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'], )
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, )
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, )
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, )
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'], )