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How to extract text from STRING to end of line?

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Top Forums Shell Programming and Scripting How to extract text from STRING to end of line?
# 1  
Old 06-17-2013
How to extract text from STRING to end of line?
Hi

I have a very large data file with several hundred columns and millions of lines.

The important data is in the last set of columns with variable numbers of tab delimited fields in front of it on each line.

Im currently trying sed to get the data out - I want anything beetween :RES and the end of line in the example two lines below (lines begin with chr):

Currently Im trying variations on

sed -n '/RES/, /$/p' BIGFILE >sedout

which gets me the first set of info before :RES but not after

can anyone help - apologies for the inexperience

chr2 166746903 . CTAA CTAATATAA 999.0 mrd10;tdb0.05;mrd15;mrp0.05;bqb0.05 INDEL;DP=1647;VDB=0.0367;AF1=0.03161;AF2=0.08017,4.387e-06;LRT=4.35e-05;LRT2=0.000173;AC1=14;DP4=1300,129,22,0;MQ=35;FQ=999;PCHI2=0.0107;PC2=0,58;PV4=0.25,7.1e-06,0.43,1.7e-13;EFF=INTRON(MODIFIER||||TTC21B|retained_intron|CODING|ENST00000243344|),INTRON(MODIFIER||||TTC21B| retained_intron|CODING|ENST00000536175|);MPB=U;ABPA=22;ASTHMA=19 GT:PLSmilieP:SP:GQ:RES 0/0:0,81,255:27:0:93:0 0/0:0,24,153:8:0:36:0 0/0:0,93,238:31:0:99:0 0/1:14,0,135:7:0:4:0 0/0:0,6,64:2:0:18:0 0/0:0,63,245:21:0:75:0 0/0:0,15,140:5:0:27:0 0/0:0,3,35:1:0:15:-1 0/0:0,0,0:0:0:12:0 0/0:0,0,0:0:0:12:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,9,87:3:0:21:0 0/0:0,0,0:0:0:12:0 0/0:0,9,87:3:0:21:0 0/0:0,120,255:40:0:99:0 0/0:0,27,160:9:0:39:0 0/0:0,0,0:0:0:12:0 0/0:0,9,87:3:0:21:0 0/0:0,0,0:0:0:12:0 0/0:0,9,75:3:0:21:0 0/0:0,6,64:2:0:18:0 0/0:0,3,35:1:0:15:-1 0/0:0,87,255:29:0:99:-1 0/0:0,12,106:4:0:24:-1 0/0:0,12,101:4:0:24:0 0/1:14,0,117:7:0:4:0 0/0:0,6,60:2:0:18:0 0/0:0,27,185:9:0:39:0 0/0:0,9,87:3:0:21:0 0/0:0,3,35:1:0:15:-1 0/0:0,81,213:27:0:93:0 0/1:32,3,0:1:0:13:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,0,0:0:0:12:0 0/0:0,24,153:8:0:36:-1 0/0:0,39,228:13:0:51:-1 0/0:0,21,168:7:0:33:0 0/0:0,3,35:1:0:15:-1 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,15,140:5:0:27:0 0/0:0,0,0:0:0:12:-1 0/0:0,6,64:2:0:18:0 0/0:0,15,122:5:0:27:-1 0/0:0,12,106:4:0:24:-1 0/0:0,0,0:0:0:12:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,57,255:19:0:69:0 0/1:35,0,132:10:0:23:0 