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generate_igv_genome.py
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generate_igv_genome.py
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"""
Generates a IGV genome file in the new JSON format from a template (including updating gene file)
"""
import argparse
import json
import operator
import os
import subprocess
import tempfile
import urllib.request
import gzip
import shutil
# global variables
genome_json = {}
"""
sorting order for non integer chromosomes
"""
sorting_order = {
'X': 100,
'Y': 101,
'MT': 102,
"chr11_KI270721v1_random": 1000,
"chr14_GL000009v2_random": 1001,
"chr14_GL000225v1_random": 1002,
"chr14_KI270722v1_random": 1003,
"chr14_GL000194v1_random": 1004,
"chr14_KI270723v1_random": 1005,
"chr14_KI270724v1_random": 1006,
"chr14_KI270725v1_random": 1007,
"chr14_KI270726v1_random": 1008,
"chr15_KI270727v1_random": 1009,
"chr16_KI270728v1_random": 1010,
"chr17_GL000205v2_random": 1011,
"chr17_KI270729v1_random": 1012,
"chr17_KI270730v1_random": 1013,
"chr1_KI270706v1_random": 1014,
"chr1_KI270707v1_random": 1015,
"chr1_KI270708v1_random": 1016,
"chr1_KI270709v1_random": 1017,
"chr1_KI270710v1_random": 1018,
"chr1_KI270711v1_random": 1019,
"chr1_KI270712v1_random": 1020,
"chr1_KI270713v1_random": 1021,
"chr1_KI270714v1_random": 1022,
"chr22_KI270731v1_random": 1023,
"chr22_KI270732v1_random": 1024,
"chr22_KI270733v1_random": 1025,
"chr22_KI270734v1_random": 1026,
"chr22_KI270735v1_random": 1027,
"chr22_KI270736v1_random": 1028,
"chr22_KI270737v1_random": 1029,
"chr22_KI270738v1_random": 1030,
"chr22_KI270739v1_random": 1031,
"chr2_KI270715v1_random": 1032,
"chr2_KI270716v1_random": 1033,
"chr3_GL000221v1_random": 1034,
"chr4_GL000008v2_random": 1035,
"chr5_GL000208v1_random": 1036,
"chr9_KI270717v1_random": 1037,
"chr9_KI270718v1_random": 1038,
"chr9_KI270719v1_random": 1039,
"chr9_KI270720v1_random": 1040,
"chr1_KI270762v1_alt": 1041,
"chr1_KI270766v1_alt": 1042,
"chr1_KI270760v1_alt": 1043,
"chr1_KI270765v1_alt": 1044,
"chr1_GL383518v1_alt": 1045,
"chr1_GL383519v1_alt": 1046,
"chr1_GL383520v2_alt": 1047,
"chr1_KI270764v1_alt": 1048,
"chr1_KI270763v1_alt": 1049,
"chr1_KI270759v1_alt": 1050,
"chr1_KI270761v1_alt": 1051,
"chr2_KI270770v1_alt": 1052,
"chr2_KI270773v1_alt": 1053,
"chr2_KI270774v1_alt": 1054,
"chr2_KI270769v1_alt": 1055,
"chr2_GL383521v1_alt": 1056,
"chr2_KI270772v1_alt": 1057,
"chr2_KI270775v1_alt": 1058,
"chr2_KI270771v1_alt": 1059,
"chr2_KI270768v1_alt": 1060,
"chr2_GL582966v2_alt": 1061,
"chr2_GL383522v1_alt": 1062,
"chr2_KI270776v1_alt": 1063,
"chr2_KI270767v1_alt": 1064,
