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awk -F'/|"' '$3~"m|M"{printf "%.1f\n", $2/12;next} {print $2+0}' infile

AWK:awk -F"/" '{gsub("\"","")}$2~"a|A"{printf ("%d\n",$1)}$2~"m|M"{printf ("%.1f\n",$1/12)}' file

perl -lne 'if(/(\d+)[ ]?\/a/i){$x=$1;$x=~s/^0*//;print"$x"}
if(/(\d+)[ ]?\/m/i){$y=$1;$y=~s/^0*//;printf "%0.1f\n",$y/12}' inputfile

I think the best way to do it is to use hash of array references, instead of arrays. Try this code: #!/usr/bin/perl
@arrchr = qw(chr02 chr02 chr02 chr02 chr02 chr03 chr03 chr04 chr04 chr05 chr05...

Try: @array = map {$x=($x{$_})?"_":$_;$x{$_}=1;($x)} @array;

#!/usr/bin/perl
print "Enter minimum coverage: ";
chomp($min_cov=<STDIN>);
print "Enter minimum novel_Allele_Starts: ";
chomp($min_nas=<STDIN>);
open I, "$ARGV[0]";
while (<I>){
@F=split;
...

"cmp" is a similar operator to "<=>", just designed to compare strings ;)

Try: @sorted=sort {$a cmp $b} keys %h;
for $i (@sorted){
print "$i\t$h{$i}\n";
}

Try: #!/usr/bin/perl
print "Enter minimum coverage: ";
chomp($min_cov=<STDIN>);
open I, "$ARGV[0]";
while (<I>){
$pos=((split "[\t ]+",$_)[4]);
$cov=((split "=",(split ";",(split "[\t...

In an opened terminal window or on the console enter export PATH=$PATH:/Volumes/USB/Perl_course/Recent/Scripts. Note that this sets the search path only for the current window (not others), and only...

The "1" at the end of AWK command is the same as putting "print" statement there. Perl version of that code:perl -anle '$F[1]+=0.1 if $.>5 && $.<9;print join " ",@F' fileOutput is a bit messed up...

$& holds string that was matched by last regex, so in s/.{100}/$&\n/g; it will contain hundred characters, to which newline is then appended. It is done to restore your formating of hundred chars per...

Yes. To be precise $#x is the last index of @x array. So to get number of elements in that array it needs to be incremented by 1.

Try: #!/usr/bin/perl
open I,"position_file";
@b=<I>;
%h=map {((split /\s+/)[1],(split /\s+/)[2]);} @b;
local $/;
open J,"main_file";
$_=<J>;
s/(>.*)//;
$n=$1;
s/\n//g;
@F=split //,$_;
for...

Weird... It is working for me:oracle@solaris:~/unix/dna$ cat file
>S5_SK1.chr01
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...

map function is used to create hash from the contents of @b array (which contains lines from postion_file). When map is executed, its code is run for each element of the @b array. When processing...

nawk '{| call nawk
x=$1|store 1rst field in variable x
sub(".*[.]","",x)|replace the string followed by the dot by nothing (extract only the chr<nn> part) into the x variable
A[$2]=x|create...

Perl solution:perl -alne '$F[0]=~s/.*\.//;push @{$a{$F[1]}},$F[3];push @{$b{$F[1]}},$F[4];$c{$F[1]}=$F[0];END{for $i (keys %a){print "$c{$i}\t$i\t",@{$a{$i}},"\t",@{$b{$i}}}}' file

nawk '{x=$1;sub(".*[.]","",x);A[$2]=x;B[$2]=B[$2]$4""}END{for(i in A) print A[i],i,B[i]}' inputfile

Ooops, i missed the $5 here you go :

nawk...

Try: #!/usr/bin/perl
open I, "$ARGV[0]";
local $/;
$_=<I>;
s/^(>.*)\n//;
print "$1\n";
s/\n//g;
$a=1;
while (/N+|[ACGT]+/g){
$s=$&;
$l=length $s;
@F=split //, $s;
for $i (@F){
...

Just one small thing.. s/// is not "sed" :) it is "substitute operator", that is present in many tools (sed, vi, Perl).

for i in S5_*; do
perl -i -pe 's/.*/>$ARGV/ if $.==1' $i
done

If you have few files starting with "S5_" in your current directory, and you run this code just once: perl -i -pe 's/.*/>$ARGV/ if $.==1' S5_*, then it will automatically change contents of all the...

Try: perl -i -pe 's/.*/>$ARGV/ if $.==1' S5_*

awk '{if( NR==1)print ">"FILENAME;else print}' S5_SK1.chr01