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awk or perl to parse file

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Top Forums Shell Programming and Scripting awk or perl to parse file
# 8  
Old 03-11-2015
you cannot simply join the lines.
Firstly, try it like so:
Code:
awk '
FNR>1 {
   for(i=1;i<=NF;i++)
     if ($i ~ /^NC_0000/) {
       n=split($i,a, "[.:>_]")
       print a[2]+0, a[5]+0, a[5]+0, substr(a[5],length(a[5])), a[n]
     }
}' OFS='\t' GJB-2.txt

This User Gave Thanks to vgersh99 For This Post:
cmccabe
# 9  
Old 03-11-2015
Thank you Smilie
# 10  
Old 03-13-2015
Quote:
Originally Posted by cmccabe
...
Code:
 perl -lane 'map{$_="NA" if $_<100}@F[5..$#F] if $.>1; print join "\t", "@F"' ${id}.txt > ${id}_parse.txt

${id} = text file attached
...
I couldn't understand the purpose of the map operator. However, the join function accepts two parameters - the join character and a list (array). "@F" is not an array. It is the string representation of the array @F, where each array element is separated by a single blank space. Examples:
Code:
$
$ # @x is the array in the one-liner below
$ perl -le '@x = qw(AA BB CC DD); print @x; print join "|", @x'
AABBCCDD
AA|BB|CC|DD

$
$ # "@x" is the string representation of the array @x in the one-liner below
$ perl -le '@x = qw(AA BB CC DD); print "@x"; print join "|", "@x"'
AA BB CC DD
AA BB CC DD

$

I added some dummy data in your file and it looks like this now (^I is the tab character and ^M$ is the Windows end-of-line character):

Code:
$
$ cat -nvET GJB-2.txt
     1  Input Variant^IErrors^IChromosomal Variant^ICoding Variant(s)^M$
     2  NM_004004.5:c.244G>C^I^INC_000013.10:g.20763477C>G^INM_004004.5:c.244G>C^IXM_005266354.1:c.244G>C^IXM_005266355.1:c.244G>C^IXM_005266356.1:c.244G>C^M$
     3  NM_004004.5:c.244G>C^I^INC_00001.10:g.20763477C>G^INM_004004.5:c.244G>C^INC_00005.10:g.77888999G>C^IXM_005266355.1:c.244G>C^IXM_005266356.1:c.244G>C^M$

$
$

The following Perl one-liner uses a regular expression to parse each token in each line as per the parse rules and prints the desired information:

Code:
$
$ perl -ne 'next if $.==1; while(/\t*NC_0000(\d+)\.\S+g\.(\d+)([A-Z])>([A-Z])/g){printf("%d\t%d\t%d\t%s\t%s\n",$1,$2,$2,$3,$4,$5)}' GJB-2.txt
13      20763477        20763477        C       G
1       20763477        20763477        C       G
5       77888999        77888999        G       C

$
$

This User Gave Thanks to durden_tyler For This Post:
cmccabe
# 11  
Old 03-16-2015
Thank you Smilie.
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