# HG changeset patch
# User peterjc
# Date 1337358312 14400
# Node ID 50a8a6917a9c4a0562670397127c6a9fc59ac620
# Parent  838b9bebfa3c475287f1b2c78d5ae6bd32dfe74c
Uploaded update (v0.0.3) to ignore blank lines in the ID file

diff -r 838b9bebfa3c -r 50a8a6917a9c tools/filters/seq_select_by_id.py
--- a/tools/filters/seq_select_by_id.py	Tue Jun 07 17:43:38 2011 -0400
+++ b/tools/filters/seq_select_by_id.py	Fri May 18 12:25:12 2012 -0400
@@ -16,11 +16,11 @@
 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
-This script is copyright 2011 by Peter Cock, The James Hutton Institute UK.
+This script is copyright 2011-2012 by Peter Cock, The James Hutton Institute UK.
 All rights reserved. See accompanying text file for licence details (MIT/BSD
 style).
 
-This is version 0.0.1 of the script.
+This is version 0.0.3 of the script.
 """
 import sys
 
@@ -39,7 +39,7 @@
     else:
         column = int(col_arg)-1
 except ValueError:
-    stop_err("Expected column number, got %s" % cols_arg)
+    stop_err("Expected column number, got %s" % col_arg)
 
 if seq_format == "fastqcssanger":
     stop_err("Colorspace FASTQ not supported.")
@@ -65,7 +65,7 @@
     """Read tabular file and record all specified identifiers."""
     handle = open(tabular_file, "rU")
     for line in handle:
-        if not line.startswith("#"):
+        if line.strip() and not line.startswith("#"):
             yield line.rstrip("\n").split("\t")[col].strip()
     handle.close()
 
@@ -105,7 +105,7 @@
     except KeyError, err:
         out_handle.close()
         if name not in records:
-            stop_err("Identifier %s not found in sequence file" % name)
+            stop_err("Identifier %r not found in sequence file" % name)
         else:
             raise err
     out_handle.close()
@@ -119,7 +119,7 @@
             out_handle.write(records.get_raw(name))
         except KeyError:
             out_handle.close()
-            stop_err("Identifier %s not found in sequence file" % name)
+            stop_err("Identifier %r not found in sequence file" % name)
         count += 1
     out_handle.close()
 
diff -r 838b9bebfa3c -r 50a8a6917a9c tools/filters/seq_select_by_id.txt
--- a/tools/filters/seq_select_by_id.txt	Tue Jun 07 17:43:38 2011 -0400
+++ b/tools/filters/seq_select_by_id.txt	Fri May 18 12:25:12 2012 -0400
@@ -1,5 +1,5 @@
-Galaxy tool to select FASTA, FASTQ or SFF sequences by ID
-=========================================================
+Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
+===============================================================
 
 This tool is copyright 2011 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
@@ -26,7 +26,7 @@
 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line:
 
-<tool file="filters/sff_select_by_id.xml" />
+<tool file="filters/seq_select_by_id.xml" />
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -35,7 +35,7 @@
 =======
 
 v0.0.1 - Initial version.
-
+v0.0.3 - Ignore blank lines in input
 
 Developers
 ==========
diff -r 838b9bebfa3c -r 50a8a6917a9c tools/filters/seq_select_by_id.xml
--- a/tools/filters/seq_select_by_id.xml	Tue Jun 07 17:43:38 2011 -0400
+++ b/tools/filters/seq_select_by_id.xml	Fri May 18 12:25:12 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.1">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.3">
 	<description>from a tabular file</description>
 	<command interpreter="python">
 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file