Editing files in different subdirectories using conditions
Clash Royale CLAN TAG#URR8PPP
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I'm completely new to linux. I have one directory /gwas_test and within this I have hundreds of folders each number from 1-200. Within each of these numbered folders is another folder (which I don't need to do anything to) and 1 file with summary statistics from genomewide association studies (what I need). I want to filter the variants at a threshold of <5e-08 and replace the older _imputed.txt file. However, I have looked all over the internet and tried things but have been unsuccessful. Any advice or any simpler code for complete novices like me would be very appreciated!
Here is the code I used:
find /panfs/panasas01/ssm/rkl/gwas_test/ -name "*_imputed.txt" -type f | while read fname;do
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
awk -v outputPath="$fileDirName"
awk '($14<=5e-08) print $1,$2,$3,$5,$6,$7,$11,$12,$14' $fname > outputPath "$fileDirName/$fname"
done
Thanks
linux awk loop-device
edited 1 min ago
Ipor Sircer
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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up vote
0
down vote
favorite
I'm completely new to linux. I have one directory /gwas_test and within this I have hundreds of folders each number from 1-200. Within each of these numbered folders is another folder (which I don't need to do anything to) and 1 file with summary statistics from genomewide association studies (what I need). I want to filter the variants at a threshold of <5e-08 and replace the older _imputed.txt file. However, I have looked all over the internet and tried things but have been unsuccessful. Any advice or any simpler code for complete novices like me would be very appreciated!
Here is the code I used:
find /panfs/panasas01/ssm/rkl/gwas_test/ -name "*_imputed.txt" -type f | while read fname;do
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
awk -v outputPath="$fileDirName"
awk '($14<=5e-08) print $1,$2,$3,$5,$6,$7,$11,$12,$14' $fname > outputPath "$fileDirName/$fname"
done
Thanks
linux awk loop-device
edited 1 min ago
Ipor Sircer
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I'm completely new to linux. I have one directory /gwas_test and within this I have hundreds of folders each number from 1-200. Within each of these numbered folders is another folder (which I don't need to do anything to) and 1 file with summary statistics from genomewide association studies (what I need). I want to filter the variants at a threshold of <5e-08 and replace the older _imputed.txt file. However, I have looked all over the internet and tried things but have been unsuccessful. Any advice or any simpler code for complete novices like me would be very appreciated!
Here is the code I used:
find /panfs/panasas01/ssm/rkl/gwas_test/ -name "*_imputed.txt" -type f | while read fname;do
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
awk -v outputPath="$fileDirName"
awk '($14<=5e-08) print $1,$2,$3,$5,$6,$7,$11,$12,$14' $fname > outputPath "$fileDirName/$fname"
done
Thanks
linux awk loop-device
edited 1 min ago
Ipor Sircer
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
I'm completely new to linux. I have one directory /gwas_test and within this I have hundreds of folders each number from 1-200. Within each of these numbered folders is another folder (which I don't need to do anything to) and 1 file with summary statistics from genomewide association studies (what I need). I want to filter the variants at a threshold of <5e-08 and replace the older _imputed.txt file. However, I have looked all over the internet and tried things but have been unsuccessful. Any advice or any simpler code for complete novices like me would be very appreciated!
Here is the code I used:
find /panfs/panasas01/ssm/rkl/gwas_test/ -name "*_imputed.txt" -type f | while read fname;do
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
fileBaseName=`basename "$fname" `
fileDirName=`dirname "$fname" `
awk -v outputPath="$fileDirName"
awk '($14<=5e-08) print $1,$2,$3,$5,$6,$7,$11,$12,$14' $fname > outputPath "$fileDirName/$fname"
done
Thanks
linux awk loop-device
linux awk loop-device
edited 1 min ago
Ipor Sircer
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 1 min ago
Ipor Sircer
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
edited 1 min ago
Ipor Sircer
9,8301921
edited 1 min ago
Ipor Sircer
9,8301921
edited 1 min ago
Ipor Sircer
9,8301921
9,8301921
asked 3 mins ago
rkl
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
asked 3 mins ago
rkl
1
asked 3 mins ago
rkl
1
1
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
New contributor
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
rkl is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
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add a comment |Â
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rkl is a new contributor. Be nice, and check out our Code of Conduct.
rkl is a new contributor. Be nice, and check out our Code of Conduct.
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