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| 1 | #!/usr/bin/env python | |
| 2 | # this function was written in python 3 by Samantha Taffner | |
| 3 | ||
| 4 | import sys | |
| 5 | import os | |
| 6 | ||
| 7 | def run(first_file, second_file, folder_location): | |
| 8 | ''' | |
| 9 | | HiCpy is designed to bridge the speed gap between the very fast short | |
| 10 | | single read alignment and the considerably slower paired-end alignment. | |
| 11 | | HiCpy works in conjuction with Bowtie to accomplish an efficient Hi-C | |
| 12 | | analysis pipeline. Bowtie is called an ultrafast memory-efficient | |
| 13 | | short read aligner and there is not any denying that for single | |
| 14 | | read sequencing it is very fast. However, it is lacking tremendously | |
| 15 | | in speed for paired-end alignment. After 2 weeks it finally finished | |
| 16 | | while using 7 processors. HiCpy shortens the time to 4 hours on a | |
| 17 | | 2 processor machine. | |
| 18 | | | |
| 19 | | Go to HiCpy manual for more information. | |
| 20 | ''' | |
| 21 | first_file_dir = first_file.split('/')
| |
| 22 | first_file_name = first_file_dir[-1] | |
| 23 | ||
| 24 | inside_folder_1 = folder_location + '/first_file' | |
| 25 | ||
| 26 | if not os.path.exists(inside_folder_1): os.makedirs(inside_folder_1) | |
| 27 | ||
| 28 | find_mapped(first_file, inside_folder_1, first_file_name) | |
| 29 | ||
| 30 | inside_folder_2 = folder_location + '/second_file' | |
| 31 | if not os.path.exists(inside_folder_2): os.makedirs(inside_folder_2) | |
| 32 | ||
| 33 | second_file_dir = second_file.split('/')
| |
| 34 | second_file_name = second_file_dir[-1] | |
| 35 | ||
| 36 | find_mapped(first_file, inside_folder_2, second_file_name) | |
| 37 | ||
| 38 | out_folder = folder_location + '/your_results' | |
| 39 | if not os.path.exists(out_folder): os.makedirs(out_folder) | |
| 40 | ||
| 41 | out_file = out_folder + '/your_results.bed' | |
| 42 | make_file = open(out_file,'w') | |
| 43 | make_file.close() | |
| 44 | ||
| 45 | pairing(inside_folder_1, inside_folder_2, out_file) | |
| 46 | ||
| 47 | ||
| 48 | ||
| 49 | def find_mapped(start_file, file_path, file_name): | |
| 50 | ||
| 51 | ||
| 52 | count = 0 | |
| 53 | ||
| 54 | f_1 = open((file_path + '/1.sam'), 'w') | |
| 55 | f_2 = open((file_path + '/2.sam'), 'w') | |
| 56 | f_3 = open((file_path + '/3.sam'), 'w') | |
| 57 | f_4 = open((file_path + '/4.sam'), 'w') | |
| 58 | f_5 = open((file_path + '/5.sam'), 'w') | |
| 59 | f_6 = open((file_path + '/6.sam'), 'w') | |
| 60 | f_7 = open((file_path + '/7.sam'), 'w') | |
| 61 | f_8 = open((file_path + '/8.sam'), 'w') | |
| 62 | f_9 = open((file_path + '/9.sam'), 'w') | |
| 63 | f_10 = open((file_path + '/10.sam'), 'w') | |
| 64 | f_11 = open((file_path + '/11.sam'), 'w') | |
| 65 | f_12 = open((file_path + '/12.sam'), 'w') | |
| 66 | f_13 = open((file_path + '/13.sam'), 'w') | |
| 67 | f_14 = open((file_path + '/14.sam'), 'w') | |
| 68 | f_15 = open((file_path + '/15.sam'), 'w') | |
| 69 | f_16 = open((file_path + '/16.sam'), 'w') | |
| 70 | f_17 = open((file_path + '/17.sam'), 'w') | |
| 71 | f_18 = open((file_path + '/18.sam'), 'w') | |
| 72 | f_19 = open((file_path + '/19.sam'), 'w') | |
| 73 | f_Y = open((file_path + '/Y.sam'), 'w') | |
| 74 | f_X = open((file_path + '/X.sam'), 'w') | |
| 75 | f_M = open((file_path + '/M.sam'), 'w') | |
| 76 | ||
| 77 | file_dict = {'1':f_1, '2':f_2, '3':f_3, '4':f_4, '5':f_5, '6':f_6, '7':f_7, '8':f_8, '9':f_9, '10':f_10, '11':f_11,
| |
| 78 | '12':f_12, '13':f_13, '14':f_14, '15':f_15, '16':f_16, '17':f_17, '18':f_18, '19':f_19, 'Y':f_Y, 'X':f_X, 'M':f_M} | |
| 79 | ||
| 80 | print('Program has started on ' + file_name + ' and it will update you every time it reaches an interval of 1,000,000')
| |
| 81 | ||
| 82 | with open(start_file, 'r') as sf: | |
| 83 | ||
| 84 | line = sf.readline() | |
| 85 | while line != "": | |
| 86 | count += 1 | |
| 87 | split_line = line.strip().split('\t')
| |
| 88 | ||
| 89 | #ex.bad ['D99KWTL1:845:C214UACXX:6:1101:7094:2225', '1:N:0:', '77', '*' | |
| 90 | #ex.good ['D99KWTL1:845:C214UACXX:6:1101:7166:2131', '83', 'chr7' | |
| 91 | if split_line[2].startswith('chr'):
| |
| 92 | chro = split_line[2] | |
| 93 | chro_num = chro.strip('chr')
| |
| 94 | file_dict[chro_num].write(line) | |
| 95 | ||
| 96 | ||
| 97 | if count % 1000000 == 0: | |
| 98 | print('current line = ', count)
| |
| 99 | ||
