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Replace specific words with nothing

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Top Forums Shell Programming and Scripting Replace specific words with nothing
# 8  
Old 12-30-2013
Quote:
Originally Posted by RavinderSingh13
Hello,

May be this will be helpful.

Code:
$ awk -F"_" 'NR==1 {print $1 OFS $2} NR==2 || NR==3 {print $1}' OFS=_ file_name
 
Output will be as follows:
 
intergenic_Nedd4
Gapvd1
Gapvd1

Thanks,
R. Singh

Ravinder :
Assume if file contains 100 lines,

intergenic_Nedd4_exon_0_F ---> will be line no 1

Gapvd1_intron_24_R---> will be line no 2 and 3

intergenic_Nedd4_exon_0_F---> will be in between somewhere within 100

What do you do ?
# 9  
Old 12-30-2013
for entries like this
Code:
filed1 field2 gene_intron_24_R ...filed10 field11 gene_intron_24_

it is just replacing only those that occur after field2. it is not replacing after field11. I should have been clear with the question
# 10  
Old 12-30-2013
Quote:
Originally Posted by raj_k
for entries like this
Code:
filed1 field2 gene_intron_24_R ...filed10 field11 gene_intron_24_

it is just replacing only those that occur after field2. it is not replacing after field11. I should have been clear with the question
It's not clear to me, show your real input and expected output.
# 11  
Old 12-30-2013
input
Code:
Id1   chr9   fox12_exon_0_F    chr9    56    72        72660772    H3K4ME2_E    726  72  promoter       intergenic_Nedd4_exon_0_F

output
Code:
Id1   chr9   fox12   chr9    56    72         72660772    H3K4ME2_E    726  72  promoter        intergenic_Nedd4

# 12  
Old 12-30-2013
Quote:
Posted by Akshay:

Ravinder :
Assume if file contains 100 lines,

intergenic_Nedd4_exon_0_F ---> will be line no 1

Gapvd1_intron_24_R ---> will be line no 2 and 3

intergenic_Nedd4_exon_0_F ---> will be in between somewhere within 100

What do you do ?
Hello Akshay,

I have just given code for the lines given by user. Will try to give a code which may apply to all.


Thanks,
R. Singh
# 13  
Old 12-30-2013
Quote:
Originally Posted by raj_k
input
Code:
Id1   chr9   fox12_exon_0_F    chr9    56    72        72660772    H3K4ME2_E    726  72  promoter       intergenic_Nedd4_exon_0_F

output
Code:
Id1   chr9   fox12   chr9    56    72         72660772    H3K4ME2_E    726  72  promoter        intergenic_Nedd4

We shall replace sub with gsub, here is code

Code:
$ awk 'gsub(/_(intron|exon)_([[:digit:]]+)_([[:upper:]])/, x) + 1' file
Id1   chr9   fox12    chr9    56    72        72660772    H3K4ME2_E    726  72  promoter       intergenic_Nedd4

This User Gave Thanks to Akshay Hegde For This Post:
raj_k
# 14  
Old 12-30-2013
Hello Raj/Akashay,

Here are the some more solutions.

1st: When we have a file in which Input is having Record seprator as new line.

Code:
sed 's/\(.*\)\(_exon.*\)/\1/g;s/\(.*\)\(_intron.*\)/\1/g' check_lines12

2nd: When we have record seprator as space then code is as follows.

Code:
awk -F" " '{for(i=1;i<=NF;i++) print $i"\n"}' check_lines12_2 | sed 's/\(.*\)\(_exon.*\)/\1/g;s/\(.*\)\(_intron.*\)/\1/g' | tr '\n' ' '
 
OR
 
cat file_name | tr ' ' '\n' | sed 's/\(.*\)\(_exon.*\)/\1/g;s/\(.*\)\(_intron.*\)/\1/g' | tr '\n' ' '

Output will be as follows in all these commands.


Code:
Id1  chr9  fox12  chr9  56  72  72660772  H3K4ME2_E  726  72  promoter  intergenic_Nedd4



NOTE: Where file_name and check_lines12_2 are the input files.


Thanks,
R. Singh
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