"chr3_JH636055v2_alt": 1065,
"chr3_KI270783v1_alt": 1066,
"chr3_KI270780v1_alt": 1067,
"chr3_GL383526v1_alt": 1068,
"chr3_KI270777v1_alt": 1069,
"chr3_KI270778v1_alt": 1070,
"chr3_KI270781v1_alt": 1071,
"chr3_KI270779v1_alt": 1072,
"chr3_KI270782v1_alt": 1073,
"chr3_KI270784v1_alt": 1074,
"chr4_KI270790v1_alt": 1075,
"chr4_GL383528v1_alt": 1076,
"chr4_KI270787v1_alt": 1077,
"chr4_GL000257v2_alt": 1078,
"chr4_KI270788v1_alt": 1079,
"chr4_GL383527v1_alt": 1080,
"chr4_KI270785v1_alt": 1081,
"chr4_KI270789v1_alt": 1082,
"chr4_KI270786v1_alt": 1083,
"chr5_KI270793v1_alt": 1084,
"chr5_KI270792v1_alt": 1085,
"chr5_KI270791v1_alt": 1086,
"chr5_GL383532v1_alt": 1087,
"chr5_GL949742v1_alt": 1088,
"chr5_KI270794v1_alt": 1089,
"chr5_GL339449v2_alt": 1090,
"chr5_GL383530v1_alt": 1091,
"chr5_KI270796v1_alt": 1092,
"chr5_GL383531v1_alt": 1093,
"chr5_KI270795v1_alt": 1094,
"chr6_GL000250v2_alt": 1095,
"chr6_KI270800v1_alt": 1096,
"chr6_KI270799v1_alt": 1097,
"chr6_GL383533v1_alt": 1098,
"chr6_KI270801v1_alt": 1099,
"chr6_KI270802v1_alt": 1100,
"chr6_KB021644v2_alt": 1101,
"chr6_KI270797v1_alt": 1102,
"chr6_KI270798v1_alt": 1103,
"chr7_KI270804v1_alt": 1104,
"chr7_KI270809v1_alt": 1105,
"chr7_KI270806v1_alt": 1106,
"chr7_GL383534v2_alt": 1107,
"chr7_KI270803v1_alt": 1108,
"chr7_KI270808v1_alt": 1109,
"chr7_KI270807v1_alt": 1110,
"chr7_KI270805v1_alt": 1111,
"chr8_KI270818v1_alt": 1112,
"chr8_KI270812v1_alt": 1113,
"chr8_KI270811v1_alt": 1114,
"chr8_KI270821v1_alt": 1115,
"chr8_KI270813v1_alt": 1116,
"chr8_KI270822v1_alt": 1117,
"chr8_KI270814v1_alt": 1118,
"chr8_KI270810v1_alt": 1119,
"chr8_KI270819v1_alt": 1120,
"chr8_KI270820v1_alt": 1121,
"chr8_KI270817v1_alt": 1122,
"chr8_KI270816v1_alt": 1123,
"chr8_KI270815v1_alt": 1124,
"chr9_GL383539v1_alt": 1125,
"chr9_GL383540v1_alt": 1126,
"chr9_GL383541v1_alt": 1127,
"chr9_GL383542v1_alt": 1128,
"chr9_KI270823v1_alt": 1129,
"chr10_GL383545v1_alt": 1130,
"chr10_KI270824v1_alt": 1131,
"chr10_GL383546v1_alt": 1132,
"chr10_KI270825v1_alt": 1133,
"chr11_KI270832v1_alt": 1134,
"chr11_KI270830v1_alt": 1135,
"chr11_KI270831v1_alt": 1136,
"chr11_KI270829v1_alt": 1137,
"chr11_GL383547v1_alt": 1138,
"chr11_JH159136v1_alt": 1139,
"chr11_JH159137v1_alt": 1140,
"chr11_KI270827v1_alt": 1141,
"chr11_KI270826v1_alt": 1142,
"chr12_GL877875v1_alt": 1143,
"chr12_GL877876v1_alt": 1144,
"chr12_KI270837v1_alt": 1145,
"chr12_GL383549v1_alt": 1146,
"chr12_KI270835v1_alt": 1147,
"chr12_GL383550v2_alt": 1148,
"chr12_GL383552v1_alt": 1149,
"chr12_GL383553v2_alt": 1150,
"chr12_KI270834v1_alt": 1151,
"chr12_GL383551v1_alt": 1152,
"chr12_KI270833v1_alt": 1153,
"chr12_KI270836v1_alt": 1154,
