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,
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...
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
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
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
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