I am a biologist who is new to linux and am having difficulty generating a script to do what I want it to do! I have tried basic grep commands, but even that does not give me back the data I want.
I have many files that are all currently in .xslx and I'm not sure if they need to be .csv or .txt for this to work... Each of these files has ~90,000 lines.
Basically I want a script that will ask me what I am looking for:
Code:
echo Please input gene name you wish to look for
read GeneName
Then I want to look through all of the lines in all of my files (~200) and see if $GeneName is present in field 13 (it may be present multiple times in the one file, or not at all).
If it is present in field 13, I want the entire line/s it is in, plus the file name/s it is found in to be printed to a .txt file.
I have tried using grep command and it just gives me back all lines from the file, not the lines containing $GeneName. I apologise I do not have a better unix background, but I have been trying for days and I just cannot generate it!!! I would appreciate any help.
There is a heading line at the top of each file, and each subsequent line starts with chr. For this example, I would be wanting to identify the lines containing WASH7P in file1.txt and file2.txt (or if this would work with .csv files?)
file1.txt
Code:
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq
chr01 14907 14907 A G het 108 52 39 snp131 rs6682375 ncRNA WASH7P . . rs6682375 . .
chr01 14930 14930 A G het 148 62 44 snp131 rs6682385 ncRNA WASH7P . . rs6682385 1000g2010nov_all 0.71
chr01 761752 761752 C T hom 225 69 69 snp131 rs1057213 ncRNA NCRNA00115 . . rs1057213 1000g2010nov_all 0.544
chr01 761800 761800 A T hom 42 11 11 snp131 rs1064272 ncRNA NCRNA00115 . . rs1064272 1000g2010nov_all 0.114
file2.txt
Code:
chr_name chr_start chr_end ref_base alt_base hom_het snp_quality tot_depth alt_depth dbSNP dbSNP131 region gene change annotation dbSNP132 1000genomes allele freq
chr01 17556 17556 C T het 43 30 9 . . ncRNA WASH7P . . . . .
chr01 69511 69511 A G hom 225 106 106 snp131 rs2691305 exonic OR4F5 nonsynonymous SNV "OR4F5:NM_001005484:exon1:c.A421G:p.T141A," rs2691305 1000g2010nov_all 0.789
chr01 761732 761732 C T hom 225 103 102 snp131 rs2286139 ncRNA NCRNA00115 . . rs2286139 1000g2010nov_all 0.537
I would like be asked to type in GeneName (i.e. WASH7P) and the output in a .txt file to be something like:
Code:
file1.txt:chr01 14907 14907 A G het 108 52 39 snp131 rs6682375 ncRNA WASH7P . . rs6682375 . .
file1.txt:chr01 14930 14930 A G het 148 62 44 snp131 rs6682385 ncRNA WASH7P . . rs6682385 1000g2010nov_all 0.71
file2.txt:chr01 17556 17556 C T het 43 30 9 . . ncRNA WASH7P . . . . .
Many thanks,
Kelly
Last edited by Franklin52; 09-14-2011 at 05:00 AM..
Reason: Please use code tags for code and data samples, thank you
Hi Kelly,
Go through this and let me know if there's any problem. Use tags while posting your queries. The code below is working fine for me and giving the expected output.
Code:
echo "the text"
read Genename
grep $Genename file1.txt > somefile.txt
You will need to convert to txt or csv first as awk/grep require text files not binary.
Try this:
Code:
echo Please input gene name you wish to look for
read GeneName
for file in *.txt
do
awk -v F=$file -vN=$GeneName '$13 ~ N { print F": "$0 }' $file
done
This User Gave Thanks to Chubler_XL For This Post:
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09-14-2011
