[med-svn] [spades] 01/08: fix Biopython imports

[Sascha Steinbiss]

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

commit b08e3a67c79d07f268d37ee3674a524bdbf59e58
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Feb 11 11:46:34 2016 +0000

    fix Biopython imports
---
 debian/patches/0114_adjust_seqio_imports.patch | 59 ++++++++++++++++++++++++++
 debian/patches/series                          |  1 +
 2 files changed, 60 insertions(+)

diff --git a/debian/patches/0114_adjust_seqio_imports.patch b/debian/patches/0114_adjust_seqio_imports.patch
new file mode 100644
index 0000000..f48c096
--- /dev/null
+++ b/debian/patches/0114_adjust_seqio_imports.patch
@@ -0,0 +1,59 @@
+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 3d8c8f0..be65510 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -14,3 +14,4 @@
 0111_use_full_config_dirs.patch
 0112_spelling.patch
 0113_adjust_paths.patch
+0114_adjust_seqio_imports.patch

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