More Help, New to awk!!!! 1

[demis001]

PHV wrote the following script to process the inputfile at the end of this post(it will work for single line process, the problem I have is to extract the last part)

awk '
BEGIN{print "loop_beg\tmature_arm\tpri_id"}
$1~/^(loop_beg|mature_arm)$/{a[$1]=$2}
$1=="pri_id"{print a["loop_beg"]"\t"a["mature_arm"]"\t"$2}
' /path/to/input
--------------------------------------------------------
input file

nucleus -0.6
star -1.3
score_randfold 1.6
score_mfe 3.1
score_freq 0
score 3.1
flank_first_end 41
flank_first_seq kkkkkk
flank_first_struct ........
flank_second_beg 107
flank_second_seq fffffffffffff
flank_second_struct ..................
freq 62
loop_beg 60
loop_end 88
loop_seq llllll
loop_struct ccccccccccccccc
mature_arm second
mature_beg 89
mature_end 106
mature_query GC40_484005_x31
mature_seq CAGAGCTGGCTGAAGGGC
mature_strand +
mature_struct ........
pre_seq ttttt
pre_struct ....................
pri_beg 1
pri_end 140
pri_id chr11_1559
pri_mfe -84.14
pri_seq ...........
pri_struct kkkkkkkkkk
star_arm first
star_beg 42
star_end 59
star_seq CCTTCAGCCAGAGCTGGC
star_struct fffff
GC40_1014_x 18 20
GC40_1014_x 18 21
GC40_484005_x 18 22

-----second record coninues----

I want to print $1 and $3 of the last part(GC40-----). Each record have more than one entry.

Output should be something like this
header1 header2 header3 header4
$2 $2 $1 $3
$1 $3
$1 $3
$2 $2 $1 $3

Help please!!!

 

[Annihilannic]

It seems like PHV has given you a good start, have you tried modifying the script to do that? If so, where are you stuck?

Annihilannic.

 

[demis001]

Many thanks,
I have tried to insert sort of if statment and really doesn't work. Here is what I have tried;

awk '
BEGIN{print "loop_beg\tmature_arm\tpri_id\tquery"}
{if($1~/^(loop_beg|mature_arm)$/a[$1]=$2})
{if($1~/^(GC40)/a[$1]=$1}
$1=="GC40"{print a["loop_beg"]"\t"a["mature_arm"]"\t"$2\t a["GC40"]"\t"$1}
' /path/to/input

 

[Annihilannic]

You don't need the if statements because each awk expression is effectively an if statement already, of the format expression { code }. Whenever the expression is true, the code is executed.

Try this slight variation:

aawk '
    BEGIN {print "loop_beg\tmature_arm\tpri_id\tquery"}
    $1~/^(loop_beg|mature_arm)$/ { a[$1]=$2 }
    $1~/^GC40/ {
        print a["loop_beg"]"\t"a["mature_arm"]"\t"$2"\t"$1"\t"$3
        a["loop_beg"]=""
        a["mature_arm"]=""
    }
'  /path/to/input

Annihilannic.

 

[demis001]

Many Many Thanks! You guys teached me and guid me a lot!

 

[feherke]

Hi

Here on Tek-Tips we used to thank for the received help by giving stars. Please click the

* [navy]Thank Annihilannic
for this valuable post![/navy]

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Feherke.

http://rootshell.be/~feherke/