I'm trying to find the snp whose postion (POS) lie between the txstart and txend in the gene data
so for this data I have the first SNP will lie between MAGI2 txstart and txend
You might have mentioned that the code you quoted above came from a different thread (Map snps into a ref gene file) in which your first input file had two fields (with headings POS and ID) instead of the three fields (with headings CHROM, POS, and ID) that you are showing in this thread.
Did you think that I wouldn't recognize code I suggested for you a week ago if you reposted it in a different thread without attribution?
Why don't you try to modify that code to print the header line you now say that you want and to align the fields captured from the first input file with where that data is located in your new specification for that input file, instead of just saying that code that you implied you wrote doesn't work?
you are so hard on me , by the way i'm not trying to confuse you or test your memory, I don't know how to modeify the code , If you can help please do so
you are so hard on me , by the way i'm not trying to confuse you or test your memory, I don't know how to modeify the code , If you can help please do so
I'm not trying to be hard on you. This site is here to help you and many, many others learn how to write code to do what you want or need to do. It is not here to act as your unpaid programming staff.
I didn't mean to imply that you were trying to confuse me or test me. I meant to say that copying someone's code without attribution and implying it is your own is plagiarism.
If you don't understand how that code works and what needs to be done to it to make it work with a different input file format, why don't you look at the awk man page on your system and try to figure out what the code is doing. If you can't figure it out, ask questions and the volunteers here will be happy to try to help you learn how it works and suggest what might need to be changed to work with your new file format.
Someone might also show you how to add a BEGIN clause to your awk script to print the heading you want in your output file. Maybe even something like:
Code:
awk '
BEGIN { print "gene ID CHROM POS txstart txend"
}
FNR == 1 {
next
}
FNR == NR {
POS[++k] = $2
ID[k] = $3
next
}
{ for(i = 1; i <= k; i++)
if(POS[i] >= $5 && POS[i] <= $6)
print $1, ID[i], $3, POS[i], $5, $6
}' pre_snpinfo_tumor.txt refFlat.txt
As always, since you haven't bothered to tell us what operating system you're using, if you're using a Solaris/SunOS system change awk to /usr/xpg4/bin/awk or nawk.
With the sample input files you provided in post #1 in this thread, the above code produces the output:
There is absolutely nothing wrong with the code I suggested in post #4 in this thread. When run on macOS Sierra release 10.12.3 using the shells bash, ksh, sh, and zsh it produces exactly the output requested in post #1 in this thread as shown in post #4 in this thread.
One might guess that you either made a mistake when copying the code, you used an editor that converted the UNIX line terminators required in a shell script into DOS or old MAC line separators, or used an editor that converted some of the characters that are part of the syntax of awk statements into "pretty-printed" versions of those characters that are not recognized by awk.
If you are absolutely positive that you didn't make any mistakes when copying the code, please:
tell us exactly what release of OS X or macOS you're using,
tell us what shell you're using,
show us the exact command that you used to invoke that awk script, and
show us the output you get from the command:
Code:
od -bc < filename
(where filename is the name of the file containing your awk script).
I copied and paste the code in the terminal that is it
by the way I'm working under a server from my University using SSH so the data are in that server
and I type unix code to get my result, put in this case it gave me errors
I have the following data set about the snps ID txt file
POS ID
78599583 rs987435
33395779 rs345783
189807684 rs955894
33907909 rs6088791
75664046 rs11180435
218890658 rs17571465
127630276 rs17011450
90919465 rs6919430
and a gene... (7 Replies)
Hi I have a file like this
input_fileCR387793 -0.8
CR387793 -5.5
CR387794 -5.3
CR387795 -0.9
AR388755 -3.0
AR388755 3.8
AR388755 4.5
Each line has annotation name and its correlated value. The annotation name and the value are seperated by a space. I want to average the value if the lines... (4 Replies)
