コード例 #1
0
ファイル: test_mapseq.py プロジェクト: bbcf/bbcflib
 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")
コード例 #2
0
ファイル: test_mapseq.py プロジェクト: bbcf/bbcflib
 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")
コード例 #3
0
ファイル: test_mapseq.py プロジェクト: bbcf/bbcflib
 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")
コード例 #4
0
ファイル: test_mapseq.py プロジェクト: bbcf/bbcflib
 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")