"chr13_KI270840v1_alt": 1155,
"chr13_KI270839v1_alt": 1156,
"chr13_KI270843v1_alt": 1157,
"chr13_KI270841v1_alt": 1158,
"chr13_KI270838v1_alt": 1159,
"chr13_KI270842v1_alt": 1160,
"chr14_KI270844v1_alt": 1161,
"chr14_KI270847v1_alt": 1162,
"chr14_KI270845v1_alt": 1163,
"chr14_KI270846v1_alt": 1164,
"chr15_KI270852v1_alt": 1165,
"chr15_KI270851v1_alt": 1166,
"chr15_KI270848v1_alt": 1167,
"chr15_GL383554v1_alt": 1168,
"chr15_KI270849v1_alt": 1169,
"chr15_GL383555v2_alt": 1170,
"chr15_KI270850v1_alt": 1171,
"chr16_KI270854v1_alt": 1172,
"chr16_KI270856v1_alt": 1173,
"chr16_KI270855v1_alt": 1174,
"chr16_KI270853v1_alt": 1175,
"chr16_GL383556v1_alt": 1176,
"chr16_GL383557v1_alt": 1177,
"chr17_GL383563v3_alt": 1178,
"chr17_KI270862v1_alt": 1179,
"chr17_KI270861v1_alt": 1180,
"chr17_KI270857v1_alt": 1181,
"chr17_JH159146v1_alt": 1182,
"chr17_JH159147v1_alt": 1183,
"chr17_GL383564v2_alt": 1184,
"chr17_GL000258v2_alt": 1185,
"chr17_GL383565v1_alt": 1186,
"chr17_KI270858v1_alt": 1187,
"chr17_KI270859v1_alt": 1188,
"chr17_GL383566v1_alt": 1189,
"chr17_KI270860v1_alt": 1190,
"chr18_KI270864v1_alt": 1191,
"chr18_GL383567v1_alt": 1192,
"chr18_GL383570v1_alt": 1193,
"chr18_GL383571v1_alt": 1194,
"chr18_GL383568v1_alt": 1195,
"chr18_GL383569v1_alt": 1196,
"chr18_GL383572v1_alt": 1197,
"chr18_KI270863v1_alt": 1198,
"chr19_KI270868v1_alt": 1199,
"chr19_KI270865v1_alt": 1200,
"chr19_GL383573v1_alt": 1201,
"chr19_GL383575v2_alt": 1202,
"chr19_GL383576v1_alt": 1203,
"chr19_GL383574v1_alt": 1204,
"chr19_KI270866v1_alt": 1205,
"chr19_KI270867v1_alt": 1206,
"chr19_GL949746v1_alt": 1207,
"chr20_GL383577v2_alt": 1208,
"chr20_KI270869v1_alt": 1209,
"chr20_KI270871v1_alt": 1210,
"chr20_KI270870v1_alt": 1211,
"chr21_GL383578v2_alt": 1212,
"chr21_KI270874v1_alt": 1213,
"chr21_KI270873v1_alt": 1214,
"chr21_GL383579v2_alt": 1215,
"chr21_GL383580v2_alt": 1216,
"chr21_GL383581v2_alt": 1217,
"chr21_KI270872v1_alt": 1218,
"chr22_KI270875v1_alt": 1219,
"chr22_KI270878v1_alt": 1220,
"chr22_KI270879v1_alt": 1221,
"chr22_KI270876v1_alt": 1222,
"chr22_KI270877v1_alt": 1223,
"chr22_GL383583v2_alt": 1224,
"chr22_GL383582v2_alt": 1225,
"chrX_KI270880v1_alt": 1226,
"chrX_KI270881v1_alt": 1227,
"chr19_KI270882v1_alt": 1228,
"chr19_KI270883v1_alt": 1229,
"chr19_KI270884v1_alt": 1230,
"chr19_KI270885v1_alt": 1231,
"chr19_KI270886v1_alt": 1232,
"chr19_KI270887v1_alt": 1233,
"chr19_KI270888v1_alt": 1234,
"chr19_KI270889v1_alt": 1235,
"chr19_KI270890v1_alt": 1236,
"chr19_KI270891v1_alt": 1237,
"chr1_KI270892v1_alt": 1238,
"chr2_KI270894v1_alt": 1239,
"chr2_KI270893v1_alt": 1240,
"chr3_KI270895v1_alt": 1241,
