Following the discussion a previous discussion (https://www.biostars.org/p/171557/), I would like to prepare a file for converting chr:pos to rs. For this, I have downloaded a list of all SNPs from UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). It looks like this:
#chrom chromEnd name
chr1 100663297 rs1235665665
chr1 1048577 rs1346354302
chr1 62914560 rs538775156
I would like it to look like this:
1:100663297 rs1235665665
1:1048577 rs1346354302
1:62914560 rs538775156
I could do it in R; however, the file is so large that it crashes my computer before it even loads. I was told that Linux commands such as grep and awk are amazing for such things, and can handle very large file efficiently. Unfortunately, I do not have a slightest idea of how even to begin writing the code in Linux to achieve my goal.
Could you please help me with this?
Thank you very much.
PS I am unsure whether the title to my question is efficient in describing my problem. Please let me know if it is not and I will edit it.
•
written
by
OAJn8634
1 answer
One way:
$ tail -n+2 in.txt | sed 's/^chr//' | awk -v OFS="\t" '{ print $1":"$2, $3 }' > out.txt
Test it out, first:
$ head -10 in.txt | tail -n+2 | ... > out.txt
Break things down by seeing how a snippet of your file looks after each step.
Let's see what you have learned: Please describe what this command line is doing. :)
Alternatively:
sed -e '1,1d' -e 's/^chr//' in > out
Or e.g.
awk 'BEGIN{OFS=FS="\t"}NR>1{sub(/^chr/,"",$1);print $0}' in > out
Edit. I didn't notice the ":" requirement. These don't actually do that..
Corrected:
sed -e '1,1d' -e 's/^chr//' -e 's/\t/:/' in > out
awk 'BEGIN{OFS=FS="\t"}NR>1{sub(/^chr/,"",$1);print $1":",$2,$3}' in > out
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This is really basic question. You should starting searching the web for how
awkworks. Have a look for examples at this tutorial side.Of course I could give you the solution. But then you will not learn that much :)
Edit : Along to finswimmer comment, here are some other links
Hello OAJn8634
Please take a look at the
manofawk,sed,grep,cutto see how to use it. Give us your best try and we will take a look how to modify it to fit your attentAwk in Bioinformatics
https://stackoverflow.com/questions/29275971/need-to-remove-the-string-chr-and-the-sign-from-the-file
Hello Bastien Hervé and finswimmer, Thank you very much for the very useful links on how get me started, and for offering to help. I really appreciate it.