read or write the format
/*
* A parser class to read or write the format
@@
-135,7
+135,7
@@
def myFormat = { ->
// read in the file specified at the top of the Groovy script
// read in the file specified at the top of the Groovy script
-FastQFile parser = new FastQFile(new FileParse(FASTQ_FILE, DataSourceType.FILE));
+FastQFile parser = new FastQFile(new FileParse(FASTQ_FILE, FASTQ_FILE_PROTOCOL));
AlignmentI al = new jalview.datamodel.Alignment(parser.getSeqsAsArray());
parser.addAnnotations(al);
jalview.gui.AlignFrame newwindow = new jalview.gui.AlignFrame(al,800,600);
AlignmentI al = new jalview.datamodel.Alignment(parser.getSeqsAsArray());
parser.addAnnotations(al);
jalview.gui.AlignFrame newwindow = new jalview.gui.AlignFrame(al,800,600);