示例#1
0
 def test_external_add_nh_flag(self):
     with execution(None) as ex:
         f = external_add_nh_flag(ex, os.path.join(path, "mapped.sam"))
         g = add_nh_flag(os.path.join(path, "mapped.sam"))
         m = md5sum(ex, f)
         m2 = md5sum(ex, g)
     self.assertEqual(m, m2)
示例#2
0
 def test_parallel_bowtie_lsf(self):
     with execution(None) as ex:
         bam = parallel_bowtie(
             ex, os.path.join(path, "selected_transcripts"), os.path.join(path, "reads.raw"), n_lines=250, via="lsf"
         )
         sam = bam_to_sam(ex, bam)
         new_sam = remove_lines_matching(ex, "@PG", sam)
         new_bam = sam_to_bam(ex, new_sam)
         m = md5sum(ex, new_bam)
     self.assertEqual(m, "find right md5sum")
示例#3
0
 def test_parallel_bowtie_local(self):
     with execution(None) as ex:
         bam = parallel_bowtie(
             ex,
             os.path.join(path, "selected_transcripts"),
             os.path.join(path, "reads.raw"),
             n_lines=250,
             via="local",
         )
         sam = bam_to_sam(ex, bam)
         new_sam = remove_lines_matching(ex, "@PG", sam)
         new_bam = sam_to_bam(ex, new_sam)
         self.assertEqual(md5sum(ex, new_bam), "2e6bd8ce814949075715b8ffddd1dcd5")
示例#4
0
 def test_parallel_bowtie_local_with_nh_flags(self):
     with execution(None) as ex:
         bam = parallel_bowtie(
             ex,
             os.path.join(path, "selected_transcripts"),
             os.path.join(path, "reads.raw"),
             n_lines=250,
             add_nh_flags=True,
             via="local",
         )
         sam = bam_to_sam(ex, bam)
         new_sam = remove_lines_matching(ex, "@PG", sam)
         new_bam = sam_to_bam(ex, new_sam)
         self.assertEqual(md5sum(ex, new_bam), "529cd218ec0a35d5d0a23fd7b842ee20")
示例#5
0
 def test_parallel_bowtie_lsf_with_nh_flags(self):
     with execution(None) as ex:
         bam = parallel_bowtie(
             ex,
             os.path.join(path, "selected_transcripts"),
             os.path.join(path, "reads.raw"),
             n_lines=250,
             add_nh_flags=True,
             via="lsf",
         )
         sam = bam_to_sam(ex, bam)
         new_sam = remove_lines_matching(ex, "@PG", sam)
         new_bam = sam_to_bam(ex, new_sam)
         m = md5sum(ex, new_bam)
     self.assertEqual(m, "7b7c270a3980492e82591a785d87538f")
示例#6
0
 def test_internal_add_nh_flag(self):
     with execution(None) as ex:
         f = add_nh_flag(os.path.join(path, "mapped.sam"))
         m = md5sum(ex, f)
     self.assertEqual(m, "50798b19517575533b8ccae5b1369a3e")