Author: tille Date: 2014-06-08 11:53:35 +0000 (Sun, 08 Jun 2014) New Revision: 17065
Removed: trunk/packages/python-biopython/trunk/debian/patches/add_missing_test_Fasttree_tool.patch trunk/packages/python-biopython/trunk/debian/patches/biopython-from-pil-import-image.patch trunk/packages/python-biopython/trunk/debian/patches/fix_cpairwise2_import_issue.patch trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch trunk/packages/python-biopython/trunk/debian/patches/use_upstream_patch_for_bwa_test.patch Modified: trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch trunk/packages/python-biopython/trunk/debian/patches/series Log: Updated patches to new upstream version Deleted: trunk/packages/python-biopython/trunk/debian/patches/add_missing_test_Fasttree_tool.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/add_missing_test_Fasttree_tool.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/add_missing_test_Fasttree_tool.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,42 +0,0 @@ -Author: Peter Cock <[email protected]> -Last-Update: Sun, 27 Apr 2014 13:21:14 +0100 -Description: Add file which is missing for no good reason - from upstream source tarball. It was obtained from - https://raw.githubusercontent.com/biopython/biopython/2b414d8a9ca0aa15ef4b4b3680b8bfc755776b56/Tests/output/test_Fasttree_tool - ---- /dev/null -+++ b/Tests/output/test_Fasttree_tool -@@ -0,0 +1,33 @@ -+test_Fasttree_tool -+Checking error conditions -+========================= -+Empty file -+Failed (good) -+ -+Single sequence -+Failed (good) -+ -+Invalid sequence -+Failed (good) -+ -+Checking normal situations -+========================== -+ -+Calling fasttree on 'Quality/example.fasta' (with 3 records) -+ -+Checking generation of tree terminals -+Success -+ -+Checking distances between tree terminals -+Success -+ -+Calling fasttree on 'Clustalw/temp horses.fasta' (with 10 records) -+ -+Checking generation of tree terminals -+Success -+ -+Checking distances between tree terminals -+Success -+ -+Done -+ Deleted: trunk/packages/python-biopython/trunk/debian/patches/biopython-from-pil-import-image.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/biopython-from-pil-import-image.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/biopython-from-pil-import-image.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,31 +0,0 @@ -Author: Jakub Wilk <[email protected]> -Last-Update: Mon, 28 Apr 2014 15:39:59 +0200 -Description: Avoid python-imaging compatibility package - python-imaging's description more or less says what you have to change: - “PIL used to provide a PIL.pth file which allowed you to `import - Image` but this is deprecated. Use `from PIL import Image` now, or - install this compatibility package to temporarily get the old behavior - back - ---- a/Tests/test_GenomeDiagram.py -+++ b/Tests/test_GenomeDiagram.py -@@ -27,7 +27,7 @@ except ImportError: - "Install reportlab if you want to use Bio.Graphics.") - - try: -- import Image -+ from PIL import Image - from reportlab.graphics import renderPM - except ImportError: - #This is an optional part of ReportLab, so may not be installed. ---- a/Tests/test_GraphicsBitmaps.py -+++ b/Tests/test_GraphicsBitmaps.py -@@ -35,7 +35,7 @@ except: - "bitmaps with Bio.Graphics.") - try: - # Skip the test if PIL is not installed -- import Image as i -+ from PIL import Image as i - del i - except: - raise MissingPythonDependencyError( Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_cpairwise2_import_issue.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_cpairwise2_import_issue.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_cpairwise2_import_issue.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,18 +0,0 @@ -Author: Peter Cock <[email protected]> -Last-Update: Fri, 9 May 2014 13:36:32 +0100 -Bugs-Debian: http://bugs.debian.org/747494 -Bugs-Upstream: https://github.com/biopython/biopython/pull/299 -Description: fix cpairwise2 import issue under python3 - see https://github.com/biopython/biopython/commit/daf3e3b5ba317fbbea1f7eebae3c5f8b06a40d6b - ---- a/Bio/pairwise2.py -+++ b/Bio/pairwise2.py -@@ -878,7 +878,7 @@ def format_alignment(align1, align2, sco - # Try and load C implementations of functions. If I can't, - # then just ignore and use the pure python implementations. - try: -- from cpairwise2 import rint, _make_score_matrix_fast -+ from .cpairwise2 import rint, _make_score_matrix_fast - except ImportError: - pass - Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,15 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Thu, 06 Mar 2014 11:51:27 +0100 -Description: Fix EMBOSS test to work with latest