# HG changeset patch
# User peterjc
# Date 1478261468 14400
# Node ID fb1313d79396148034eebfbf20ef70fa23130cb5
# Parent  03e134cae41a7d518e89a70dc50ffb70313ec58a
Uploaded v0.2.5, ignore blank names in tabular files (based on contribution from Gildas Le Corguille)

diff -r 03e134cae41a -r fb1313d79396 tools/seq_filter_by_id/README.rst
--- a/tools/seq_filter_by_id/README.rst	Tue May 17 05:59:24 2016 -0400
+++ b/tools/seq_filter_by_id/README.rst	Fri Nov 04 08:11:08 2016 -0400
@@ -89,6 +89,8 @@
 v0.2.3  - Ignore blank lines in ID file (contributed by Gildas Le Corguillé).
         - Defensive quoting of filenames etc in the command definition
           (internal change only).
+v0.2.4  - Corrected error message wording.
+v0.2.5  - Ignore empty names, common in R output (Gildas Le Corguillé).
 ======= ======================================================================
 
 
diff -r 03e134cae41a -r fb1313d79396 tools/seq_filter_by_id/seq_filter_by_id.py
--- a/tools/seq_filter_by_id/seq_filter_by_id.py	Tue May 17 05:59:24 2016 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.py	Fri Nov 04 08:11:08 2016 -0400
@@ -74,7 +74,7 @@
 options, args = parser.parse_args()
 
 if options.version:
-    print "v0.2.3"
+    print "v0.2.5"
     sys.exit(0)
 
 in_file = options.input
@@ -93,7 +93,7 @@
 if logic not in ["UNION", "INTERSECTION"]:
     sys.exit("Logic agrument should be 'UNION' or 'INTERSECTION', not %r" % logic)
 if options.id_list and args:
-    sys.exit("Cannot accepted IDs via both -t and as tabular files")
+    sys.exit("Cannot accept IDs via both -t in the command line, and as tabular files")
 elif not options.id_list and not args:
     sys.exit("Expected matched pairs of tabular files and columns (or -t given)")
 if len(args) % 2:
@@ -181,7 +181,7 @@
     '\r': '__cr__',
     '\t': '__tc__',
     '#': '__pd__',
-    }
+}
 
 # Read tabular file(s) and record all specified identifiers
 ids = None  # Will be a set
@@ -206,15 +206,19 @@
                 continue
             parts = line.rstrip("\n").split("\t")
             for col in columns:
-                file_ids.add(clean_name(parts[col]))
+                name = clean_name(parts[col])
+                if name:
+                    file_ids.add(name)
     else:
         # Single column, special case speed up
         col = columns[0]
         for line in handle:
-            if not line.strip(): #skip empty lines
+            if not line.strip():  # skip empty lines
                 continue
             if not line.startswith("#"):
-                file_ids.add(clean_name(line.rstrip("\n").split("\t")[col]))
+                name = clean_name(line.rstrip("\n").split("\t")[col])
+                if name:
+                    file_ids.add(name)
     print "Using %i IDs from column %s in tabular file" % (len(file_ids), ", ".join(str(col + 1) for col in columns))
     if ids is None:
         ids = file_ids
diff -r 03e134cae41a -r fb1313d79396 tools/seq_filter_by_id/seq_filter_by_id.xml
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml	Tue May 17 05:59:24 2016 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Fri Nov 04 08:11:08 2016 -0400
@@ -1,8 +1,7 @@
-<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.3">
+<tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.5">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.64">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
diff -r 03e134cae41a -r fb1313d79396 tools/seq_filter_by_id/tool_dependencies.xml
--- a/tools/seq_filter_by_id/tool_dependencies.xml	Tue May 17 05:59:24 2016 -0400
+++ b/tools/seq_filter_by_id/tool_dependencies.xml	Fri Nov 04 08:11:08 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.64">
-        <repository changeset_revision="b64c8edb7e45" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0c7526e8ea70" name="package_biopython_1_64" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>