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# 1  
Old 12-13-2013
Adding a line before
Hi
I had a question related to adding a particular line in my file.

My file looks like this

Code:
sorce1       LEN   assumption   695     3570    0.770047        -       .       ID=f000001.1;source_id=A.off_LEN_10008424;
sorce1       LEN   descriptive     3334    3570    .       -       0       Parent=f000001.1;
sorce1       LEN   extra     913     993     .       -       0       Parent=f000001.1;
sorce1       LEN   descriptive     695     736     .       -       0       Parent=f000001.1;

sorce1       LEN   assumption    8859    11328   0.628724        +       .       ID=f000002.1;source_id=A.off_LEN_10008425;
sorce1       LEN   descrptive     8859    9032    .       +       0       Parent=f000002.1;

sorce1       LEN   assumption    24331   34483   1       -       .       ID=f000003.1;source_id=A.off_LEN_10008426;part_support_id=CUFF1.1.1;
sorce1       LEN   extra     34479   34483   .       -       0       Parent=f000003.1;

For every line which has assumption in 3rd column, I have to add a line which has same entry as the line which is bolded.

The bolded line needs to have the 3rd column entry " assumption " to be replaced by predictive.

An example:
Code:

sorce1       LEN   predictive    695     3570    0.770047        -       .       ID=f000001;source_id=A.off_LEN_10008424;
sorce1       LEN   assumption   695     3570    0.770047        -       .       ID=f000001.1;source_id=A.off_LEN_10008424;
sorce1       LEN   descriptive     3334    3570    .       -       0       Parent=f000001.1;
sorce1       LEN   extra     913     993     .       -       0       Parent=f000001.1;
sorce1       LEN   descriptive     695     736     .       -       0       Parent=f000001.1;

sorce1       LEN   predictive    8859    11328   0.628724        +       .       ID=f000002;source_id=A.off_LEN_10008425;
sorce1       LEN   assumption    8859    11328   0.628724        +       .       ID=f000002.1;source_id=A.off_LEN_10008425;
sorce1       LEN   descrptive     8859    9032    .       +       0       Parent=f000002.1;

sorce1       LEN   predictive    24331   34483   1       -       .       ID=f000003;source_id=A.off_LEN_10008426;part_support_id=CUFF1.1.1;
sorce1       LEN   assumption    24331   34483   1       -       .       ID=f000003.1;source_id=A.off_LEN_10008426;part_support_id=CUFF1.1.1;
sorce1       LEN   extra     34479   34483   .       -       0       Parent=f000003.1;

Please do help on what I could do to add a line for every statement which has assumption in 3rd column

Thanks
Last edited by Scrutinizer; 12-13-2013 at 04:05 AM.. Reason: code tags
# 2  
Old 12-13-2013
You could try:
Code:
awk '$3=="assumption"{$0=$0 ORS $0; sub($3, "predictive")}1' file

But you would also need to adjust the ID in the last column, no?

Perhaps sed:
Code:
sed 's/\(.*\)assumption\(.*\)\(ID=[^.]*\)[^;]*\(;.*\)/\1predictive\2\3\4\
&/' file

Last edited by Scrutinizer; 12-13-2013 at 04:21 AM..
This User Gave Thanks to Scrutinizer For This Post:
sa@@
# 3  
Old 12-13-2013
Code:
#!/usr/bin/env perl

open( $fh, "<", "file") or die "Cannot open file: $!\n";

while( my $line = <$fh>) {
	chomp($line);
	my @array = split /\s+/, $line;			# split to get 3rd field	
	if ( $array[2] eq "assumption"){
		my $new = $line;					# save current line
		$new =~ s/assumption/predictive/;	        # replace assumption
		$line = $new."\n" . $line ;			# store new version
	}
	print $line."\n";						

}

This User Gave Thanks to brianadams For This Post:
sa@@
# 4  
Old 12-14-2013
Quote:
Originally Posted by Scrutinizer
You could try:
Code:
awk '$3=="assumption"{$0=$0 ORS $0; sub($3, "predictive")}1' file

But you would also need to adjust the ID in the last column, no?

Perhaps sed:
Code:
sed 's/\(.*\)assumption\(.*\)\(ID=[^.]*\)[^;]*\(;.*\)/\1predictive\2\3\4\
&/' file

I tried both the codes.
The first awk code did makethe necessary changes in 3rd column but didnt do the ID change.

As per your advice the 2nd sed command will help in making the changes in ID.
However the 2nd sed command just replaced the entire line having assumption in 3rd column with a line having predictive in 3rd column

I wanted to add a line which has the same contents as line of assumption but change in ID value.
(ddint want to remove the already existing line. )
I hope its not confusing.

Thanks a lot though.
# 5  
Old 12-14-2013
Code:
perl -lape 'if($F[2] eq assumption) {$_.="$/$_"; $_=~s/$F[2](.*?ID=\w+)\.\d/predictive\1/}' file

Last edited by jethrow; 12-14-2013 at 05:42 PM..
This User Gave Thanks to jethrow For This Post:
sa@@
# 6  
Old 12-14-2013
Quote:
Originally Posted by sa@@
I tried both the codes.
The first awk code did makethe necessary changes in 3rd column but didnt do the ID change.