0/1:14,0,137:7:0:4:0 0/0:0,12,100:4:0:24:0 0/0:0,12,106:4:0:24:0 0/0:0,52,238:29:0:64:-1 0/0:0,72,239:24:0:84:0 0/0:0,60,255:20:0:72:0 0/0:0,21,168:7:0:33:0 0/0:0,55,255:30:0:67:0 0/0:0,42,177:14:0:54:0 0/0:0,39,255:13:0:51:0 0/0:0,3,35:1:0:15:0 0/0:0,181,255:60:0:99:0 0/0:0,18,169:6:0:30:-1 0/0:0,21,145:7:0:33:0 0/0:2,0,212:11:0:10:0 0/0:0,12,94:4:0:24:0 0/0:0,6,70:2:0:18:0 0/0:0,18,156:6:0:30:0 0/0:0,9,98:3:0:21:0 0/1:72,0,23:4:0:41:0 0/1:25,0,29:2:0:13:0 0/1:14,0,137:7:0:4:0 0/0:0,0,0:0:0:12:0 0/0:0,66,255:22:0:78:-1 0/0:0,18,135:6:0:30:0 0/0:0,6,64:2:0:18:0 0/0:0,6,64:2:0:18:0 0/0:0,132,255:44:0:99:0 0/0:8,0,125:8:0:5:-1 0/1:35,0,132:10:0:23:0 0/0:0,15,115:5:0:27:-1 0/0:0,6,70:2:0:18:-1 0/0:0,15,122:5:0:27:0 0/1:41,0,136:8:0:29:-1 0/0:0,6,64:2:0:18:0 0/1:26,0,55:3:0:14:-1 0/0:0,27,185:9:0:39:0 0/0:2,0,139:11:0:10:0 0/0:0,30,165:10:0:42:-1 0/0:0,6,64:2:0:18:0 0/0:0,33,238:11:0:45:0 0/0:0,18,135:6:0:30:0 0/0:0,42,178:14:0:54:0 0/0:0,6,64:2:0:18:0 0/0:0,12,106:4:0:24:0 0/0:0,12,106:4:0:24:0 0/0:0,24,178:8:0:36:0 0/0:0,51,182:17:0:63:0 0/0:0,6,64:2:0:18:0 0/0:0,15,140:5:0:27:-1 0/0:0,24,153:8:0:36:-1 0/0:0,6,64:2:0:18:0 0/0:0,6,64:2:0:18:-1 0/0:0,24,178:8:0:36:0 0/0:0,15,122:5:0:27:-1 0/0:0,6,64:2:0:18:-1 0/0:0,0,0:0:0:12:0 0/0:0,18,154:6:0:30:0 0/0:0,3,35:1:0:15:0 0/0:0,3,35:1:0:15:0 0/0:0,15,122:5:0:27:0 0/0:0,12,106:4:0:24:0 0/0:0,30,165:10:0:42:-1 0/0:0,0,0:0:0:12:-1 0/0:0,6,64:2:0:18:0 0/0:0,0,0:0:0:12:-1 0/0:0,3,33:1:0:15:0 0/0:0,12,105:4:0:24:0 0/0:0,3,35:1:0:15:0 0/0:0,3,35:1:0:15:0 0/0:0,54,245:18:0:66:0 0/0:0,15,122:5:0:27:0 0/0:0,9,87:3:0:21:0 0/0:0,15,122:5:0:27:0 0/0:0,12,106:4:0:24:0 0/0:0,0,0:0:0:12:-1 0/0:0,21,145:7:0:33:-1 0/0:0,9,68:3:0:21:0 0/0:0,15,122:5:0:27:0 0/0:0,9,87:3:0:21:-1 0/0:0,24,151:8:0:36:0 0/0:0,18,148:6:0:30:0 0/0:0,12,106:4:0:24:0 0/0:0,63,184:21:0:75:0 0/0:0,9,87:3:0:21:-1 0/0:0,9,98:3:0:21:0 0/0:0,9,87:3:0:21:0 0/1:14,0,117:7:0:4:0 0/0:0,0,0:0:0:12:0 0/0:0,42,231:14:0:54:0 0/0:0,0,0:0:0:12:0 0/0:0,81,255:27:0:93:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,21,145:7:0:33:0 0/0:0,24,178:8:0:36:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:-1 0/0:0,0,0:0:0:12:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,54,211:18:0:66:0 0/0:0,3,35:1:0:15:0 0/0:0,18,135:6:0:30:0 0/0:0,3,35:1:0:15:0 0/0:0,54,208:18:0:66:0 0/0:0,12,122:4:0:24:0 0/0:0,3,35:1:0:15:0 0/0:0,15,122:5:0:27:0 0/0:0,9,99:3:0:21:0 0/0:0,12,106:4:0:24:0 