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'],
)