As per your advice the 2nd sed command will help in making the changes in ID.
However the 2nd sed command just replaced the entire line having assumption in 3rd column with a line having predictive in 3rd column

I wanted to add a line which has the same contents as line of assumption but change in ID value.
(ddint want to remove the already existing line. )
I hope its not confusing.

Thanks a lot though.
I am not sure I understand what you mean. The 2nd command does not replace but adds a "predictive" line:

Code:
$ sed 's/\(.*\)assumption\(.*\)\(ID=[^.]*\)[^;]*\(;.*\)/\1predictive\2\3\4\
&/' file
sorce1       LEN   predictive   695     3570    0.770047        -       .       ID=f000001;source_id=A.off_LEN_10008424;
sorce1       LEN   assumption   695     3570    0.770047        -       .       ID=f000001.1;source_id=A.off_LEN_10008424;
sorce1       LEN   descriptive     3334    3570    .       -       0       Parent=f000001.1;
sorce1       LEN   extra     913     993     .       -       0       Parent=f000001.1;
sorce1       LEN   descriptive     695     736     .       -       0       Parent=f000001.1;

sorce1       LEN   predictive    8859    11328   0.628724        +       .       ID=f000002;source_id=A.off_LEN_10008425;
sorce1       LEN   assumption    8859    11328   0.628724        +       .       ID=f000002.1;source_id=A.off_LEN_10008425;
sorce1       LEN   descrptive     8859    9032    .       +       0       Parent=f000002.1;

sorce1       LEN   predictive    24331   34483   1       -       .       ID=f000003;source_id=A.off_LEN_10008426;part_support_id=CUFF1.1.1;
sorce1       LEN   assumption    24331   34483   1       -       .       ID=f000003.1;source_id=A.off_LEN_10008426;part_support_id=CUFF1.1.1;
sorce1       LEN   extra     34479   34483   .       -       0       Parent=f000003.1;
$

The command uses two lines the first line ends with a \ as the last character on the line.

Some sed's may be able to do this:
Code:
sed 's/\(.*\)assumption\(.*\)\(ID=[^.]*\)[^;]*\(;.*\)/\1predictive\2\3\4\n&/' file

awk version:
Code:
awk '
  $3=="assumption"{
    split($NF,F,/[.;]/)
    $0=$0 ORS $0
    sub($3, "predictive")
    sub(F[1]"\."F[2], F[1])
  }
  1
' file

Last edited by Scrutinizer; 12-14-2013 at 03:47 AM..
This User Gave Thanks to Scrutinizer For This Post:
sa@@
# 7  
Old 02-16-2014
additional doubts
To add on to my previous query,I have some additional questions using the code
Code:
sed 's/\(.*\)assumption\(.*\)\(ID=[^.]*\)[^;]*\(;.*\)/\1predictive\2\3\4\n&/' file

In my file, I have some instance where there are variants for the id name :For example One variant of id is f000012.1 and the other is f000012.2
File looks like this

Code:
sorce1       LEN   assumption    354569    361011   0.628724        +       .       ID=f000012.1;source_id=A.off_LEN_10008425;
sorce1       LEN   descriptive        354600    360111    .       +       0       Parent=f000012.1;

sorce1       LEN   assumption    350567    354686    0.628724        +       .       ID=f000012.2;source_id=A.off_LEN_10008425;
sorce1       LEN   descriptive     350567    353321    .       +       0                       Parent=f000012.2;


Using the mentioned command adds 2 lines

Code:
sorce1       LEN   predictive   354569    361011   0.628724        +       .       ID=f000012.1;source_id=A.off_LEN_10008425;

sorce1       LEN   assumption    354569    361011   0.628724        +       .       ID=f000012.1;source_id=A.off_LEN_10008425;
sorce1       LEN   descriptive        354600    360111    .       +       0       Parent=f000012.1;


sorce1       LEN  predictive     350567    354686    0.628724        +       .       ID=f000012.2;source_id=A.off_LEN_10008425;

sorce1       LEN   assumption    350567    354686    0.628724        +       .       ID=f000012.2;source_id=A.off_LEN_10008425;
sorce1       LEN   descrptive     350567    353321    .       +       0                       Parent=f000012.2;

---------- Post updated at 12:37 PM ---------- Previous update was at 12:35 PM ----------

Instead of two separate predictive lines for same id ,
Is there a way I could only a single line with predictive with using the earliest start point ie : and farthest away end point to represent the predictive statement?


The ID should have only the name without the variants like this
Code:
sorce1       LEN   predictive    350567    361011    0.628724        +       .       ID=f000012;source_id=A.off_LEN_10008425;

This should happen only for cases having variants of IDS ie have two ids one with.1 and .2
For other cases,it should follow the normal procedure of just adding a single line

Can this be possible?
Last edited by Scrutinizer; 02-17-2014 at 01:23 AM.. Reason: corrected formatting
 
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