0/0:0,15,122:5:0:27:0 0/0:0,33,220:11:0:45:0 0/0:0,33,197:11:0:45:-1 0/0:0,18,135:6:0:30:-1 0/0:0,21,145:7:0:33:-1 0/0:0,30,165:10:0:42:0 0/0:0,45,208:15:0:57:0 0/0:0,72,255:24:0:84:-1 0/0:0,15,132:5:0:27:0 0/0:0,21,168:7:0:33:0 0/0:0,21,153:7:0:33:-1 0/0:0,21,168:7:0:33:0 0/0:0,33,169:11:0:45:0 0/0:0,9,87:3:0:21:0 0/0:0,18,135:6:0:30:0 0/0:0,6,64:2:0:18:0 0/0:0,3,35:1:0:15:0 0/0:0,102,214:34:0:99:0 0/0:0,3,35:1:0:15:-1 0/0:0,24,153:8:0:36:0 0/0:0,6,64:2:0:18:0 0/0:0,9,87:3:0:21:0 0/0:0,0,0:0:0:12:-1 0/0:0,6,64:2:0:18:-1 0/0:0,18,135:6:0:30:0 0/0:0,0,0:0:0:12:0 0/0:0,3,35:1:0:15:0 0/0:0,12,122:4:0:24:-1 0/0:0,148,255:49:0:99:0 0/0:0,24,153:8:0:36:0 0/0:0,6,64:2:0:18:-1 0/0:0,3,35:1:0:15:0 0/0:0,15,122:5:0:27:0 0/0:0,9,87:3:0:21:0 0/0:0,3,35:1:0:15:0 0/0:0,3,35:1:0:15:0 0/0:0,18,135:6:0:30:0 0/0:0,18,153:6:0:30:-1 0/0:0,3,35:1:0:15:0 0/0:0,9,99:3:0:21:-1 0/0:0,9,87:3:0:21:0 0/0:0,3,35:1:0:15:-1 0/0:0,24,178:8:0:36:0 0/0:0,12,122:4:0:24:0 0/0:0,18,156:6:0:30:0 0/0:0,6,64:2:0:18:0 0/0:0,24,153:8:0:36:0 0/0:0,39,204:13:0:51:0 0/0:0,9,98:3:0:21:0 0/0:0,9,87:3:0:21:0
chr2 166747345 . TA TAACCAA 999.0 mrd10;sb0.05;tdb0.05;mrd15;mrp0.05 INDEL;DP=2010;VDB=0.0367;AF1=0.04555;AF2=0.1009,7.652e-06;LRT=9.18e-06;LRT2=3.71e-05;AC1=20;DP4=1559,232,39,0;MQ=35;FQ=999;PCHI2=0.00469;PC2=0,71;PV4=0.0069,1,1,4e-23;EFF=INTRON(MODIFIER||||TTC21B|retained_intron|CODING|ENST00000243344|),INTRON(MODIFIER||||TTC21B| retained_intron|CODING|ENST00000536175|),SPLICE_SITE_DONOR(HIGH||||TTC21B|retained_intron|CODING|ENS T00000243344|),SPLICE_SITE_DONOR(HIGH||||TTC21B|retained_intron|CODING|ENST00000536175|);MPB=U;ABPA= 25;ASTHMA=33 GT:PLSmilieP:SP:GQ:RES 0/0:0,90,255:30:0:99:0 0/0:0,18,126:6:0:28:0 0/0:0,168,255:66:0:99:0 0/0:0,39,203:13:0:49:0 0/0:0,36,243:12:0:46:0 0/0:0,105,237:35:0:99:0 0/0:0,3,35:1:0:13:-1 0/0:0,9,87:3:0:19:0 0/0:0,3,35:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,3,35:1:0:13:0 0/0:0,3,35:1:0:13:0 0/0:0,3,35:1:0:13:0 0/1:23,0,29:2:0:13:0 0/0:0,3,35:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,6,70:2:0:16:0 0/0:0,78,255:26:0:88:0 0/0:0,69,185:23:0:79:0 0/0:0,3,35:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,3,35:1:0:13:0 0/1:35,3,0:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,0,0:0:0:11:0 0/0:0,60,255:20:0:70:-1 0/0:0,3,35:1:0:13:0 0/1:29,0,18:2:0:19:0 0/1:25,0,29:2:0:15:0 0/0:26,32,85:3:0:16:-1 0/0:0,54,224:18:0:64:0 0/0:0,0,0:0:0:11:0 