import numpy as np
from .samflag import samflags
[docs]def find_chromosome_reads(chromosome, N_reads: int):
"""Find the reads inside each chromosome
Parameters
----------
chromosome : str
The name of the chromosome , either in arabic numbers 1, 2 , or roman "I", "II"
N_reads : int
Returns
-------
flags, start_position, readlength
"""
# Initialize arrays
start_position = np.empty(shape=(N_reads), dtype=int)
flags = np.empty(shape=(N_reads), dtype=int)
readlength = np.empty(shape=(N_reads), dtype=int)
for index, reads in enumerate(chromosome):
read = str(reads).split("\t")
start_position[index] = int(read[3]) + 1
# GET FLAG FOR EACH READ. IF READ ON FORWARD STRAND, ASSIGN VALUE 1, IF READ ON REVERSE STRAND ASSIGN VALUE -1, IF READ UNMAPPED OR SECONDARY ALIGNMENT ASSIGN VALUE 0
# flag_array[read_counter] = int(read[1])
samprop = samflags(flag=int(read[1]), verbose=False)[1]
if "read reverse strand" in samprop:
flags[index] = -1
else:
flags[index] = 1
if "not primary alignment" in samprop or "read unmapped" in samprop:
flags[index] = 0
cigarmatch_list = []
if not reads.cigartuples == None:
for cigar_type, cigar_length in reads.cigartuples:
if cigar_type == 0:
cigarmatch_list.append(cigar_length)
elif cigar_type == 2:
cigarmatch_list.append(cigar_length)
match_length = sum(cigarmatch_list)
readlength[index] = match_length # int(len(read[9]))
return flags, start_position, readlength
