Shell Programming and Scripting

I have a text file with the geneIds separated by space in each line. The number Ids in lines are different.

The file is like:

Code:

 abc qwe tyu ghj jkl dfg sdf
 cvb sdk fgh tyu
 uio iop tyu rty eru wer rty iop
 asd sdf dfg fgh zxc

I want to format the file like:

Code:

 abc
 qwe
 tyu
 ghj
 jkl
 dfg
 sdf

 cvb
 sdk
 fgh
 tyu
 
 uio
 iop
 tyu
 .
 . 
 iop
 
 asd 
 sdf
 .
 . 
 .
 zxc

Any help would be appreciated. Thanks!

Code:

$ 
$ cat f02
abc qwe tyu ghj jkl dfg sdf
cvb sdk fgh tyu
uio iop tyu rty eru wer rty iop
asd sdf dfg fgh zxc
$ 
$ perl -pne 'BEGIN {$\="\n"}s/ /\n/g' f02
abc
qwe
tyu
ghj
jkl
dfg
sdf

cvb
sdk
fgh
tyu

uio
iop
tyu
rty
eru
wer
rty
iop

asd
sdf
dfg
fgh
zxc

$ 
$

Code:

awk '{$1=$1}1' OFS="\n" ORS="\n\n" infile

This awk works if you have a space in front of some of the line or not
cvb vs cvb
@durden_tylor, you have removed this space in f02
perl gives an extra blank row due to this space

sed works too ...

Code:

sed -e "s/$/\n/" -e "s/[ \n]/\n/g" infile

sed has same problem as perl
it adds double blank line, since there is a space infront of the line

Code:

abc
qwe
tyu
ghj
jkl
dfg
sdf


cvb
sdk
fgh
tyu


uio
...
...

The OP did not specify an operating system, so I'll mention that because of \n in the replacement text, that sed script will fail on most non-Linux systems.

Regards,
Alister

---------- Post updated at 01:17 PM ---------- Previous update was at 01:09 PM ----------

If we assume that the sample data and sample output in the OP are exactly correct, then your solution is incorrect. The sample output has a leading space which your solution discards. Additionally, your solution adds a concluding blank line which does not appear in the sample output.

The OP should clarify exactly what they want because there is a discrepancy between the problem description and the sample input/output. The post's text appears to state (due to the grammar, it's impossible to be certain) that input fields are delimited by a single space (supported by the sample data). If that's correct, then, in the absence of special consideration (which isn't mentioned in the post) a leading space represents an empty first field which should become a blank line. However, this would cause an ambiguity in the output format, since a blank line could represent an empty field or a record separator.

If we assume that the leading space on every line of the input and output is an artifact of copy/pasting, a simple, portable solution which treats the input as newline delimited records of single-space delimited fields and converts it to blank-line delimited records (with the exception that the final record is not followed by a blank line) of newline delimited fields:

Code:

sed 'y/ /\n/; $!G'

Regards,
Alister

I do see now that the OPs output request also has space in front

Code:

awk '{$1=" "$1}1' OFS="\n " ORS="\n\n"

This gives space in front of all line.
But we do not know for sure of is this he wants