awk help

[SDPA_Pet]

Can any one help me with awk.

The attached file is an example. I have 10 functions and 6 comparsions. The first column is the function name and column 2- 7 are p value.

I need to write a awk command to keep the functions which have five out of six p value less than 0.05

I want to select functions like this

function1 0.01 0.01 0.01 0.01 0.01 0.1

Thanks
Ben

[Richard Finney]

cat file | awk '{n=0;if($2<0.05)n++; if($3<0.05)n++; if($4<0.05)n++; if($5<0.05)n++; if($6<0.05)n++; if($7<0.05)n++; if (n==5) print $0}'

Note this only picks if 5, if you want >= 5 change "==" to ">="

[GenoMax]

If you need 5 out of 6 then the following should work:

$ awk '{count = 0; for (i=2; i<=NF; i++) if ($i < 0.05) count++; if (count == 5) print $0}' data.txt

Note: Richard beat me to it but I will leave this here since as always more than one way of doing things.

[SDPA_Pet]

If you need 5 out of 6 then the following should work:

$ awk '{count = 0; for (i=2; i<=NF; i++) if ($i < 0.05) count++; if (count == 5) print $0}' data.txt

Note: Richard beat me to it but I will leave this here since as always more than one way of doing things.

Hi GEnoMax

"i<NF", What does NF mean?

Thanks

[SDPA_Pet]

If you need 5 out of 6 then the following should work:

$ awk '{count = 0; for (i=2; i<=NF; i++) if ($i < 0.05) count++; if (count == 5) print $0}' data.txt

Note: Richard beat me to it but I will leave this here since as always more than one way of doing things.

Hi GenoMax,

Can you help me the attached dataset. I want to extract all the data meet these conditions:

either column4 or column 6 data >=1

I try this but it doesn't work

awk '{n=0;if($4>=1)n++; if($6>=1)n++; if (n>=1) print $0}' t-test-story.txt

Thank you.

[GenoMax]

Hi GEnoMax

"i<NF", What does NF mean?

Thanks

NF is total number of fields in a record (a line).

[SDPA_Pet]

Hi GenoMax,

Can you help me with the new file? I don't know why my script doesn't work.

[GenoMax]

Hi GenoMax,

Can you help me the attached dataset. I want to extract all the data meet these conditions:

either column4 or column 6 data >=1

Thank you.

Try this:

$ awk '{FS="\t"; if ($4 > 1 || $6 > 1 ) print $0}' t-test-story.txt

[musta1234]

Need help converting tab to fasta

Hello all!! I need help converting tab to fasta... I am a newbie and know only a little bash scripting. I need to convert a tab delimited SNP file into either a single fasta file or a multiple fasta files for each column using a the first line as identifier.

The closest I got was a script that enters a loop and can only be stopped by ctrl-C


#!/bin/bash


echo ">" > carat.txt

counter=1
#My tab file has 64 columns
while : [ $counter -lt 64]
do

less <SNP.txt |awk "{print$"$counter"}"| cat carat.txt - >$counter.fa
counter=$(($counter +1))

done

exit



SNP_001 SNP_002 SNP_003....
T T T T
C C C C
C C C C
C C C C
A A A A
A A A A
T T T T
T T T T
C C C C
G G G G
G G G G
C C C C

[musta1234]

Moved

this post is also copied to a new thread to increase exposure... thanks

[GenoMax]

this post is also copied to a new thread to increase exposure... thanks

Are you basically looking to transpose the matrix your posted and covert it to a multi-fasta file?