0/0:0,0,0:0:0:11:0 0/0:0,75,238:25:0:85:0 0/1:35,3,0:1:0:13:0 0/0:0,9,94:3:0:19:-1 0/0:0,0,0:0:0:11:-1 0/0:0,0,0:0:0:11:0 0/0:0,21,167:7:0:31:0 0/0:0,90,213:30:0:99:0 0/1:25,0,58:4:0:15:0 0/0:0,0,0:0:0:11:0 0/0:0,3,35:1:0:13:0 0/0:0,9,87:3:0:19:0 0/0:0,0,0:0:0:11:0 0/0:0,18,169:6:0:28:0 0/0:0,3,35:1:0:13:-1 0/0:0,15,122:5:0:25:0 0/0:0,6,64:2:0:16:-1 0/0:0,0,0:0:0:11:-1 0/0:0,0,0:0:0:11:0 0/0:0,12,106:4:0:22:0 0/0:0,12,119:4:0:22:0 0/0:0,102,255:34:0:99:0 0/0:0,24,151:8:0:34:0 0/0:0,12,106:4:0:22:0 0/0:0,9,98:3:0:19:0 0/0:0,9,98:3:0:19:0 0/0:0,87,255:29:0:97:-1 0/0:0,90,255:30:0:99:0 0/0:0,93,255:31:0:99:-1 0/0:0,22,163:14:0:32:-1 0/0:0,60,255:20:0:70:-1 0/0:0,57,255:19:0:67:-1 0/0:0,42,255:14:0:52:0 0/0:0,15,137:5:0:25:0 0/0:0,175,255:58:0:99:-1 0/0:0,21,166:7:0:31:-1 0/1:29,0,29:2:0:19:-1 0/0:0,48,234:16:0:58:0 0/0:35,35,35:1:0:11:0 0/1:26,0,55:3:0:16:0 0/0:0,12,110:4:0:22:-1 0/1:19,0,87:4:0:9:0 0/0:0,3,35:1:0:13:-1 0/1:16,0,93:5:0:7:0 0/0:0,6,70:2:0:16:-1 0/0:0,0,0:0:0:11:-1 0/0:0,72,185:24:0:82:0 0/0:0,6,70:2:0:16:0 0/0:29,32,61:2:0:13:-1 0/0:0,3,35:1:0:13:-1 0/0:0,202,255:67:0:99:0 0/1:35,0,124:9:0:25:-1 0/1:19,0,76:4:0:9:0 0/0:29,59,243:12:0:40:-1 0/0:0,6,64:2:0:16:-1 0/1:23,0,73:4:0:13:0 0/0:0,12,120:4:0:22:0 0/0:0,6,70:2:0:16:0 0/0:0,12,91:4:0:22:0 0/0:0,39,248:13:0:49:0 0/1:44,0,95:8:0:34:-1 0/0:17,32,134:6:0:25:-1 0/0:0,3,35:1:0:13:0 0/0:0,48,255:16:0:58:0 0/0:0,27,187:9:0:37:0 0/0:0,81,255:27:0:91:0 0/0:0,6,64:2:0:16:0 0/0:0,9,87:3:0:19:-1 0/0:0,9,87:3:0:19:-1 0/0:0,30,208:10:0:40:0 0/0:0,78,255:26:0:88:0 0/0:0,21,145:7:0:31:-1 0/0:0,21,183:7:0:31:0 0/0:0,57,235:19:0:67:0 0/0:0,21,184:7:0:31:0 0/0:0,0,0:0:0:11:0 0/0:0,3,35:1:0:13:-1 0/0:0,3,35:1:0:13:0 0/0:0,18,154:6:0:28:-1 0/0:0,21,141:7:0:31:0 0/0:0,15,140:5:0:25:0 0/0:0,24,180:8:0:34:-1 0/0:0,0,0:0:0:11:0 0/0:0,0,0:0:0:11:0 0/0:0,6,64:2:0:16:0 0/0:0,9,87:3:0:19:-1 0/0:0,9,87:3:0:19:-1 0/0:0,6,70:2:0:16:0 0/0:0,0,0:0:0:11:0 0/0:0,0,0:0:0:11:0 0/0:0,15,117:5:0:25:0 0/0:0,12,122:4:0:22:0 0/0:0,12,106:4:0:22:0 0/0:0,75,255:25:0:85:0 0/0:0,39,175:13:0:49:0 0/0:0,30,162:10:0:40:-1 0/0:0,6,70:2:0:16:0 0/0:0,0,0:0:0:11:-1 0/0:0,0,0:0:0:11:0 0/0:0,18,148:6:0:28:-1 0/0:0,0,0:0:0:11:0 0/0:0,30,191:10:0:40:0 0/0:0,18,144:6:0:28:0 0/0:0,45,255:15:0:55:0 0/0:0,0,0:0:0:11:0 0/0:0,12,106:4:0:22:-1 0/0:0,82,252:35:0:92:-1 0/0:0,6,64:2:0:16:0 0/0:0,0,0:0:0:11:0 0/0:29,32,44:2:0:13:0 0/0:0,9,83:3:0:19:0 0/0:0,6,64:2:0:16:0 0/0:0,39,228:13:0:49:0 