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testfile.output.csv
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 2 columns, instead of 46 in line 2.
103 lines (103 loc) · 53.2 KB
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testfile.output.csv
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Command:,vxtractor.pl -h HMMs/bacteria/ -c testfile.output.csv -o testfile.output.fasta -a testfile.fasta
Options:,Don't include HMM in fasta
Sequence,V1leftlong,V1leftshort,V1rightlong,V1rightshort,V2leftlong,V2leftshort,V2rightlong,V2rightshort,V3leftlong,V3leftshort,V3rightlong,V3rightshort,V4leftlong,V4leftshort,V4rightlong,V4rightshort,V5leftlong,V5leftshort,V5rightlong,V5rightshort,V6leftlong,V6leftshort,V6rightlong,V6rightshort,V7leftlong,V7leftshort,V7rightlong,V7rightshort,V8leftlong,V8leftshort,V8rightlong,V8rightshort,V9leftlong,V9leftshort,V9rightlong,V9rightshort,V1,V2,V3,V4,V5,V6,V7,V8,V9
"'AF418950.1.1453","'1-40","'3-40","'notfound","'57-80","'86-136","'86-136","'183-232","'183-232","'312-356","'320-356","'398-440","'398-428","'463-504","'463-504","'590-638","'590-638","'693-737","'707-737","'780-831","'780-818","'860-910","'872-910","'965-1013","'965-999","'980-1033","'996-1033","'1094-1132","'1094-1118","'1119-1160","'1139-1160","'1218-1265","'1218-1247","'1279-1328","'1289-1328","'1374-1409","'1374-1409","'41-56 HMM=shortright","'137-182","'357-397","'505-589","'738-779","'911-964","'1034-1093","'1161-1217","'1329-1373","'"
"'AJ292687.1.1469","'2-40","'3-40","'59-106","'59-80","'89-139","'89-139","'204-253","'204-253","'333-377","'341-377","'424-460","'425-448","'483-524","'483-524","'610-658","'610-658","'713-757","'727-757","'801-852","'801-839","'881-931","'893-931","'990-1038","'990-1024","'1005-1058","'1021-1058","'1120-1158","'1120-1144","'1145-1186","'1165-1186","'1244-1291","'1244-1273","'1305-1354","'1315-1354","'1394-1427","'1394-1427","'41-58","'140-203","'378-423","'525-609","'758-800","'932-989","'1059-1119","'1187-1243","'1355-1393","'"
"'X81956.1.1478","'1-40","'3-40","'64-110","'notfound","'93-143","'93-143","'192-241","'192-241","'321-365","'329-365","'412-455","'412-443","'478-519","'478-519","'605-654","'605-654","'708-751","'722-751","'794-845","'794-832","'874-925","'886-925","'981-1029","'981-1015","'996-1049","'1012-1049","'1109-1147","'1109-1133","'1134-1175","'1154-1175","'1232-1279","'1232-1261","'1293-1342","'1303-1342","'1388-1425","'1388-1425","'41-63 HMM=longright","'144-191","'366-411","'520-604","'752-793","'926-980","'1050-1108","'1176-1231","'1343-1387","'"
"'AY218772.1.1518","'1-40","'3-40","'75-122","'75-102","'105-155","'105-155","'226-275","'226-275","'355-399","'363-399","'461-505","'461-493","'528-569","'528-569","'655-704","'655-704","'757-801","'771-801","'845-896","'845-883","'925-974","'937-974","'1029-1077","'1029-1063","'1044-1097","'1060-1097","'1161-1199","'1161-1185","'1186-1226","'1206-1224","'1284-1331","'1284-1313","'1345-1394","'1356-1394","'1442-1479","'1442-1479","'41-74","'156-225","'400-460","'570-654","'802-844","'975-1028","'1098-1160","'1227-1283","'1395-1441","'"
"'AB088944.1.1446","'1-40","'4-40","'69-114","'69-96","'99-149","'99-149","'214-263","'214-263","'343-386","'351-386","'446-490","'446-478","'513-554","'513-554","'640-689","'640-689","'743-787","'757-787","'830-881","'830-868","'910-960","'922-960","'1009-1057","'1009-1043","'1024-1077","'1040-1077","'1138-1176","'1138-1162","'1163-1204","'1183-1204","'1261-1308","'1261-1290","'1322-1371","'1332-1371","'1410-1445","'1410-1445","'41-68","'150-213","'387-445","'555-639","'788-829","'961-1008","'1078-1137","'1205-1260","'1372-1409","'"
