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Hi Fehrke, Here is the logic which I don't understand on the second code abs($2)>m{m=abs($2)? why >?

Fehrke, Thank you as always!! Both options produced the result I wanted. But I have a difficaulty to construe the code. Thanks

$XXXX00000182183 A B C D 2336458 0.38052728 0.47743206 0.7575053 -0.6718711 2336459 0.28057157 0.15925342 1.6066561 -0.6718711 2336464 0.51131811 0.09128078 2.0090009 -0.6718711 2336466 -0.24900861 0.13113013 -1.7475722 -0.6718711 2336469 0.38724031 0.06652635...

test.... cat *.txt My question was the later: putting the code in code box... Thanks for providing the the tag... Supper... Demis

Annihilannic, How can you copy the and pest the code snippets like this from shell terminal? would you please tell me how to do it? Sorry it is off the topic, Thanks

Thank you, I have wrote using Perl this time. I thought it might be easier in awk. I have solved the problem using Perl

Thank you, Something wrong with the split(f1iter, idxA, SUBSEP) part. Result of the script is: 1,ENST00000327169,60240 1 358460,357522,OR4F29 1,ENST00000327169,60030 1 358460,357522,OR4F29 1,ENST00000327169,60090 1 358460,357522,OR4F29 1,ENST00000327169,60120 1 358460,357522,OR4F29...

Data2 looks like this: ENSG00000177693 ENST00000326183 1 1 59871 58954 ENSP00000317482 OR4F5 HGNC (curated) uc001aal.1 AL627309 79501 ENSG00000177799 ENST00000327169 1 1 358460 357522 ENSP00000318226 OR4F29 HGNC (curated) uc001aaw.1 BK004219 26683 ENSG00000185097 ENST00000332831 1 -1 611897...

Sorry for the confusion, I want the desired output. I can able to modify the script to get the desired output. But, I have no “nawk” on my Linux box. I have tried with “gawk” and “awk” and the script does not gave me any output using the with the demo file I have provided. Thanks

Need help, data1 1 59851 59880 CATTCTAGTGTAAAGTTTTAGATCTTATAT 1 59881 59910 AACTGTGAGATTAATCTCAGATAATGACAC 1 59911 59940 AAAATATAGTGAAGTTGGTAAGTTATTTAG 1 59941 59970 TAAAGCTCATGAAAATTGTGCCCTCCATTC 1 59971 60000 CCATATAATTTAGTAATTGTCTAGGAACTT 1...

I want to add respective column for repeat item on $1. If there is no repeat sequence on $1, I want the exact count in each col. Please would you help me guys! ---------------------------------------------------------- data Name a b c d e f g h GGGACGG 2 0 7 10 2 0 4 0 GGGAGGG 0 0 4 26 8 3 0 0...

Would you please help me in formating the folling file. File looks like the folloing. I want to capture, The "AC" and ID row and print $2 and $3 if the file contain "hsa_" in column three. See the result file I want at the end of this file. -----------data---------------- AC MIPF0000001 ID...

Hi feherke, Yours only search exact match. Is there any possiblity to change to pattern match similar to PVH. file1: TCGTCTGCCGT TCGTCTGCCGTTTT TCGTCTGCCGTTTTT TCGTCTGCCGTTTTTT TCTCTGAGGGTCG TCTCTGAGGGTCGG TCTCTGAGGGTCGGT file2 TCGTCTGCCGT TCGTCTGCCGTTTTTTCCTTG...

Sorry for confusing term I have used Annihilannic, What meant was, "it is inefficient based on processing time". It took more than 5 houre to count 250(file1) short reads within >10 millions sequence(file2) under 32gb momory computing linux machine Thank you guys, It helps a lot.

Hi All, The script by PHV works fine but memory ineffecient. If file2 is 10 millions lines, the Process tries to read in memory and print the final output. Is there any better option to print the result after each loop? Demis001

Thanks as usual PHV, it does the job I want... Demis001

Hi guys, Is there easy way to searcha and count the following. File1 TCGTCTGCCGTTTTTT TCTCTGAGGGTCGGT File2 TCGTCTGCCGTTTTTT TCGTCTGCCGTTTTTTCCTTG TCGTCTGCCGTTTTTTCCTTTTCATCTTAAAAAAAA TCGTCTGCCGTTTTTTCGTTGGCAACAATAAAGTCT TCGTCTGCCGTTTTTTG TCGTCTGCCGTTTTTTG TCGTCTGCCGTTTTTTG...

Is there any way I can negate the following line. I want to print none-overlap lines between two files. Rather than "in a", I want "not in a" awk 'NR==FNR{a[$2","$3","$6]=$0;next}$2","$3","$6 in a{print a[$2","$3","$6]"\t"$0}' $* Thanks D

Zedlan, yours didn't work!

Thanks, It works