0/0:0,12,102:4:0:22:0 0/0:0,48,210:16:0:58:0 0/0:0,0,0:0:0:11:0 0/0:0,0,0:0:0:11:-1 0/0:0,3,35:1:0:13:0 0/0:0,12,128:4:0:22:-1 0/0:0,3,35:1:0:13:0 0/0:0,3,35:1:0:13:0 0/0:0,6,64:2:0:16:-1 0/0:0,9,82:3:0:19:0 0/0:0,6,64:2:0:16:0 0/0:0,0,0:0:0:11:-1 0/0:0,3,35:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,3,35:1:0:13:0 0/0:0,3,35:1:0:13:0 0/0:0,0,0:0:0:11:0 0/0:0,6,64:2:0:16:-1 0/0:0,21,187:7:0:31:0 0/0:0,78,255:26:0:88:0 0/0:0,15,111:5:0:25:0 0/0:0,30,191:10:0:40:0 0/0:0,30,164:10:0:40:0 0/0:0,6,64:2:0:16:-1 0/0:0,6,64:2:0:16:-1 0/0:0,9,84:3:0:19:0 0/0:0,75,255:25:0:85:-1 0/0:0,63,255:21:0:73:0 0/0:0,39,200:13:0:49:-1 0/0:0,24,174:8:0:34:0 0/0:0,75,255:25:0:85:-1 0/0:0,81,213:27:0:91:0 0/0:0,72,244:24:0:82:-1 0/0:0,3,35:1:0:13:-1 0/0:0,6,64:2:0:16:0 0/0:0,18,133:6:0:28:0 0/1:16,0,93:5:0:7:-1 0/0:0,63,213:21:0:73:0 0/0:0,3,35:1:0:13:0 0/0:0,51,255:17:0:61:0 0/0:0,18,135:6:0:28:0 0/0:0,0,0:0:0:11:-1 0/0:0,123,215:41:0:99:-1 0/0:0,39,203:13:0:49:0 0/0:0,6,64:2:0:16:-1 0/0:0,15,137:5:0:25:0 0/0:0,0,0:0:0:11:-1 0/0:35,35,35:1:0:11:-1 0/0:0,0,0:0:0:11:-1 0/0:0,36,173:12:0:46:-1 0/0:0,6,64:2:0:16:0 0/0:26,32,85:3:0:16:0 0/0:0,12,103:4:0:22:0 0/0:0,229,255:76:0:99:0 0/0:0,96,255:32:0:99:-1 0/0:0,24,153:8:0:34:0 0/0:29,32,61:2:0:13:0 0/0:17,32,132:6:0:25:0 0/0:0,18,150:6:0:28:-1 0/0:0,3,35:1:0:13:-1 0/0:0,3,35:1:0:13:-1 0/0:0,13,151:11:0:23:-1 0/0:0,6,70:2:0:16:0 0/0:0,12,122:4:0:22:-1 0/0:0,6,64:2:0:16:0 0/0:26,32,85:3:0:16:0 0/0:23,32,97:4:0:19:-1 0/0:14,32,144:7:0:28:-1 0/0:0,12,106:4:0:22:0 0/0:0,21,144:7:0:31:0 0/0:10,0,135:7:0:3:-1 0/0:0,117,255:39:0:99:0 0/0:0,66,211:22:0:76:0 0/0:0,3,35:1:0:13:0 0/0:0,30,163:10:0:40:0
# 2  
Old 06-17-2013
It would be better to past your input file under code tags

This will extract you the last column on a tab delimited file..

Code:
awk -F"\t" '{print $NF}' file

# 3  
Old 06-17-2013
Code:
sed "s/.*:RES//" file

This User Gave Thanks to anbu23 For This Post:
Manchesterpaul
# 4  
Old 06-17-2013
Something like this
Code:
awk -F":RES" '/:RES/ {print ":RES" $2}'

This will print from :RES to end of line for all lines containing :RES
This User Gave Thanks to Jotne For This Post:
Manchesterpaul
# 5  
Old 06-17-2013
many thanks

the sed command worked well

---------- Post updated at 06:07 AM ---------- Previous update was at 06:05 AM ----------

as did the awk - many thanks
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