Help with While []... done in bash

[musta1234]

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 the first line as identifier.

The closest I got was a script that generates the required .fasta files but 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

[GenoMax]

See if this thread helps: http://stackoverflow.com/questions/1...a-file-in-bash

[blakeoft]

Is your input the following:

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

and do you want to get

TCCCAATTCGGC
TCCCAATTCGGC
TCCCAATTCGGC
TCCCAATTCGGC

back as a result?

[GenoMax]

I think @musta1234 wants the matrix transposed and then converted to a multi-fasta file.

>SNP_001
TCCCAATTCGGC
>SNP_002
TCCCAATTCGGC
>SNP_003
TCCCAATTCGGC

[musta1234]

Thats right

Sorry for the sloppy explanation, but all the nucleotides are from a tab delimited file and Genomax stated the way I want it perfectly.


>SNP_001
TCCCAATTCGGC
>SNP_002
TCCCAATTCGGC
>SNP_003
TCCCAATTCGGC

......

SNP_XXX
ATGCATGCATGC

Thanks

[GenoMax]

This is a bash shell script based on a solution in the stackoverflow thread I had posted above.

Save the code in a file (script.sh in example below) and then run as follows:

$ sh script.sh your_data file

#!/bin/bash 
declare -a array=( )                      # we build a 1-D-array

read -a line < "$1"                       # read the headline

COLS=${#line[@]}                          # save number of columns

index=0
while read -a line; do
    for (( COUNTER=0; COUNTER<${#line[@]}; COUNTER++ )); do
        array[$index]=${line[$COUNTER]}
        ((index++))
    done
done < "$1"

for (( ROW = 0; ROW < COLS; ROW++ )); do
        printf ">"
  for (( COUNTER = ROW; COUNTER < ${#array[@]}; COUNTER += COLS )); do
    printf "%s" ${array[$COUNTER]}
    if [ $COUNTER == $ROW ]
    then
        printf "\n"
    fi
  done
  printf "\n" 
done

[musta1234]

Thanks

I will definitely give it a try...

[musta1234]

Works GREAT!!!

Hey Genomax and all!!

The code works great... handles a file with 160 columns and 128,000 lines very well.

Thanks

This is a bash shell script based on a solution in the stackoverflow thread I had posted above.




Save the code in a file (script.sh in example below) and then run as follows:

$ sh script.sh your_data file

#!/bin/bash 
declare -a array=( )                      # we build a 1-D-array

read -a line < "$1"                       # read the headline

COLS=${#line[@]}                          # save number of columns

index=0
while read -a line; do
    for (( COUNTER=0; COUNTER<${#line[@]}; COUNTER++ )); do
        array[$index]=${line[$COUNTER]}
        ((index++))
    done
done < "$1"

for (( ROW = 0; ROW < COLS; ROW++ )); do
        printf ">"
  for (( COUNTER = ROW; COUNTER < ${#array[@]}; COUNTER += COLS )); do
    printf "%s" ${array[$COUNTER]}
    if [ $COUNTER == $ROW ]
    then
        printf "\n"
    fi
  done
  printf "\n" 
done