"chr4_KI270896v1_alt": 1242,
"chr5_KI270897v1_alt": 1243,
"chr5_KI270898v1_alt": 1244,
"chr6_GL000251v2_alt": 1245,
"chr7_KI270899v1_alt": 1246,
"chr8_KI270901v1_alt": 1247,
"chr8_KI270900v1_alt": 1248,
"chr11_KI270902v1_alt": 1249,
"chr11_KI270903v1_alt": 1250,
"chr12_KI270904v1_alt": 1251,
"chr15_KI270906v1_alt": 1252,
"chr15_KI270905v1_alt": 1253,
"chr17_KI270907v1_alt": 1254,
"chr17_KI270910v1_alt": 1255,
"chr17_KI270909v1_alt": 1256,
"chr17_JH159148v1_alt": 1257,
"chr17_KI270908v1_alt": 1258,
"chr18_KI270912v1_alt": 1259,
"chr18_KI270911v1_alt": 1260,
"chr19_GL949747v2_alt": 1261,
"chr22_KB663609v1_alt": 1262,
"chrX_KI270913v1_alt": 1263,
"chr19_KI270914v1_alt": 1264,
"chr19_KI270915v1_alt": 1265,
"chr19_KI270916v1_alt": 1266,
"chr19_KI270917v1_alt": 1267,
"chr19_KI270918v1_alt": 1268,
"chr19_KI270919v1_alt": 1269,
"chr19_KI270920v1_alt": 1270,
"chr19_KI270921v1_alt": 1271,
"chr19_KI270922v1_alt": 1272,
"chr19_KI270923v1_alt": 1273,
"chr3_KI270924v1_alt": 1274,
"chr4_KI270925v1_alt": 1275,
"chr6_GL000252v2_alt": 1276,
"chr8_KI270926v1_alt": 1277,
"chr11_KI270927v1_alt": 1278,
"chr19_GL949748v2_alt": 1279,
"chr22_KI270928v1_alt": 1280,
"chr19_KI270929v1_alt": 1281,
"chr19_KI270930v1_alt": 1282,
"chr19_KI270931v1_alt": 1283,
"chr19_KI270932v1_alt": 1284,
"chr19_KI270933v1_alt": 1285,
"chr19_GL000209v2_alt": 1286,
"chr3_KI270934v1_alt": 1287,
"chr6_GL000253v2_alt": 1288,
"chr19_GL949749v2_alt": 1289,
"chr3_KI270935v1_alt": 1290,
"chr6_GL000254v2_alt": 1291,
"chr19_GL949750v2_alt": 1292,
"chr3_KI270936v1_alt": 1293,
"chr6_GL000255v2_alt": 1294,
"chr19_GL949751v2_alt": 1295,
"chr3_KI270937v1_alt": 1296,
"chr6_GL000256v2_alt": 1297,
"chr19_GL949752v1_alt": 1298,
"chr6_KI270758v1_alt": 1299,
"chr19_GL949753v2_alt": 1300,
"chr19_KI270938v1_alt": 1301,
"chrUn_KI270302v1": 1302,
"chrUn_KI270304v1": 1303,
"chrUn_KI270303v1": 1304,
"chrUn_KI270305v1": 1305,
"chrUn_KI270322v1": 1306,
"chrUn_KI270320v1": 1307,
"chrUn_KI270310v1": 1308,
"chrUn_KI270316v1": 1309,
"chrUn_KI270315v1": 1310,
"chrUn_KI270312v1": 1311,
"chrUn_KI270311v1": 1312,
"chrUn_KI270317v1": 1313,
"chrUn_KI270412v1": 1314,
"chrUn_KI270411v1": 1315,
"chrUn_KI270414v1": 1316,
"chrUn_KI270419v1": 1317,
"chrUn_KI270418v1": 1318,
"chrUn_KI270420v1": 1319,
"chrUn_KI270424v1": 1320,
"chrUn_KI270417v1": 1321,
"chrUn_KI270422v1": 1322,
"chrUn_KI270423v1": 1323,
"chrUn_KI270425v1": 1324,
"chrUn_KI270429v1": 1325,
"chrUn_KI270442v1": 1326,
"chrUn_KI270466v1": 1327,
"chrUn_KI270465v1": 1328,
"chrUn_KI270467v1": 1329,
"chrUn_KI270435v1": 1330,
"chrUn_KI270438v1": 1331,
"chrUn_KI270468v1": 1332,
"chrUn_KI270510v1": 1333,
"chrUn_KI270509v1": 1334,