EMBOSS release - ---- a/Tests/test_Emboss.py -+++ b/Tests/test_Emboss.py -@@ -73,6 +73,8 @@ def get_emboss_version(): - assert stderr is None # Send to stdout instead - for line in stdout.split("\n"): - if line.strip()=="Reports the current EMBOSS version number": -+ pass -+ elif line.strip()=="Report the current EMBOSS version number": - pass - elif line.startswith("Writes the current EMBOSS version number"): - pass Modified: trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -4,9 +4,9 @@ Forwarded-Upstream: yes Description: Remove non DFSG free DTD ---- a/Bio/Entrez/DTDs/modules.ent -+++ b/Bio/Entrez/DTDs/modules.ent -@@ -350,13 +350,6 @@ Version Reason/Occasion +--- biopython-1.64.orig/Bio/Entrez/DTDs/modules.ent ++++ biopython-1.64/Bio/Entrez/DTDs/modules.ent +@@ -350,13 +350,6 @@ "mathmlsetup.ent" > Modified: trunk/packages/python-biopython/trunk/debian/patches/series =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/series 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/series 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,6 +1 @@ -fix_test_emboss.patch -add_missing_test_Fasttree_tool.patch -use_upstream_patch_for_bwa_test.patch -biopython-from-pil-import-image.patch remove_mathml-qname.patch -fix_cpairwise2_import_issue.patch Deleted: trunk/packages/python-biopython/trunk/debian/patches/use_upstream_patch_for_bwa_test.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/use_upstream_patch_for_bwa_test.patch 2014-06-08 08:29:42 UTC (rev 17064) +++ trunk/packages/python-biopython/trunk/debian/patches/use_upstream_patch_for_bwa_test.patch 2014-06-08 11:53:35 UTC (rev 17065) @@ -1,191 +0,0 @@ -Author: Saket Choudhary <[email protected]> -Last-Update: Tue, 29 Apr 2014 01:37:43 +0530 -Description: Skip bwa aln tests if it is an unrecognized command -Comment: Taken over from upstream commit d884ee6e12a798b974b3a3996e22b5292ab79be6 -Forwarded-Upstream: yes - ---- a/Tests/test_BWA_tool.py -+++ b/Tests/test_BWA_tool.py -@@ -9,12 +9,12 @@ from Bio import MissingExternalDependenc - import sys - import os - import unittest --from Bio import SeqIO --from Bio import AlignIO --from Bio.Sequencing.Applications import BwaIndexCommandline, BwaAlignCommandline --from Bio.Sequencing.Applications import BwaSamseCommandline, BwaSampeCommandline --from Bio.Sequencing.Applications import BwaBwaswCommandline --from Bio.Application import ApplicationError -+#TODO from Bio.Sequencing.Applications import BwaBwaswCommandline -+from Bio.Sequencing.Applications import BwaIndexCommandline -+from Bio.Sequencing.Applications import BwaAlignCommandline -+from Bio.Sequencing.Applications import BwaSamseCommandline -+from Bio.Sequencing.Applications import BwaSampeCommandline -+ - - ################################################################# - -@@ -29,11 +29,8 @@ if sys.platform == "win32": - prog_files = os.environ["PROGRAMFILES"] - except KeyError: - prog_files = r"C:\Program Files" -- #A default path of C:\Program Files\bwa.exe was chosen -- #but this path can be edited depending on where bwa is located -- -- likely_dirs = ["bwa", "BWA", "Bwa", "bwa-0.6.2"] -- likely_exes = ["bwa.exe", "BWA.exe", "Bwa.exe"] -+ likely_dirs = ["bwa", "bwa-0.6.2", ""] -+ likely_exes = ["bwa"] - for folder in likely_dirs: - if os.path.isdir(os.path.join(prog_files, folder)): - for filename in likely_exes: -@@ -50,52 +47,96 @@ else: - #really the bwa tool's output - bwa_found = False - if "not found" not in output and "bwa" in output \ -- and "alignment via Burrows-Wheeler transformation" in output: -+ and "alignment via Burrows-Wheeler transformation" in output: - bwa_exe = "bwa" - - if not bwa_exe: -- raise MissingExternalDependencyError(\ -- "Install bwa and correctly set the file path to the program if you want to use it from Biopython") -+ raise MissingExternalDependencyError("Install bwa and correctly set" -+ " the file path to the program if" -+ " you want to use it from Biopython") - - - class BwaTestCase(unittest.TestCase): - """Class for implementing BWA test cases""" - def setUp(self): -- self.reference_file = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "human_g1k_v37_truncated.fasta") -- self.infile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "HNSCC1_1_truncated.fastq") -- self.infile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "HNSCC1_2_truncated.fastq") -- self.saifile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "1.sai") -- self.saifile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "2.sai") -- self.samfile1 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "1.sam") -- self.samfile2 = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "2.sam") -- self.samfile = os.path.join(os.path.dirname(os.path.abspath(__file__)), "BWA", "out.sam") -+ self.reference_file = "BWA/human_g1k_v37_truncated.fasta" -+ self.reference_extensions = ['amb', 'ann', 'bwt', 'pac', 'sa'] -+ self.infile1 = "BWA/HNSCC1_1_truncated.fastq" -+ self.infile2 = "BWA/HNSCC1_2_truncated.fastq" -+ self.saifile1 = "BWA/1.sai" -+ self.saifile2 = "BWA/2.sai" -+ self.samfile1 = "BWA/1.sam" -+ self.samfile2 = "BWA/2.sam" -+ self.samfile = "BWA/out.sam" -+ self.files_to_clean = [self.saifile1, self.saifile2, -+ self.samfile1, self.samfile2, -+ self.samfile] -+ -+ def tearDown(self): -+ for filename in self.files_to_clean: -+ if os.path.isfile(filename): -+ os.remove(filename) -+ for extension in self.reference_extensions: -+ index_file = self.reference_file + "." + extension -+ if os.path.exists(index_file): -+ os.remove(index_file) - - def test_index(self): - """Test for creating index files for the reference genome fasta file""" -- cmdline = BwaIndexCommandline() -+ cmdline = BwaIndexCommandline(bwa_exe) - cmdline.set_parameter("infile", self.reference_file) - cmdline.set_parameter("algorithm", "bwtsw") - stdout, stderr = cmdline() -- output = stdout.startswith("[bwt_gen]") -+ for extension in self.reference_extensions: -+ index_file = self.reference_file + "." + extension -+ self.assertTrue(os.path.exists(index_file), -+ "Index File %s not found" -+ % (index_file)) - self.assertTrue(stdout.startswith("[bwt_gen]"), -- "FASTA indexing failed:\n%s\nStdout:%s" \ -+ "FASTA indexing failed:\n%s\nStdout:%s" - % (cmdline, stdout)) - - def do_aln(self, in_file, out_file): - """Test for generating sai files given the reference and read file""" -- cmdline = BwaAlignCommandline() -+ cmdline = BwaAlignCommandline(bwa_exe) - cmdline.set_parameter("reference", self.reference_file) - cmdline.read_file = in_file - self.assertTrue(os.path.isfile(in_file)) - stdout, stderr = cmdline(stdout=out_file) - - self.assertTrue("fail to locate the index" not in stderr, -- "Error aligning sequence to reference:\n%s\nStderr:%s" \ -+ "Error aligning sequence to reference:\n%s\nStderr:%s" - % (cmdline, stderr)) - -+ def skip_aln_tests(self): -+ """As reported on http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011342.html -+ 'bwa aln' is failing for bwa[0.7.6a-r433] -+ Tests using 'aln' should be skipped in that case""" -+ -+ aln_output = getoutput("bwa aln") -+ if "unrecognized" in aln_output: -+ return True -+ return False -+ -+ def create_fasta_index(self): -+ """Creates index for fasta file -+ BWA requires an indexed fasta for each alignment operation. -+ This should be called to create an index before any alignment -+ operation. -+ -+ """ -+ cmdline = BwaIndexCommandline(bwa_exe) -+ cmdline.set_parameter("infile", self.reference_file) -+ cmdline.set_parameter("algorithm", "bwtsw") -+ stdout, stderr = cmdline() -+ - def test_samse(self): - """Test for single end sequencing """ -- cmdline = BwaSamseCommandline() -+ if self.skip_aln_tests(): -+ return -+ self.create_fasta_index() -+ self.do_aln(self.infile1, self.saifile1) -+ cmdline = BwaSamseCommandline(bwa_exe) - cmdline.set_parameter("reference", self.reference_file) - cmdline.set_parameter("read_file", self.infile1) - cmdline.set_parameter("sai_file", self.saifile1) -@@ -104,16 +145,20 @@ class BwaTestCase(unittest.TestCase): - with open(self.samfile1, "r") as handle: - headline = handle.readline() - self.assertTrue(headline.startswith("@SQ"), -- "Error generating sam files:\n%s\nOutput starts:%s" \ -+ "Error generating sam files:\n%s\nOutput starts:%s" - % (cmdline, headline)) - - def test_sampe(self): - """Test for generating samfile by paired end sequencing""" -+ if self.skip_aln_tests(): -+ return -+ self.create_fasta_index() -+ - ##Generate sai files from paired end data - self.do_aln(self.infile1, self.saifile1) - self.do_aln(self.infile2, self.saifile2) - -- cmdline = BwaSampeCommandline() -+ cmdline = BwaSampeCommandline(bwa_exe) - cmdline.set_parameter("reference", self.reference_file) - cmdline.set_parameter("sai_file1", self.saifile1) - cmdline.set_parameter("sai_file2", self.saifile2) -@@ -124,10 +169,11 @@ class BwaTestCase(unittest.TestCase): - with open(self.samfile, "r") as handle: - headline = handle.readline() - self.assertTrue(headline.startswith("@SQ"), -- "Error generating sam files:\n%s\nOutput starts:%s" \ -+ "Error generating sam files:\n%s\nOutput starts:%s" - % (cmdline, headline)) - - - if __name__ == "__main__": - runner = unittest.TextTestRunner(verbosity=2) - unittest.main(testRunner=runner) -+ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
