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commit b08e3a67c79d07f268d37ee3674a524bdbf59e58 Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> +--- 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
