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• since bash doesn't have the equivalent of zsh's (N) glob qualifier or ksh93's ~(N) glob operator, before using a glob in a for loop (at least), you need to set the nullglob option:

  shopt -s nullglob
  for infile in *_1.fastq.Block*; do...
  

  If you don't and there's no matching file, you'll loop over a literal *_1.fastq.Block*

• You can set IFS for read only with: IFS=_ read -ra ADDR <<< "$infile" (see also the quotes around $infile which are needed in older versions of bash). That way, $IFS is only changed while read runs¹ and it's restored to its previous value after read returns.

• IFS=. read -ra <<< "$var" is a poor method for splitting. First is only works for single line $vars which is not necessarily the case of file names, and also it's quite inefficient. That involves either storing the contents of $var into a tempfile or feed it via a pipe depending on the version of bash and/or the size of $var and then reading it one byte at a time until a newline is found.

  Here, you could use the split+glob operator instead:

  IFS=:; set -o noglob
  addr=( $infile )
  

  Or switch to better shells with proper splitting operators.

  Another approach here, you be to do:

  regex='^(.*)_1\.fastq\.(Block.*)$'
  if [[ $infile =~ $regex ]]; then
    outfile=${BASH_REMATCH[1]}_2.fastq.${BASH_REMATCH[2]}
    ...
  

  With the caveat that regex matching only works with valid text, which again is not a guarantee for file names.

  Here, you could also use standard sh parameter expansion operators:

  new_file=${infile%_1.fastq.Block*}_2.fastq.Block${infile##*_1.fastq.Block}
  

  Or the ksh93-style:

  new_file=${infile/_1.fastq.Block/_2.fastq.Block}
  

• since bash doesn't have the equivalent of zsh's (N) glob qualifier or ksh93's ~(N) glob operator, before using a glob in a for loop (at least), you need to set the nullglob option:

  shopt -s nullglob
  for infile in *_1.fastq.Block*; do...
  

  If you don't and there's no matching file, you'll loop over a literal *_1.fastq.Block*

• You can set IFS for read only with: IFS=_ read -ra ADDR <<< "$infile" (see also the quotes around $infile which are needed in older versions of bash). That way, $IFS is only changed while read runs¹ and it's restored to its previous value after read returns.

• IFS=. read -ra <<< "$var" is a poor method for splitting. First is only works for single line $vars which is not necessarily the case of file names, and also it's quite inefficient. That involves either storing the contents of $var into a tempfile or feed it via a pipe depending on the version of bash and/or the size of $var and then reading it one byte at a time until a newline is found.

  Here, you could use the split+glob operator instead:

  IFS=:; set -o noglob
  addr=( $infile )
  

  (or addr=( $infile'' ) to not ignore a trailing :.)

  Or switch to better shells with proper splitting operators.

  Another approach here would be to do:

  regex='^(.*)_1\.fastq\.(Block.*)$'
  if [[ $infile =~ $regex ]]; then
    outfile=${BASH_REMATCH[1]}_2.fastq.${BASH_REMATCH[2]}
    ...
  

  With the caveat that regex matching only works with valid text, which again is not a guarantee for file names.

  Here, you could also use standard sh parameter expansion operators:

  new_file=${infile%_1.fastq.Block*}_2.fastq.Block${infile##*_1.fastq.Block}
  

  Or the ksh93-style:

  new_file=${infile/_1.fastq.Block/_2.fastq.Block}
  

  (note the variations in behaviour among all those approaches if _1.fastq.Block occurs more than once in the file name).

In

echo $second_file

Since you forgot to quote the parameter expansion, it's subject to split+glob, so with IFS=., ABC_2.fastq.Block12 is first split into, ABC_2, fastq and Block12 and each word subject to globbing, with no effect here since none of the words contain glob operators.

So 3 arguments are passed to echo which it prints space separated.

To print the contents of a variable followed by a newline character, you need:

printf '%s\n' "$var"

For more details, see:

• When is double-quoting necessary?
• Why is printf better than echo?

Now, a few more comments on your code:

• since bash doesn't have the equivalent of zsh's (N) glob qualifier or ksh93's ~(N) glob operator, before using a glob in a for loop (at least), you need to set the nullglob option:

  shopt -s nullglob
  for infile in *_1.fastq.Block*; do...
  

  If you don't and there's no matching file, you'll loop over a literal *_1.fastq.Block*

• You can set IFS for read only with: IFS=_ read -ra ADDR <<< "$infile" (see also the quotes around $infile which are needed in older versions of bash). That way, $IFS is only changed while read runs¹ and it's restored to its previous value after read returns.

• IFS=. read -ra <<< "$var" is a poor method for splitting. First is only works for single line $vars which is not necessarily the case of file names, and also it's quite inefficient. That involves either storing the contents of $var into a tempfile or feed it via a pipe depending on the version of bash and/or the size of $var and then reading it one byte at a time until a newline is found.

