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Commit ca45ca09 authored by tjc's avatar tjc
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write out gzip files by default

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12079 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 700953af
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...@@ -262,11 +262,12 @@ public class ReadAndWriteEntry ...@@ -262,11 +262,12 @@ public class ReadAndWriteEntry
System.out.println("-i\t[y|n] ignore obsolete features, default is y"); System.out.println("-i\t[y|n] ignore obsolete features, default is y");
System.out.println("-s\tspace separated list of sequences to read and write out"); System.out.println("-s\tspace separated list of sequences to read and write out");
System.out.println("-o\t[EMBL|GFF] output format, default is EMBL"); System.out.println("-o\t[EMBL|GFF] output format, default is EMBL");
System.out.println("-a\t[y|n] for EMBL submission format change to n, default is y");
System.out.println("-pp\t[y|n] read polypeptide domain features, default is n");
// note that read_only and noprompt -D parameters redundant now // note that read_only and noprompt -D parameters redundant now
System.out.println("New parameters:"); System.out.println("Advanced parameters:");
System.out.println("-z\t[y|n] gzip output, default is y");
System.out.println("-a\t[y|n] for EMBL submission format change to n, default is y");
System.out.println("-pp\t[y|n] read polypeptide domain features, default is n");
System.out.println("-c\tthe URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (if not using default)"); System.out.println("-c\tthe URL for your Chado database e.g. db.genedb.org:5432/snapshot?genedb_ro (if not using default)");
System.out.println("-u\t[swing|console|script] the UI mode : run in swing (with popup dialog boxes) mode, run in console mode (choices entered in the console window), or in script mode (all choices default to continue, all parameters passed on command line) "); System.out.println("-u\t[swing|console|script] the UI mode : run in swing (with popup dialog boxes) mode, run in console mode (choices entered in the console window), or in script mode (all choices default to continue, all parameters passed on command line) ");
System.out.println("-p\tthe password for connecting to the Chado database"); System.out.println("-p\tthe password for connecting to the Chado database");
...@@ -280,6 +281,7 @@ public class ReadAndWriteEntry ...@@ -280,6 +281,7 @@ public class ReadAndWriteEntry
int format = DocumentEntryFactory.EMBL_FORMAT; int format = DocumentEntryFactory.EMBL_FORMAT;
boolean include_diana_extensions = true; boolean include_diana_extensions = true;
String suffix = ".embl"; String suffix = ".embl";
boolean gzip = true;
String filePath = ""; String filePath = "";
...@@ -304,6 +306,12 @@ public class ReadAndWriteEntry ...@@ -304,6 +306,12 @@ public class ReadAndWriteEntry
include_diana_extensions = false; include_diana_extensions = false;
} }
if (key.equals("-z"))
{
if(i + 1 < args.length && args[i + 1].toLowerCase().equals("n"))
gzip = false;
}
if (key.equals("-o")) if (key.equals("-o"))
{ {
if(i + 1 < args.length && args[i + 1].toLowerCase().equals("gff")) if(i + 1 < args.length && args[i + 1].toLowerCase().equals("gff"))
...@@ -375,13 +383,17 @@ public class ReadAndWriteEntry ...@@ -375,13 +383,17 @@ public class ReadAndWriteEntry
files.toArray(names); files.toArray(names);
} }
if (filePath.length() != 0) if(filePath.length() != 0)
{ {
filePath += "/"; filePath += "/";
} }
if(gzip)
suffix = suffix + ".gz";
for(int i=0;i < names.length; i++) for(int i=0;i < names.length; i++)
{ {
System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix); System.out.println("read :: "+names[i]+" write :: "+names[i]+suffix);
logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix); logger4j.info("read :: "+names[i]+" write :: "+names[i]+suffix);
......
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