| 100 | line = sf.readline() | |
| 101 | print('All done')
| |
| 102 | ||
| 103 | ||
| 104 | def pairing(folder_1, folder_2, out_file): | |
| 105 | ||
| 106 | print("I'm now working on making the bed file for you")
| |
| 107 | ||
| 108 | with open((out_file), 'w') as wf: | |
| 109 | ||
| 110 | #make a list from 1-x and M. This list is used to to iterate over so all | |
| 111 | #files are accessed | |
| 112 | ||
| 113 | file_list = ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17', '18', '19','M','X','Y'] | |
| 114 | ||
| 115 | #access all files in folder_1 = store_file | |
| 116 | ||
| 117 | for ch in file_list: | |
| 118 | store_dict = {}
| |
| 119 | store_file_counter = 0 | |
| 120 | read_file_counter = 0 | |
| 121 | print("I'm working on chromsome ", ch)
| |
| 122 | store_file = open((folder_1 +'/'+ ch + '.sam'), 'r') | |
| 123 | ||
| 124 | line = store_file.readline() | |
| 125 | ||
| 126 | #read threw store_file and store in dict | |
| 127 | while line != "": | |
| 128 | store_file_counter += 1 | |
| 129 | ||
| 130 | #counter for to keep user updated on progress | |
| 131 | if store_file_counter % 1000000 == 0: | |
| 132 | print('current line store_file_counter is = ', store_file_counter)
| |
| 133 | list_line = line.strip().split('\t')
| |
| 134 | ||
| 135 | #work on getting .bed format for store_file | |
| 136 | chro = list_line[2] | |
| 137 | position = list_line[3] | |
| 138 | sign = list_line[1] | |
| 139 | if sign == '+': | |
| 140 | ending_pos = int(position) + 35 | |
| 141 | bed = chro + '\t' + position + '\t' + str(ending_pos) | |
| 142 | elif sign == '-': | |
| 143 | ending_pos = int(position) - 35 | |
| 144 | bed = chro + '\t' + str(ending_pos) + '\t' + position | |
| 145 | ||
| 146 | ||
| 147 | #work on getting xy_location | |
| 148 | s_0 = list_line[0] | |
| 149 | s_0_split = s_0.split(':')
| |
| 150 | s_6 = s_0_split[6].split(' ')
| |
| 151 | ||
| 152 | xy_location = s_0_split[5] + s_6[0] | |
| 153 | ||
| 154 | #add to store_dict chromosome number, sign, and bed format | |
| 155 | store_dict[xy_location] = [position, sign, bed] | |
| 156 | line = store_file.readline() | |
| 157 | ||
| 158 | ||
| 159 | #access file '1' = read_file from folder_2 | |
| 160 | ||
| 161 | read_file = open((folder_2 +'/'+ ch + '.sam'), 'r') | |
| 162 | line_2 = read_file.readline() | |
| 163 | ||
| 164 | #read threw read_file find if it is in stored dict | |
| 165 | ||
| 166 | while line_2 != "": | |
| 167 | read_file_counter += 1 | |
| 168 | ||
| 169 | #counter for to keep user updated on progress | |
| 170 | if read_file_counter % 1000000 == 0: | |
| 171 | print('current line read_file_counter is = ', read_file_counter)
| |
| 172 | ||
| 173 | list_line = line_2.strip().split('\t')
| |
| 174 | ||
| 175 | #work on getting xy_location | |
| 176 | s_0 = list_line[0] | |
| 177 | s_0_split = s_0.split(':')
| |
| 178 | s_6 = s_0_split[6].split(' ')
| |
| 179 | xy_location_read_file = s_0_split[5] + s_6[0] | |
| 180 | ||
| 181 | #find matching xy_location in store dictionary | |
| 182 | if xy_location_read_file in store_dict.keys(): | |
| 183 | ||
| 184 | ||
| 185 | #work on getting .bed format for read_file | |
| 186 | chro = list_line[2] | |
| 187 | position = list_line[3] | |
| 188 | ||
| 189 | #find out if absolute value of read_file position - store_position | |
| 190 | # is > 1000 | |
| 191 | if abs(int(store_dict[xy_location_read_file][0]) - int(position)) > 1000: | |
| 192 | sign = list_line[1] | |
| 193 | ||
| 194 | #write + sign next to - sign frag | |
| 195 | if sign == '+': | |
| 196 | ending_pos = int(position) + 35 | |
| 197 | bed = chro + '\t' + position + '\t' + str(ending_pos) | |
| 198 | to_write = bed + '\t' + store_dict[xy_location_read_file][2] + '\n' | |
| 199 | wf.write(to_write) | |
| 200 | elif sign == '-': | |
| 201 | ending_pos = int(position) - 35 | |
| 202 | bed = chro + '\t' + str(ending_pos) + '\t' + position | |
| 203 | to_write = store_dict[xy_location_read_file][2] + '\t' + bed + '\n' | |
| 204 | wf.write(to_write) | |
| 205 | ||
| 206 | ||
| 207 | line_2 = read_file.readline() | |
| 208 | ||
| 209 | print("I'done with the pairing")
| |
| 210 | ||
| 211 | if __name__ == '__main__': | |
| 212 | ||
| 213 | run("/Users/Bea/Desktop/samantha_folder/sam/5_11_13/R1_cDNA_35bp.sam", "/Users/Bea/Desktop/samantha_folder/sam/5_11_13/R3_cDNA_35bp.sam", "/Users/Bea/Desktop/5_15_13")
| |
| 214 | #started 9:32 AM ended at 9:58 AM |
