Restructure package

* remove src/ directory * Move CONTRIB, INSTALL, LICENCE, CHANGELOG to top level * move seqmagick script to seqmagick/scripts
fhcrc · Apr 7, 2011 · 386c72e · 386c72e
1 parent 788e0a9
commit 386c72e
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Showing 12 changed files with 13 additions and 2 deletions.
diff --git a/src/seqmagick/CHANGELOG → CHANGELOG b/src/seqmagick/CHANGELOG → CHANGELOG
diff --git a/src/seqmagick/CONTRIB → CONTRIB b/src/seqmagick/CONTRIB → CONTRIB
diff --git a/src/seqmagick/INSTALL → INSTALL b/src/seqmagick/INSTALL → INSTALL
diff --git a/src/seqmagick/LICENSE → LICENSE b/src/seqmagick/LICENSE → LICENSE
diff --git a/scripts/seqmagick b/scripts/seqmagick
@@ -0,0 +1,5 @@
+#!/usr/bin/env python
+
+from seqmagick.scripts import cli
+
+cli.main()
diff --git a/src/seqmagick/README → seqmagick/README b/src/seqmagick/README → seqmagick/README
diff --git a/src/seqmagick/__init__.py → seqmagick/__init__.py b/src/seqmagick/__init__.py → seqmagick/__init__.py
diff --git a/src/seqmagick/fileformat.py → seqmagick/fileformat.py b/src/seqmagick/fileformat.py → seqmagick/fileformat.py
diff --git a/src/seqmagick/magickwrap.py → seqmagick/magickwrap.py b/src/seqmagick/magickwrap.py → seqmagick/magickwrap.py
@@ -362,6 +362,13 @@ def _cut_sequences(self, records, start, end):
                                'cutting sequences based on specified range (' + start + '-' + end + ').'
         start = start - 1
         for record in records:
+            record = SeqRecord(record.seq[start:end], id=record.id,
+                    name=record.name, description=record.description)
+
+            # TODO: Make this a little cleaner?
+            # Include quality scores if present
+
+
             yield SeqRecord(record.seq[start:end], id=record.id,
                             description=record.description)
 

diff --git a/seqmagick/scripts/__init__.py b/seqmagick/scripts/__init__.py
diff --git a/src/seqmagick/scripts/seqmagick → seqmagick/scripts/cli.py b/src/seqmagick/scripts/seqmagick → seqmagick/scripts/cli.py
diff --git a/src/seqmagick/setup.py → setup.py b/src/seqmagick/setup.py → setup.py
@@ -6,7 +6,6 @@
       version = '0.1',
       description = 'Tools for converting and working with sequence files.',
       author = 'Erick Matsen <ematsen@gmail.com>, Brian Hodges <bhodges@fhcrc.org>',
-      package_dir = {'seqmagick': '.'},
-      packages = ['seqmagick'],
+      packages = ['seqmagick', 'seqmagick.scripts'],
       scripts = ['scripts/seqmagick'],
       )