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wilkening_rna_seq_experiment.py
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wilkening_rna_seq_experiment.py
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import three_t_fill_experiment
import os
from Sequencing import utilities, fastq, adapters
from Sequencing.Parallel import map_reduce
from collections import Counter
class WilkeningRNASeqExperiment(three_t_fill_experiment.ThreeTFillExperiment):
num_stages = 2
specific_results_files = []
specific_figure_files = []
specific_outputs = []
specific_work = []
specific_cleanup = []
def __init__(self, **kwargs):
super(WilkeningRNASeqExperiment, self).__init__(**kwargs)
full_adapter_in_R2 = utilities.reverse_complement(self.barcode) + utilities.reverse_complement(adapters.primers['PE']['R1'])
self.adapter_in_R2 = full_adapter_in_R2[:19]
def trim_reads(self, read_pairs):
total_reads = 0
long_enough_reads = 0
trimmed_lengths = Counter()
barcodes = Counter()
truncated_in_R1 = self.adapter_in_R1[1:]
truncated_in_R2 = self.adapter_in_R2[1:]
for R1, R2 in read_pairs:
total_reads += 1
barcodes[R2.seq[:len(self.barcode)]] += 1
# Check for weird thing where expected overhang base doesn't
# exist in primer dimers.
R1_dimer_distance = adapters.adapter_hamming_distance(R1.seq,
truncated_in_R1,
len(R1.seq),
len(truncated_in_R1),
len(self.barcode),
)
R2_dimer_distance = adapters.adapter_hamming_distance(R2.seq,
truncated_in_R2,
len(R2.seq),
len(truncated_in_R2),
len(self.barcode),
)
if R1_dimer_distance <= 3 and R2_dimer_distance <= 3:
position = len(self.barcode)
else:
position = adapters.consistent_paired_position(R1.seq,
R2.seq,
self.adapter_in_R1,
self.adapter_in_R2,
19,
3,
)
if position != None:
trimmed_lengths[position] += 1
if position - len(self.barcode) < 12:
continue
else:
position = len(R1.seq)
long_enough_reads += 1
payload_slice = slice(len(self.barcode), position)
processed_R1 = fastq.Read(R1.name, R1.seq[payload_slice], R1.qual[payload_slice])
processed_R2 = fastq.make_record(R2.name, R2.seq[payload_slice], R2.qual[payload_slice])
yield processed_R1, processed_R2
trimmed_lengths = utilities.counts_to_array(trimmed_lengths)
self.write_file('trimmed_lengths', trimmed_lengths)
self.write_file('barcodes', barcodes)
self.summary.extend(
[('Total read pairs', total_reads),
('Long enough', long_enough_reads),
]
)
if __name__ == '__main__':
script_path = os.path.realpath(__file__)
map_reduce.controller(WilkeningRNASeqExperiment, script_path)