"chrUn_KI270518v1": 1335,
"chrUn_KI270508v1": 1336,
"chrUn_KI270516v1": 1337,
"chrUn_KI270512v1": 1338,
"chrUn_KI270519v1": 1339,
"chrUn_KI270522v1": 1340,
"chrUn_KI270511v1": 1341,
"chrUn_KI270515v1": 1342,
"chrUn_KI270507v1": 1343,
"chrUn_KI270517v1": 1344,
"chrUn_KI270529v1": 1345,
"chrUn_KI270528v1": 1346,
"chrUn_KI270530v1": 1347,
"chrUn_KI270539v1": 1348,
"chrUn_KI270538v1": 1349,
"chrUn_KI270544v1": 1350,
"chrUn_KI270548v1": 1351,
"chrUn_KI270583v1": 1352,
"chrUn_KI270587v1": 1353,
"chrUn_KI270580v1": 1354,
"chrUn_KI270581v1": 1355,
"chrUn_KI270579v1": 1356,
"chrUn_KI270589v1": 1357,
"chrUn_KI270590v1": 1358,
"chrUn_KI270584v1": 1359,
"chrUn_KI270582v1": 1360,
"chrUn_KI270588v1": 1361,
"chrUn_KI270593v1": 1362,
"chrUn_KI270591v1": 1363,
"chrUn_KI270330v1": 1364,
"chrUn_KI270329v1": 1365,
"chrUn_KI270334v1": 1366,
"chrUn_KI270333v1": 1367,
"chrUn_KI270335v1": 1368,
"chrUn_KI270338v1": 1369,
"chrUn_KI270340v1": 1370,
"chrUn_KI270336v1": 1371,
"chrUn_KI270337v1": 1372,
"chrUn_KI270363v1": 1373,
"chrUn_KI270364v1": 1374,
"chrUn_KI270362v1": 1375,
"chrUn_KI270366v1": 1376,
"chrUn_KI270378v1": 1377,
"chrUn_KI270379v1": 1378,
"chrUn_KI270389v1": 1379,
"chrUn_KI270390v1": 1380,
"chrUn_KI270387v1": 1381,
"chrUn_KI270395v1": 1382,
"chrUn_KI270396v1": 1383,
"chrUn_KI270388v1": 1384,
"chrUn_KI270394v1": 1385,
"chrUn_KI270386v1": 1386,
"chrUn_KI270391v1": 1387,
"chrUn_KI270383v1": 1388,
"chrUn_KI270393v1": 1389,
"chrUn_KI270384v1": 1390,
"chrUn_KI270392v1": 1391,
"chrUn_KI270381v1": 1392,
"chrUn_KI270385v1": 1393,
"chrUn_KI270382v1": 1394,
"chrUn_KI270376v1": 1395,
"chrUn_KI270374v1": 1396,
"chrUn_KI270372v1": 1397,
"chrUn_KI270373v1": 1398,
"chrUn_KI270375v1": 1399,
"chrUn_KI270371v1": 1400,
"chrUn_KI270448v1": 1401,
"chrUn_KI270521v1": 1402,
"chrUn_GL000195v1": 1403,
"chrUn_GL000219v1": 1404,
"chrUn_GL000220v1": 1405,
"chrUn_GL000224v1": 1406,
"chrUn_KI270741v1": 1407,
"chrUn_GL000226v1": 1408,
"chrUn_GL000213v1": 1409,
"chrUn_KI270743v1": 1410,
"chrUn_KI270744v1": 1411,
"chrUn_KI270745v1": 1412,
"chrUn_KI270746v1": 1413,
"chrUn_KI270747v1": 1414,
"chrUn_KI270748v1": 1415,
"chrUn_KI270749v1": 1416,
"chrUn_KI270750v1": 1417,
"chrUn_KI270751v1": 1418,
"chrUn_KI270752v1": 1419,
"chrUn_KI270753v1": 1420,
"chrUn_KI270754v1": 1421,
"chrUn_KI270755v1": 1422,
"chrUn_KI270756v1": 1423,
"chrUn_KI270757v1": 1424,
"chrUn_GL000214v1": 1425,
"chrUn_KI270742v1": 1426,
"chrUn_GL000216v2": 1427,
"chrUn_GL000218v1": 1428,
"chrY_KI270740v1_random": 1429
}
def parse_args():
"""
parses the arguments
:return: argparse object containing all provided arguments
"""
print("parsing args...")
