Create a single fastq ids in each row

Question

[harry]

See below are some fastq ids:

A00868:56:HK2YWDRXX:1:2103:1832:17472,A00868:56:HK2YWDRXX:1:2106:21775:8547,A00868:56:HK2YWDRXX:1:2113:26883:13761,A00868:56:HK2YWDRXX:1:2120:23276:14278,A00868:56:HK2YWDRXX:1:2126:27091:5196,A00868:56:HK2YWDRXX:1:2131:23583:12493,A00868:56:HK2YWDRXX:1:2136:1787:17769,A00868:56:HK2YWDRXX:1:2171:1515:29606,A00868:56:HK2YWDRXX:1:2172:17020:32127,A00868:56:HK2YWDRXX:1:2174:4969:10848,A00868:56:HK2YWDRXX:1:2175:1777:25363,A00868:56:HK2YWDRXX:1:2211:18719:5635,A00868:56:HK2YWDRXX:1:2212:25780:9784,A00868:56:HK2YWDRXX:1:2212:24144:36511,A00868:56:HK2YWDRXX:1:2265:4137:11318,A00868:56:HK2YWDRXX:1:2270:15745:24345,A00868:56:HK2YWDRXX:1:2271:20663:36057,A00868:56:HK2YWDRXX:2:2103:22941:4085,A00868:56:HK2YWDRXX:2:2104:25400:18176,A00868:56:HK2YWDRXX:2:2117:16260:17597,A00868:56:HK2YWDRXX:2:2134:11912:1297,A00868:56:HK2YWDRXX:2:2173:17924:12399,A00868:56:HK2YWDRXX:2:2214:13566:19288,A00868:56:HK2YWDRXX:2:2215:8088:29778,A00868:56:HK2YWDRXX:2:2231:22001:24220,A00868:56:HK2YWDRXX:2:2240:7057:12962,A00868:56:HK2YWDRXX:2:2247:4291:31187,A00868:56:HK2YWDRXX:2:2275:18629:30217,A00868:56:HK2YWDRXX:1:2116:24053:5697,A00868:56:HK2YWDRXX:1:2136:16911:23109,A00868:56:HK2YWDRXX:2:2101:15492:33051,A00868:56:HK2YWDRXX:2:2134:21549:9126,A00868:56:HK2YWDRXX:2:2178:32560:27821,A00868:56:HK2YWDRXX:2:2216:2329:23688,A00868:56:HK2YWDRXX:2:2238:15772:11616,A00868:56:HK2YWDRXX:2:2242:14199:14810,A00868:56:HK2YWDRXX:2:2258:18249:20854,A00868:56:HK2YWDRXX:2:2265:8901:23516
A00868:56:HK2YWDRXX:1:2160:31476:14826,A00868:56:HK2YWDRXX:1:2257:30581:6104,A00868:56:HK2YWDRXX:2:2108:4300:34366,A00868:56:HK2YWDRXX:2:2141:4182:19476,A00868:56:HK2YWDRXX:2:2146:23041:20541,A00868:56:HK2YWDRXX:2:2118:4209:25942,A00868:56:HK2YWDRXX:2:2142:22679:20134,A00868:56:HK2YWDRXX:2:2150:16306:7905,A00868:56:HK2YWDRXX:2:2244:31620:15984
A00868:56:HK2YWDRXX:1:2125:5927:25629,A00868:56:HK2YWDRXX:1:2215:16649:30796
A00868:56:HK2YWDRXX:1:2139:3568:19006,A00868:56:HK2YWDRXX:1:2233:19108:31015,A00868:56:HK2YWDRXX:1:2244:25654:8281,A00868:56:HK2YWDRXX:2:2234:26684:24251,A00868:56:HK2YWDRXX:1:2276:24415:33348

In each row, there are multiple fastq ids and I want in each row a single id like below:

A00868:56:HK2YWDRXX:1:2103:1832:17472
A00868:56:HK2YWDRXX:1:2106:21775:8547
A00868:56:HK2YWDRXX:1:2113:26883:13761
A00868:56:HK2YWDRXX:1:2120:23276:14278
A00868:56:HK2YWDRXX:1:2125:5927:25629

So please tell me there is any command to create a single id in each row. Thanks in advance

Answer 1

[Istvan Albert]

assuming your input is in a file called ids you can use the UNIX command line tool called tr to transform commas into newlines like so:

cat ids | tr ',' '\n' | head

prints:

A00868:56:HK2YWDRXX:1:2103:1832:17472
A00868:56:HK2YWDRXX:1:2106:21775:8547
A00868:56:HK2YWDRXX:1:2113:26883:13761
A00868:56:HK2YWDRXX:1:2120:23276:14278
A00868:56:HK2YWDRXX:1:2126:27091:5196
A00868:56:HK2YWDRXX:1:2131:23583:12493
A00868:56:HK2YWDRXX:1:2136:1787:17769
A00868:56:HK2YWDRXX:1:2171:1515:29606
A00868:56:HK2YWDRXX:1:2172:17020:32127
A00868:56:HK2YWDRXX:1:2174:4969:10848

[swbarnes2]

You might want to do a sort and uniq to make sure there are no duplicates.

[harry]

Thanks, Istvan Albert. It working very well.