Esempio n. 1
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 def map_tophat(self):
     mapping_tools.map_tophat([self.file_names['preprocessed_reads']],
                              self.file_names['bowtie2_index_prefix'],
                              self.file_names['genes'],
                              self.file_names['transcriptome_index'],
                              self.file_names['tophat_dir'],
                             )
Esempio n. 2
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 def map_tophat(self):
     mapping_tools.map_tophat([self.file_names['trimmed_reads']],
                              self.file_names['bowtie2_index_prefix'],
                              self.file_names['genes'],
                              self.file_names['transcriptome_index'],
                              self.file_names['tophat_dir'],
                              no_sort=True,
                             )
Esempio n. 3
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 def map_tophat(self):
     mapping_tools.map_tophat(
         [self.file_names['trimmed_reads']],
         self.file_names['bowtie2_index_prefix'],
         self.file_names['genes'],
         self.file_names['transcriptome_index'],
         self.file_names['tophat_dir'],
         no_sort=True,
     )
Esempio n. 4
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    def map_tophat(self):
        mapping_tools.map_tophat([self.file_names['five_prime_boundaries']],
                                 self.file_names['bowtie2_index_prefix'],
                                 self.file_names['genes'],
                                 self.file_names['transcriptome_index'],
                                 self.file_names['five_prime_tophat_dir'],
                                 no_sort=True,
                                )

        mapping_tools.map_tophat([self.file_names['three_prime_boundaries']],
                                 self.file_names['bowtie2_index_prefix'],
                                 self.file_names['genes'],
                                 self.file_names['transcriptome_index'],
                                 self.file_names['three_prime_tophat_dir'],
                                 no_sort=True,
                                )
    def map_tophat(self):
        mapping_tools.map_tophat([self.file_names['R1_preprocessed']],
                                 self.file_names['bowtie2_index_prefix'],
                                 self.file_names['genes'],
                                 self.file_names['transcriptome_index'],
                                 self.file_names['R1_tophat_dir'],
                                 no_sort=True,
                                )

        mapping_tools.map_tophat([self.file_names['R2_preprocessed']],
                                 self.file_names['bowtie2_index_prefix'],
                                 self.file_names['genes'],
                                 self.file_names['transcriptome_index'],
                                 self.file_names['R2_tophat_dir'],
                                 no_sort=True,
                                )
Esempio n. 6
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 def remap_polyA_trimmed(self, reads):
     trim.trim_polyA_from_unmapped(reads,
                                   self.file_names['unmapped_trimmed_fastq'],
                                   second_time=True,
                                  )
     if os.path.getsize(self.file_names['unmapped_trimmed_fastq']) == 0:
         # tophat crashes on an empty file, so create empty files of all the
         # output of tophat that we need to exist.
         if not os.path.isdir(self.file_names['tophat_remapped_polyA_dir']):
             os.mkdir(self.file_names['tophat_remapped_polyA_dir'])
         template = pysam.Samfile(self.file_names['accepted_hits'], 'rb')
         empty_accepted_hits = pysam.Samfile(self.file_names['remapped_accepted_hits'], 'wb', template=template)
         empty_accepted_hits.close()
         empty_unmapped = pysam.Samfile(self.file_names['remapped_unmapped_bam'], 'wb', template=template)
         empty_unmapped.close()
     else:
         mapping_tools.map_tophat([self.file_names['unmapped_trimmed_fastq']],
                                  self.file_names['bowtie2_index_prefix'],
                                  self.file_names['genes'],
                                  self.file_names['transcriptome_index'],
                                  self.file_names['tophat_remapped_polyA_dir'],
                                 )