print("Choose the data file which holds the information of the gene \

that you are looking for. Format gene name, chromosome, start position, end position.")

Tk().withdraw()

text_file_path = askopenfilename()

print("Choose the BAM file that you are extracting reads from.")

Tk().withdraw()

bam_file_path = askopenfilename()

sample_name = raw_input("What is the name of the sample the reads are coming from: ")

sequence_size = raw_input("What is the length of each read's sequence: ")

path = text_file_path.split('/')

path.pop()

path = '/'.join(path)

path = '/' + path

directory_path = path + '/' + sample_name

if os.path.isdir(directory_path) == False:

os.mkdir(directory_path)

fin = open(text_file_path, 'r')

for line in fin:

try:

gene_info = line.split("\t")

gene_name = gene_info[0]

chromosome = 'chr' + gene_info[1]

start_position = gene_info[2]

end_position = gene_info[3]

samfile = pysam.Samfile(bam_file_path, "rb")

iter = samfile.fetch(chromosome, int(start_position), int(end_position))

file_name = directory_path + '/' + gene_name + '.txt'

gene_file = open(file_name, 'w')

for x in iter:

current_read = str(x)

read_info = current_read.split("\t")

read_start = read_info[3]

read_end = str(int(read_info[3]) + int(sequence_size))

read_mapping_quality = read_info[4]

read_sequence = read_info[9]

selected_read_info = [read_start, read_end, read_mapping_quality, read_sequence]

output_string = '\t'.join(selected_read_info) + '\n'

gene_file.write(output_string)

gene_file.close()

except:

print("Error Found")

print("Done")

fin.close()