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Delete lines in a file

 
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# 1  
Old 04-03-2013
Delete lines in a file
Hi

This is a sample of my data file.

Code:
##field      PH01000000      1       4869017
#PH01000000G0240
WWW278545G0240  P.he_model_v1.0     erine    119238  121805  .       -       .       ID=PH01000000G0240;Description="zinc finger, C3HC4 type domain containing protein, expressed"
WWW278545G0240  P.he_model_v1.0     RA    119238  121805  .       -       .       ID=PH01000000G0240.mRNA;Parent=PH01000000G0240
WWW278545G0240  P.he_model_v1.0     NGS     120721  121773  .       -       .       ID=PH01000000G0240.CDS;Parent=PH01000000G0240

#PH01000000G0250
WWW278545G0250  P.he_model_v1.0     erine    125260  126544  .       -       .       ID=PH01000000G0250;Description="FERONIA receptor-like kinase, putative, expressed"
WWW278545G0250  P.he_model_v1.0     RA    125260  126544  .       -       .       ID=PH01000000G0250.mRNA;Parent=PH01000000G0250
WWW278545G0250  P.he_model_v1.0     NGS    125971  126544  .       -       .       ID=PH01000000G0250.CDS;Parent=PH01000000G0250

#PH01000000G0290
WWW278545G0290  P.he_model_v1.0     erine    151334  153926  .       +       .       ID=PH01000000G0290;Description="DUF581 domain containing protein, expressed"
WWW278545G0290  P.he_model_v1.0     RA    151334  153926  .       +       .       ID=PH01000000G0290.mRNA;Parent=PH01000000G0290

I want to use some basic vi command or any comand to delete all those lines whose third column entry is RA or NGS.

I want to retain only those lines whos 3rd column is erine.

Is this possible?

Thanks
Last edited by Scrutinizer; 04-13-2013 at 12:55 PM.. Reason: code tags
# 2  
Old 04-03-2013
Please use code tags as required by forum rules!

If it has to be the third column, grep erinealone would not do. Try
Code:
awk '$3=="erine" {print}' file

Should you want the entire file, incl. headers and empty lines, but RA and NGS removed, try
Code:
awk '$3 ~ /RA|NGS/ {next}' file

This User Gave Thanks to RudiC For This Post:
sonia102
# 3  
Old 04-03-2013
Or, using grep:
Code:
$ grep "^[^ ]\+ [^ ]\+ erine " temp.x
WWW278545G0240 P.he_model_v1.0 erine 119238 121805 . - . ID=PH01000000G0240;Description="zinc finger, C3HC4 type domain containing protein, expressed"
WWW278545G0250 P.he_model_v1.0 erine 125260 126544 . - . ID=PH01000000G0250;Description="FERONIA receptor-like kinase, putative, expressed"
WWW278545G0290 P.he_model_v1.0 erine 151334 153926 . + . ID=PH01000000G0290;Description="DUF581 domain containing protein, expressed"

And see how great it looks with those code tags! Smilie
This User Gave Thanks to hanson44 For This Post:
sonia102
# 4  
Old 04-07-2013
Awesome~~
THANKSSmilieSmilie
# 5  
Old 04-12-2013
Hi Rudic,
I used this command
Code:
awk '$3 ~ /RA|NGS/ {next}' file > newfile

but it gave me th new file of 0 data. Is it becoz there is an occurance of RA and NGS at a position other than 3rd column?

Sorry i didnt add this section of the orginial file earlier.

Code:
WWW278545G0250 P.he_model_v1.0 erine 125260 126544 . - . ID=PH01000000G0250;Description="FERONIA receptor-like kinase, putative, expressed"
WWW278545G0250 P.he_model_v1.0 RA 125260 126544 . - . ID=PH01000000G0250.RA;Parent=PH01000000G0250
WWW278545G0250 P.he_model_v1.0 NGS 125971 126544 . - . ID=PH01000000G0250.NGS;Parent=PH01000000G0250

Is there a way to keep all the lines of the original except those having $3 as RA and NGS?

Thanks

---------- Post updated at 12:34 PM ---------- Previous update was at 12:29 PM ----------

the first code did remove the required entries but it deleted all other entries as well so had to revert back to second option but it didnt work for me..
I couldnt figure out why it didnt work SmilieSmilie
Last edited by Scrutinizer; 04-13-2013 at 12:56 PM.. Reason: code tags
# 6  
Old 04-12-2013
Hello there,

I'm totally new using a program and the default script is generating a error.
it's the script#!/bin/sh
#
# Path to packmol executable (change it if you want,
# a blank line suposes that it is in the path):
#
path=
export OMP_NUM_THREADS=$1
ulimit -s unlimited
if [ "$path" \> " " ]; then
$path/packmol < $2
else
packmol < $2
fi


and the error say line 12: $2: ambiguous redirect
i dont understand
can you help me?
regards

Moderator's Comments:
Mod Comment Please start a new thread for this..
Last edited by Scrutinizer; 04-13-2013 at 09:56 AM..
# 7  
Old 04-13-2013
RudiC and Sonia102,
In this case awk needs a {print} at the end.
Last edited by MadeInGermany; 04-13-2013 at 08:11 AM..
 
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