[med-svn] [spades] 06/08: remove unnecessary patch

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository spades.

commit 3f32c1ce80087f81c7d9f6bd8ac2cbf255a54a48
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 15:11:52 2016 +0000

    remove unnecessary patch
---
 debian/patches/0114_adjust_seqio_imports.patch | 59 --------------------------
 debian/patches/series                          |  1 -
 2 files changed, 60 deletions(-)

diff --git a/debian/patches/0114_adjust_seqio_imports.patch b/debian/patches/0114_adjust_seqio_imports.patch
deleted file mode 100644
index f48c096..0000000
--- a/debian/patches/0114_adjust_seqio_imports.patch
+++ /dev/null
@@ -1,59 +0,0 @@
-Description: use correct SeqIO imports 
- Upstream's Biopython imports are missing the 'from Bio' part. Adding this
- to allow usage of Debian's packaged Biopython.
-Author: Sascha Steinbiss <sascha at steinbiss.name> 
---- a/src/spades_pipeline/truspades/break_by_coverage.py
-+++ b/src/spades_pipeline/truspades/break_by_coverage.py
-@@ -7,7 +7,7 @@
- ############################################################################
- 
- 
--import SeqIO
-+from Bio import SeqIO
- from SeqIO import SeqRecord
- 
- import sys
---- a/src/spades_pipeline/truspades/moleculo_filter_contigs.py
-+++ b/src/spades_pipeline/truspades/moleculo_filter_contigs.py
-@@ -9,7 +9,7 @@
- 
- import sam_parser
- 
--import SeqIO
-+from Bio import SeqIO
- 
- import sys
- 
---- a/src/spades_pipeline/truspades/moleculo_postprocessing.py
-+++ b/src/spades_pipeline/truspades/moleculo_postprocessing.py
-@@ -6,7 +6,7 @@
- 
- import moleculo_filter_contigs
- import break_by_coverage
--import SeqIO
-+from Bio import SeqIO
- import sys
- import generate_quality
- import sam_parser
---- a/src/spades_pipeline/truspades/reference_construction.py
-+++ b/src/spades_pipeline/truspades/reference_construction.py
-@@ -16,7 +16,7 @@
- import itertools
- import traceback
- 
--import SeqIO
-+from Bio import SeqIO
- import alignment
- import parallel_launcher
- import sam_parser
---- a/truspades.py
-+++ b/truspades.py
-@@ -24,7 +24,7 @@
- sys.path.append(os.path.join(python_modules_home, "spades_pipeline", "truspades"))
- sys.path.append(os.path.join(python_modules_home, "spades_pipeline"))
- 
--import SeqIO
-+from Bio import SeqIO
- import parallel_launcher
- import reference_construction
- import launch_options
diff --git a/debian/patches/series b/debian/patches/series
index be65510..3d8c8f0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -14,4 +14,3 @@
 0111_use_full_config_dirs.patch
 0112_spelling.patch
 0113_adjust_paths.patch
-0114_adjust_seqio_imports.patch

-- 
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