"'AY278624.1.1473","'1-40","'3-40","'75-122","'75-101","'105-155","'105-155","'220-269","'220-269","'349-393","'357-393","'452-496","'452-484","'519-560","'519-560","'646-695","'646-695","'749-793","'763-793","'832-883","'832-870","'912-962","'924-962","'1013-1061","'1013-1047","'1028-1081","'1044-1081","'1143-1181","'1143-1167","'1168-1209","'1188-1209","'1266-1313","'1266-1295","'1327-1376","'1337-1376","'1417-1450","'1417-1450","'41-74","'156-219","'394-451","'561-645","'794-831","'963-1012","'1082-1142","'1210-1265","'1377-1416","'"
"'AB200224.1.1490","'1-40","'3-40","'75-122","'75-101","'105-155","'105-155","'220-269","'220-269","'349-393","'357-393","'456-496","'456-484","'519-560","'519-560","'646-695","'646-695","'749-793","'763-793","'833-884","'833-871","'913-963","'925-963","'1012-1060","'1012-1046","'1027-1080","'1043-1080","'1142-1180","'1142-1166","'1167-1208","'1187-1208","'1265-1312","'1265-1294","'1326-1375","'1336-1375","'1414-1449","'1414-1449","'41-74","'156-219","'394-455","'561-645","'794-832","'964-1011","'1081-1141","'1209-1264","'1376-1413","'"
"'ABJL02000006.58.1568","'1-40","'3-40","'71-118","'71-97","'101-151","'101-151","'215-264","'215-264","'344-387","'352-387","'451-491","'451-479","'514-555","'514-555","'641-690","'641-690","'744-788","'758-788","'828-879","'828-866","'908-958","'920-958","'1007-1055","'1007-1041","'1022-1075","'1038-1075","'1137-1175","'1137-1161","'1162-1203","'1182-1203","'1260-1307","'1260-1289","'1321-1370","'1331-1370","'1409-1444","'1409-1444","'41-70","'152-214","'388-450","'556-640","'789-827","'959-1006","'1076-1136","'1204-1259","'1371-1408","'"
"'AY218622.1.1479","'1-40","'3-40","'69-115","'69-96","'99-149","'99-149","'213-262","'213-262","'342-385","'350-385","'444-488","'444-476","'511-552","'511-552","'638-687","'638-687","'740-784","'754-784","'824-875","'824-862","'904-953","'916-952","'1003-1051","'1003-1037","'1018-1071","'1034-1071","'1133-1171","'1133-1157","'1158-1199","'1178-1199","'1255-1302","'1255-1284","'1316-1365","'1326-1365","'1404-1439","'1404-1439","'41-68","'150-212","'386-443","'553-637","'785-823","'954-1002","'1072-1132","'1200-1254","'1366-1403","'"
"'EU421894.1.1477","'1-40","'3-40","'63-110","'63-90","'93-143","'93-143","'208-257","'208-257","'337-381","'345-381","'440-484","'440-472","'507-548","'507-548","'634-683","'634-683","'738-782","'752-782","'820-871","'820-858","'900-950","'912-950","'999-1047","'999-1033","'1014-1067","'1030-1067","'1129-1167","'1129-1153","'1154-1195","'1174-1195","'1252-1299","'1252-1281","'1313-1362","'1323-1362","'1401-1435","'1401-1435","'41-62","'144-207","'382-439","'549-633","'783-819","'951-998","'1068-1128","'1196-1251","'1363-1400","'"
"'AF050539.1.1448","'1-40","'3-40","'71-118","'71-98","'101-151","'101-151","'216-265","'216-265","'345-389","'353-389","'448-492","'448-480","'515-556","'515-556","'642-691","'642-691","'745-789","'759-789","'829-880","'829-867","'909-959","'921-959","'1010-1058","'1010-1044","'1025-1078","'1041-1078","'1140-1178","'1140-1164","'1165-1206","'1185-1206","'1263-1310","'1263-1292","'1324-1373","'1334-1373","'1412-1447","'1412-1447","'41-70","'152-215","'390-447","'557-641","'790-828","'960-1009","'1079-1139","'1207-1262","'1374-1411","'"
"'EF509046.1.1456","'1-38","'3-37","'68-114","'68-93","'97-147","'97-147","'213-262","'213-262","'342-387","'352-387","'429-473","'429-461","'496-537","'496-537","'622-671","'622-671","'725-769","'739-769","'809-860","'809-847","'889-939","'901-939","'995-1043","'995-1029","'1010-1063","'1026-1063","'1123-1161","'1123-1147","'1148-1189","'1168-1189","'1247-1294","'1247-1276","'1308-1357","'1318-1357","'1403-1440","'1403-1440","'39-67","'148-212","'388-428","'538-621","'770-808","'940-994","'1064-1122","'1190-1246","'1358-1402","'"