parser = argparse.ArgumentParser(description="Generates a IGV genome JSON")
parser.add_argument("template_file", help="Template JSON containing all links to the input files.")
parser.add_argument("hgnc_file", help="file path to the the HGNC table file (containing HGNC id <-> gene name mapping")
parser.add_argument("output", help="file path for the generated output IGV genome JSON file")
return parser.parse_args()
def parse_json(template_file: str):
"""
parses the template file
:param template_file: file path to the json template file
"""
global genome_json
with open(template_file, 'r') as json_file:
genome_json = json.load(json_file)
return
def download_files(output_folder: str):
"""
downloads all distant files in the template json and links to them
:param output_folder: target folder for the downloads
:return: modified JSON template with links to the local files
"""
global genome_json
# download all required files
for key in ["fastaURL", "indexURL", "cytobandURL", "aliasURL"]:
url = genome_json[key]
filename = os.path.basename(url)
print("Downloading file '" + filename + "'...")
urllib.request.urlretrieve(url, os.path.join(output_folder, filename))
genome_json[key] = filename
# download tracks
for track in genome_json["tracks"]:
url = track["url"]
filename = os.path.basename(url)
print("Downloading file '" + filename + "'...")
urllib.request.urlretrieve(url, os.path.join(output_folder, filename))
track["url"] = filename
# load optional index
if "indexURL" in track:
url = track["indexURL"]
filename = os.path.basename(url)
print("Downloading file '" + filename + "'...")
urllib.request.urlretrieve(url, os.path.join(output_folder, filename))
track["indexURL"] = filename
return
def load_hgnc_file(hgnc_filepath):
print("Parsing HGNC file...")
hgnc_mapping = {}
with open(hgnc_filepath, 'r', encoding="utf8") as hgnc_file:
for line in hgnc_file:
if line.startswith("hgnc_id\tsymbol\tname"):
# skip header
continue
elif line.startswith("HGNC:"):
# parse line
split_line = line.split('\t')
hgnc_id = int(split_line[0].split(':')[1])
symbol = split_line[1].strip()
hgnc_mapping[hgnc_id] = symbol
print("\t " + str(len(hgnc_mapping.keys())) + " ids parsed.")
return hgnc_mapping
def sort_gff3(content):
"""
sorts the content gff3 file based on the sorting order defined above
:param content: content of the gff file (without headers)
:return: sorted list of lists
"""
print("sorting gff3 data...")
# preprocess chromosome column and positioning column
for line in content:
if line[0] in sorting_order:
line[0] = sorting_order[line[0]]
elif line[0].startswith("GL0"):
line[0] = 10000 + int(float(line[0][2:]) * 10) #move GL0000XX.X to the end
elif line[0].startswith("KI"):
line[0] = 20000 + int(float(line[0][2:]) * 10) #move KI0000XX.X to the end
else:
line[0] = int(line[0])
line[3] = int(line[3])
line[4] = int(line[4])
# sort content
content.sort(key=operator.itemgetter(0, 3))
# create reverse sorting_order:
reverse_sorting_order = {}
for k, v in sorting_order.items():
reverse_sorting_order[v] = k
# replace placeholder with original chromosome names:
for line in content:
if line[0] in reverse_sorting_order:
line[0] = reverse_sorting_order[line[0]]
return content
def update_gene_file(hgnc_mapping, output_folder):
"""
:param hgnc_mapping:
:return:
"""
print("Modifying GFF3 files (updating gene names) ...")
global genome_json
# modify all gff3 track files:
for track in genome_json["tracks"]:
if "format" in track and track["format"] == "gff3":
print("Modifying GFF3 file '" + track["url"] + "'...")