  Here, you could use the split+glob operator instead:

  IFS=:; set -o noglob
  addr=( $infile )
  

  Or switch to better shells with proper splitting operators.

^{¹ Though beware that if a trap is handled whilst read is running, the code in that trap will have the modified $IFS}

In

echo $second_file

Since you forgot to quote the parameter expansion, it's subject to split+glob, so with IFS=., ABC_2.fastq.Block12 is first split into, ABC_2, fastq and Block12 and each word subject to globbing, with no effect here since none of the words contain glob operators.

So 3 arguments are passed to echo which it prints space separated.

To print the contents of a variable followed by a newline character, you need:

printf '%s\n' "$var"

For more details, see:

• When is double-quoting necessary?
• Why is printf better than echo?

Now, a few more comments on your code:

• since bash doesn't have the equivalent of zsh's (N) glob qualifier or ksh93's ~(N) glob operator, before using a glob in a for loop (at least), you need to set the nullglob option:

  shopt -s nullglob
  for infile in *_1.fastq.Block*; do...
  

  If you don't and there's no matching file, you'll loop over a literal *_1.fastq.Block*

• You can set IFS for read only with: IFS=_ read -ra ADDR <<< "$infile" (see also the quotes around $infile which are needed in older versions of bash). That way, $IFS is only changed while read runs¹ and it's restored to its previous value after read returns.

• IFS=. read -ra <<< "$var" is a poor method for splitting. First is only works for single line $vars which is not necessarily the case of file names, and also it's quite inefficient. That involves either storing the contents of $var into a tempfile or feed it via a pipe depending on the version of bash and/or the size of $var and then reading it one byte at a time until a newline is found.

  Here, you could use the split+glob operator instead:

  IFS=:; set -o noglob
  addr=( $infile )
  

  Or switch to better shells with proper splitting operators.

  Another approach here, you be to do:

  regex='^(.*)_1\.fastq\.(Block.*)$'
  if [[ $infile =~ $regex ]]; then
    outfile=${BASH_REMATCH[1]}_2.fastq.${BASH_REMATCH[2]}
    ...
  

  With the caveat that regex matching only works with valid text, which again is not a guarantee for file names.

  Here, you could also use standard sh parameter expansion operators:

  new_file=${infile%_1.fastq.Block*}_2.fastq.Block${infile##*_1.fastq.Block}
  

  Or the ksh93-style:

  new_file=${infile/_1.fastq.Block/_2.fastq.Block}
  

^{¹ Though beware that if a trap is handled whilst read is running, the code in that trap will have the modified $IFS}

In

echo $second_file

Since you forgot to quote the parameter expansion, it's subject to split+glob, so with IFS=., ABC_2.fastq.Block12 is first split into, ABC_2, fastq and Block12 and each word subject to globbing, with no effect here since none of the words contain glob operators.

So 3 arguments are passed to echo which it prints space separated.

To print the contents of a variable followed by a newline character, you need:

printf '%s\n' "$var"

For more details, see:

• When is double-quoting necessary?
• Why is printf better than echo?

In

echo $second_file

Since you forgot to quote the parameter expansion, it's subject to split+glob, so with IFS=., ABC_2.fastq.Block12 is first split into, ABC_2, fastq and Block12 and each word subject to globbing, with no effect here since none of the words contain glob operators.

So 3 arguments are passed to echo which it prints space separated.

To print the contents of a variable followed by a newline character, you need:

printf '%s\n' "$var"

For more details, see:

• When is double-quoting necessary?
• Why is printf better than echo?

Now, a few more comments on your code:

• since bash doesn't have the equivalent of zsh's (N) glob qualifier or ksh93's ~(N) glob operator, before using a glob in a for loop (at least), you need to set the nullglob option:

  shopt -s nullglob
  for infile in *_1.fastq.Block*; do...
  

  If you don't and there's no matching file, you'll loop over a literal *_1.fastq.Block*

• You can set IFS for read only with: IFS=_ read -ra ADDR <<< "$infile" (see also the quotes around $infile which are needed in older versions of bash). That way, $IFS is only changed while read runs¹ and it's restored to its previous value after read returns.

• IFS=. read -ra <<< "$var" is a poor method for splitting. First is only works for single line $vars which is not necessarily the case of file names, and also it's quite inefficient. That involves either storing the contents of $var into a tempfile or feed it via a pipe depending on the version of bash and/or the size of $var and then reading it one byte at a time until a newline is found.

  Here, you could use the split+glob operator instead:

  IFS=:; set -o noglob
  addr=( $infile )
  

  Or switch to better shells with proper splitting operators.

^{¹ Though beware that if a trap is handled whilst read is running, the code in that trap will have the modified $IFS}