"'AY531639.1.1463","'1-40","'3-40","'57-104","'57-84","'87-137","'87-137","'201-250","'201-250","'330-374","'338-374","'427-470","'427-458","'493-534","'493-534","'620-669","'620-669","'723-767","'737-767","'804-855","'804-842","'884-934","'896-934","'989-1037","'989-1023","'1004-1057","'1020-1057","'1117-1155","'1117-1140","'1142-1183","'1162-1183","'1241-1288","'1241-1270","'1302-1351","'1312-1351","'1393-1428","'1393-1428","'41-56","'138-200","'375-426","'535-619","'768-803","'935-988","'1058-1116","'1184-1240","'1352-1392","'"
"'Y11329.1.1467","'1-40","'3-40","'55-100","'55-81","'85-135","'85-135","'196-245","'196-245","'325-369","'333-369","'422-465","'422-453","'488-529","'488-529","'615-664","'615-664","'718-762","'732-762","'802-853","'802-840","'882-932","'894-932","'986-1034","'986-1020","'1001-1054","'1017-1054","'1113-1151","'1113-1137","'1138-1179","'1158-1179","'1237-1284","'1237-1266","'1298-1346","'1307-1346","'1390-1424","'1390-1424","'41-54","'136-195","'370-421","'530-614","'763-801","'933-985","'1055-1112","'1180-1236","'1347-1389","'"
"'AJ431215.1.1477","'1-40","'3-40","'75-122","'75-101","'105-155","'105-155","'218-267","'218-267","'347-390","'355-390","'430-474","'430-462","'497-538","'497-538","'624-673","'624-673","'727-771","'741-771","'814-865","'814-852","'894-944","'906-944","'1000-1048","'1000-1034","'1015-1068","'1031-1068","'1128-1166","'1128-1152","'1153-1194","'1173-1194","'1251-1298","'1251-1280","'1312-1361","'1322-1361","'1406-1438","'1406-1438","'41-74","'156-217","'391-429","'539-623","'772-813","'945-999","'1069-1127","'1195-1250","'1362-1405","'"
"'AY034820.1.1455","'1-40","'3-40","'71-118","'71-98","'101-151","'101-151","'199-248","'199-248","'328-372","'336-372","'411-455","'411-443","'478-519","'478-519","'605-654","'605-654","'708-752","'722-752","'795-846","'795-833","'875-925","'887-925","'979-1027","'979-1013","'994-1047","'1010-1047","'1107-1145","'1107-1131","'1132-1173","'1152-1173","'1230-1277","'1230-1259","'1291-1340","'1301-1340","'1383-1417","'1383-1417","'41-70","'152-198","'373-410","'520-604","'753-794","'926-978","'1048-1106","'1174-1229","'1341-1382","'"
"'EF602860.1.1494","'1-38","'3-38","'64-111","'64-91","'94-144","'94-144","'216-265","'216-265","'345-389","'354-389","'453-497","'453-485","'520-561","'520-561","'647-696","'647-696","'750-794","'764-794","'834-885","'834-872","'914-964","'926-964","'1022-1070","'1022-1056","'1037-1090","'1053-1090","'1152-1190","'1152-1176","'1177-1218","'1197-1218","'1276-1323","'1276-1305","'1337-1386","'1347-1386","'1433-1469","'1433-1469","'39-63","'145-215","'390-452","'562-646","'795-833","'965-1021","'1091-1151","'1219-1275","'1387-1432","'"
"'EF603409.1.1488","'1-38","'3-37","'65-112","'65-92","'95-145","'95-145","'217-266","'217-266","'346-390","'355-390","'454-498","'454-486","'521-562","'521-562","'648-697","'648-697","'751-795","'765-795","'835-886","'835-873","'915-965","'927-965","'1023-1071","'1023-1057","'1038-1091","'1054-1091","'1153-1191","'1153-1177","'1178-1219","'1198-1219","'1277-1324","'1277-1306","'1338-1387","'1348-1387","'1434-1470","'1434-1470","'39-64","'146-216","'391-453","'563-647","'796-834","'966-1022","'1092-1152","'1220-1276","'1388-1433","'"
