CODEWITHSUNDEEP
bashshellhttp-redirectsed
Abir Shaked
Abir Shaked

Reputation: 1

Bash script to stdout stuck with redirect

My bash script is the following: 

#!/bin/bash
if [ ! -f "$1" ]; then
  exit
fi
while read line;do
  str1="[GAC]*T"
  num=$"(echo $line | tr -d -c 'T' | wc -m)"
  for((i=0;i<$num;i++))do
    echo $line | sed "s/$str1/&\n/" | head -n1 -q
    str1="${str1}[GAC]*T"
  done
  str1="[GAC]*T"
done < "$1

While it works normally as it should (take the filename input and print it line by line until the letter T and next letter T and so on) it prints to the terminal.

Input:

GATTT
ATCGT

Output:

GAT
GATT
GATTT
AT
ATCGT

When I'm using the script with | tee outputfile the outputfile is correct but when using the script with > outputfile the terminal hangs / is stuck and does not finish. Moreover it works with bash -x scriptname inputfile > outputfile but is stuck with bash scriptname inputfile > outputfile.

Upvotes: 0

Views: 373

Answers (2)

builder-7000
builder-7000

Reputation: 7627

I made modifications to your original script, please try:

if [ ! -f "$1" ]; then                                               
  exit                                                                   
fi                                                                       
while IFS='' read -r line || [[ -n "$line" ]];do                         
  str1="[GAC]*T"                                                         
  num=$(echo $line | tr -d -c 'T' | wc -m)                               
  for((i=0;i<$num;i++));do                                               
    echo $line | sed "s/$str1/&\n/" | head -n1 -q                        
    str1="${str1}[GAC]*T"                                                
  done                                                                   
  str1="[GAC]*T"                                                         
done < "$1"

For input:

GATTT                                                                    
ATCGT

This script outputs:

GAT
GATT
GATTT
AT
ATCGT

Modifications made to your original script were:

  • Line while read line; do changed to while IFS='' read -r line || [[ -n "$line" ]]; do. Why I did this is explained here: Read a file line by line assigning the value to a variable

  • Line num=$"(echo $line | tr -d -c 'T' | wc -m)" changed to num=$(echo $line | tr -d -c 'T' | wc -m)

  • Line for((i=0;i<$num;i++))do changed to for((i=0;i<$num;i++));do

  • Line done < "$1 changed to done < "$1"

Now you can do: ./scriptname inputfile > outputfile

Upvotes: 1

user unknown
user unknown

Reputation: 36250

Try:

sed -r 's/([^T]*T+)/\1\n/g' gatc.txt > outputfile

instead of your script.

It takes some optional non-Ts, followed by at least one T and inserts a newline after the T. 

cat gatc.txt 
GATGATTGATTTATATCGT
sed -r 's/([^T]*T+)/\1\n/g' gatc.txt 
GAT
GATT
GATTT
AT
AT
CGT

For multiple lines, to delete empty lines in the end:

echo "GATTT
ATCGT" |  sed -r 's/([^T]*T+)/\1\n/g;' | sed '/^$/d'
GATTT
AT
CGT

Upvotes: 0

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