# unzip and modify
n_comment_lines = 0
n_unmodified_lines = 0
n_modified_lines = 0
n_ignored = 0
comment_lines = []
content_lines = []
with gzip.open(os.path.join(output_folder, track["url"]), 'rb') as compressed_gff3:
for line in compressed_gff3:
line = line.decode('utf-8')
# skip comments
if line.startswith("#"):
if line.strip() == "###":
# ignore
n_ignored += 1
continue
comment_lines.append(line)
n_comment_lines += 1
continue
# detect HGNC ids
annotation_column = line.split('\t')[8]
if "[Source:HGNC Symbol%3BAcc:" in annotation_column:
kv_list = annotation_column.split(';')
idx_name = -1
idx_description = -1
for idx in range(len(kv_list)):
if kv_list[idx].startswith("Name="):
idx_name = idx
elif kv_list[idx].startswith("description="):
idx_description = idx
if idx_description > -1:
# extract HGNC id
hgnc_id = int(kv_list[idx_description].split('[')[1].split(']')[0].split(':')[-1])
if hgnc_id not in hgnc_mapping.keys():
print("Warning: HGNC id " + str(hgnc_id) + " not found in HGNC file!")
# store line unmodified
content_lines.append(line.split('\t'))
n_unmodified_lines += 1
continue
if idx_name > -1:
kv_list[idx_name] = "Name=" + hgnc_mapping[hgnc_id]
else:
kv_list.append("Name=" + hgnc_mapping[hgnc_id])
split_line = line.split('\t')
split_line[8] = ";".join(kv_list)
content_lines.append(split_line)
n_modified_lines += 1
else:
# no HGNC identifier -> store unmodified
content_lines.append(line.split('\t'))
n_unmodified_lines += 1
# stats
print("\tcomment lines: " + str(n_comment_lines))
print("\tunmodified lines: " + str(n_unmodified_lines))
print("\tmodified lines: " + str(n_modified_lines))
print("\tignored lines: " + str(n_ignored))
# sort content
content_lines = sort_gff3(content_lines)
# write modified file to disk
print("Writing modified file to disk...")
with open(os.path.join(output_folder, os.path.splitext(track["url"])[0]), 'wt') as modified_gff3:
for line in comment_lines:
modified_gff3.write(line)
for line in content_lines:
modified_gff3.write("\t".join(str(e) for e in line))
# bgzip
print("Compressing file...")
print("\tignored lines: " + str(n_ignored))
rc = subprocess.call(["bgzip", "-f", os.path.join(output_folder, os.path.splitext(track["url"])[0])])
if rc != 0:
raise RuntimeError("bgzip failed with return code " + str(rc) + "!")
# tabix
print("Indexing file...")
rc = subprocess.call(["tabix", "-p", "gff", os.path.join(output_folder, track["url"])])
if rc != 0:
raise RuntimeError("tabix failed with return code " + str(rc) + "!")
# add index to JSON
track["indexURL"] = track["url"] + ".tbi"
return
def update_alias_file(output_folder):
"""
Extends the alias tab file
"""
print("Updating alias file...")
alias_file_name = genome_json["aliasURL"]
file_buffer = []
with open(os.path.join(output_folder, alias_file_name), 'r') as alias_file:
for line in alias_file:
if line.startswith("chrM"):
# add 'chrMT' and 'M' as valid aliases
line = line.strip() + "\tchrMT\tM\n"
file_buffer.append(line)
with open(os.path.join(output_folder, alias_file_name), 'w') as alias_file:
alias_file.writelines(file_buffer)
return
def main():
args = parse_args()
# read template
parse_json(args.template_file)
# download files to local storage
output_folder = os.path.dirname(args.output)
download_files(output_folder)
# load hgnc file
hgnc_mapping = load_hgnc_file(args.hgnc_file)
# update gene file
update_gene_file(hgnc_mapping, output_folder)
# update alias file
update_alias_file(output_folder)
# store modified JSON file
with open(args.output, 'w') as output_file:
print("Writing genome JSON file...")
json.dump(genome_json, output_file, indent=4)
print("\nfinished.")
if __name__ == '__main__':
main()