sed

sed is also one of the most commonly used test-editing command in Linux, which is short for stream editor. sed command edits the text from standard input in a line-by-line approach.

sed syntax

sed [OPTIONS] PROCESS [FILENAME]

Examples

sample input

head ../02_Linux_basics/sumstats.txt
#CHROM  POS ID  REF ALT A1  TEST    OBS_CT  OR  LOG(OR)_SE  Z_STAT  P   ERRCODE
1   13273   1:13273:G:C G   C   C   ADD 503 0.7461490.282904    -1.03509    0.300628    .
1   14599   1:14599:T:A T   A   A   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14604   1:14604:A:G A   G   G   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14930   1:14930:A:G A   G   G   ADD 503 1.643590.242872 2.04585 0.0407708   .
1   69897   1:69897:T:C T   C   T   ADD 503 1.691420.200238 2.62471 0.00867216  .
1   86331   1:86331:A:G A   G   G   ADD 503 1.418870.238055 1.46968 0.141649    .
1   91581   1:91581:G:A G   A   A   ADD 503 0.9313040.123644    -0.575598   0.564887    .
1   122872  1:122872:T:G    T   G   G   ADD 503 1.048280.182036 0.259034    0.795609    .
1   135163  1:135163:C:T    C   T   T   ADD 503 0.6766660.242611    -1.60989    0.107422    .

Example 1: Replacing strings

s for substitute g for global

Replacing strings

"Replace the separator from : to _"

head 02_Linux_basics/sumstats.txt | sed 's/:/_/g'
#CHROM  POS ID  REF ALT A1  TEST    OBS_CT  OR  LOG(OR)_SE  Z_STAT  P   ERRCODE
1   13273   1_13273_G_C G   C   C   ADD 503 0.7461490.282904    -1.03509    0.300628    .
1   14599   1_14599_T_A T   A   A   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14604   1_14604_A_G A   G   G   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14930   1_14930_A_G A   G   G   ADD 503 1.643590.242872 2.04585 0.0407708   .
1   69897   1_69897_T_C T   C   T   ADD 503 1.691420.200238 2.62471 0.00867216  .
1   86331   1_86331_A_G A   G   G   ADD 503 1.418870.238055 1.46968 0.141649    .
1   91581   1_91581_G_A G   A   A   ADD 503 0.9313040.123644    -0.575598   0.564887    .
1   122872  1_122872_T_G    T   G   G   ADD 503 1.048280.182036 0.259034    0.795609    .
1   135163  1_135163_C_T    C   T   T   ADD 503 0.6766660.242611    -1.60989    0.107422    .

Example 2: Delete header(the first line)

-d for deletion

Delete header(the first line)

head 02_Linux_basics/sumstats.txt | sed '1d'
1   13273   1:13273:G:C G   C   C   ADD 503 0.7461490.282904    -1.03509    0.300628    .
1   14599   1:14599:T:A T   A   A   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14604   1:14604:A:G A   G   G   ADD 503 1.676930.240899 2.14598 0.0318742   .
1   14930   1:14930:A:G A   G   G   ADD 503 1.643590.242872 2.04585 0.0407708   .
1   69897   1:69897:T:C T   C   T   ADD 503 1.691420.200238 2.62471 0.00867216  .
1   86331   1:86331:A:G A   G   G   ADD 503 1.418870.238055 1.46968 0.141649    .
1   91581   1:91581:G:A G   A   A   ADD 503 0.9313040.123644    -0.575598   0.564887    .
1   122872  1:122872:T:G    T   G   G   ADD 503 1.048280.182036 0.259034    0.795609    .
1   135163  1:135163:C:T    C   T   T   ADD 503 0.6766660.242611    -1.60989    0.107422    .