"'Z95721.1.1546","'1-40","'4-40","'66-113","'66-93","'96-146","'96-146","'224-273","'224-273","'353-397","'361-397","'462-506","'462-494","'529-570","'529-570","'656-705","'656-705","'759-803","'773-803","'847-898","'847-885","'927-977","'939-977","'1027-1075","'1027-1061","'1042-1095","'1058-1095","'1157-1195","'1157-1181","'1182-1223","'1202-1223","'1281-1328","'1281-1310","'1342-1390","'1351-1390","'1438-1475","'1438-1475","'41-65","'147-223","'398-461","'571-655","'804-846","'978-1026","'1096-1156","'1224-1280","'1391-1437","'"
"'AY570609.1.1512","'1-40","'3-40","'66-113","'66-93","'96-146","'96-146","'221-270","'221-270","'350-394","'358-394","'459-503","'459-491","'526-567","'526-567","'653-702","'653-702","'756-800","'770-800","'841-892","'841-879","'921-971","'933-971","'1025-1073","'1025-1059","'1040-1093","'1056-1093","'1155-1193","'1155-1179","'1180-1221","'1200-1221","'1279-1326","'1279-1308","'1340-1388","'1349-1388","'1434-1471","'1434-1471","'41-65","'147-220","'395-458","'568-652","'801-840","'972-1024","'1094-1154","'1222-1278","'1389-1433","'"
"'DQ447175.1.1508","'1-40","'3-40","'68-115","'68-95","'98-146","'98-146","'221-270","'221-270","'350-394","'358-394","'459-503","'459-491","'526-567","'526-567","'653-702","'653-702","'756-800","'770-800","'841-892","'841-879","'921-971","'933-971","'1025-1073","'1025-1059","'1040-1093","'1056-1093","'1155-1193","'1155-1179","'1180-1221","'1200-1221","'1279-1326","'1279-1308","'1340-1388","'1349-1388","'1434-1470","'1434-1470","'41-67","'147-220","'395-458","'568-652","'801-840","'972-1024","'1094-1154","'1222-1278","'1389-1433","'"
"'EU804430.1.1439","'1-40","'3-40","'55-101","'55-82","'84-134","'84-134","'184-233","'184-233","'313-357","'321-357","'396-440","'396-428","'463-504","'463-504","'590-639","'590-639","'693-737","'707-737","'777-828","'777-815","'857-907","'869-907","'963-1011","'963-997","'978-1031","'994-1031","'1091-1129","'1091-1115","'1116-1157","'1136-1157","'1214-1261","'1214-1243","'1275-1323","'1284-1323","'1367-1396","'1367-1396","'41-54","'135-183","'358-395","'505-589","'738-776","'908-962","'1032-1090","'1158-1213","'1324-1366","'"
"'EF212897.1.1484","'1-40","'3-40","'73-119","'73-100","'102-152","'102-152","'217-266","'217-266","'346-390","'354-390","'454-498","'454-486","'521-562","'521-562","'648-697","'648-697","'751-795","'765-795","'838-889","'838-875","'918-968","'930-968","'1020-1068","'1020-1054","'1035-1088","'1051-1088","'1148-1186","'1148-1172","'1173-1214","'1193-1214","'1272-1319","'1272-1301","'1333-1381","'1342-1381","'1427-1464","'1427-1464","'41-72","'153-216","'391-453","'563-647","'796-837","'969-1019","'1089-1147","'1215-1271","'1382-1426","'"
"'AB166772.1.1499","'1-40","'3-40","'67-113","'67-94","'96-146","'96-146","'209-258","'209-258","'338-382","'346-382","'446-490","'446-478","'513-554","'513-554","'640-689","'640-689","'743-787","'757-787","'831-882","'831-869","'911-961","'923-961","'1015-1063","'1015-1049","'1030-1083","'1046-1083","'1143-1181","'1143-1167","'1168-1209","'1188-1209","'1267-1314","'1267-1296","'1328-1376","'1337-1376","'1422-1459","'1422-1459","'41-66","'147-208","'383-445","'555-639","'788-830","'962-1014","'1084-1142","'1210-1266","'1377-1421","'"
"'AB092606.1.1485","'1-40","'3-40","'69-115","'69-96","'98-148","'98-148","'211-260","'211-260","'340-384","'348-384","'448-492","'448-480","'515-556","'515-556","'642-691","'642-691","'745-789","'759-789","'831-882","'831-869","'911-961","'923-961","'1015-1063","'1015-1049","'1030-1083","'1046-1083","'1138-1176","'1138-1162","'1163-1204","'1183-1204","'1262-1309","'1262-1291","'1323-1371","'1332-1371","'1417-1454","'1417-1454","'41-68","'149-210","'385-447","'557-641","'790-830","'962-1014","'1084-1137","'1205-1261","'1372-1416","'"
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