@Bartus
I have 2 questions about a script relating to the parts in red
1. How can I combine the two IF statements in the WHILE loop so that I get output only if those conditions are met.
2. How so I print sorted results of hash of hashes in the END part
Script
Code:
#!/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;
$F[8]=~/coverage=([^;]+)/;
if ($1>=$min_cov){
$cov{$F[0]}{$F[3]}+=$1;
$F[8]=~/novelAlleleStarts=([^;]+)/;
if ($1>=$min_nas){
$nas{$F[0]}{$F[3]}+=$1;
}
$n{$F[0]}{$F[3]}++;
$h{$F[0]}++;
}
}
END{
for $i (keys %cov){
for $j (keys %{$cov{$i}}){
print "$i\t$j\t";
printf "%.1f\t", ($cov{$i}{$j}/$n{$i}{$j});
printf "%.1f\n", ($nas{$i}{$j}/$n{$i}{$j});
}
}
for $i (keys %h){
@sorted=sort {$a cmp $b} keys %h;
}
for $i (@sorted){
print "$i\t$h{$i}\n";
$t+=$h{$i};
}
}
sample file for running script
Code:
SK1.chr10 SOLiD_diBayes SNP 3120 3120 1.000000 . . genotype=A;reference=G;coverage=179;refAlleleCounts=32;refAlleleStarts=21;refAlleleMeanQV=15;novelAlleleCounts=117;novelAlleleStarts=27;novelAlleleMeanQV=17;diColor1=23;diColor2=23;het=0;flag=h8,
SK1.chr01 SOLiD_diBayes SNP 8621 8621 0.000000 . . genotype=C;reference=T;coverage=198;refAlleleCounts=5;refAlleleStarts=5;refAlleleMeanQV=18;novelAlleleCounts=150;novelAlleleStarts=49;novelAlleleMeanQV=18;diColor1=21;diColor2=21;het=0;flag=h4,h10,h9,
SK1.chrm SOLiD_diBayes SNP 8844 8844 1.000000 . . genotype=C;reference=A;coverage=205;refAlleleCounts=38;refAlleleStarts=21;refAlleleMeanQV=24;novelAlleleCounts=164;novelAlleleStarts=51;novelAlleleMeanQV=27;diColor1=01;diColor2=01;het=0;flag=h8,
SK1.chr07 SOLiD_diBayes SNP 8852 8852 1.000000 . . genotype=T;reference=C;coverage=161;refAlleleCounts=31;refAlleleStarts=16;refAlleleMeanQV=24;novelAlleleCounts=127;novelAlleleStarts=47;novelAlleleMeanQV=23;diColor1=11;diColor2=11;het=0;flag=h8,
SK1.chr07 SOLiD_diBayes SNP 8865 8865 0.999102 . . genotype=G;reference=A;coverage=74;refAlleleCounts=11;refAlleleStarts=7;refAlleleMeanQV=26;novelAlleleCounts=59;novelAlleleStarts=29;novelAlleleMeanQV=24;diColor1=12;diColor2=12;het=0;flag=h8,
I'm not able to figure it out, can you please enlighten on this?
Cheers and have a nice day
Hi,
I am trying to make a script that creates a list of all active (alive) processes sorted by size and then print this list on screen.
Could anyone help me?
Thaks a lot (7 Replies)
Hi -
I am guessing this is fairly simple for someone .. but I can not quite figure it out. I need a sed command to print just parts of lines from a file.
e.g. filea.txt
4710451 : Success : MODIFY : cn=user1,dc=org,dc=uk
Message log started
Message log ended
4710452 : Success : MODIFY :... (7 Replies)
Hey, I found a way to print the lines which is just before a regular expression, not including the expression.
sed -n '/regexp/{n;p;}' myfile
Now I'm looking for a way to print all lines, exept the regular expression and also the line before the same regular expression.
Use code tags. (1 Reply)
Hello,
I want to print a number of lines of a file after a specific expression of a line.
I have this sed command but it prints only 1 line after the expression.
How could I adapt it to print for instance 10 lines after or 15 lines after ?
sed -n '/regexp/{n;p;}'
Thx & Regs,
Rany. (5 Replies)
CA_RELEASE has a value of 6. I need to check if that this is a numeric value. if not error.
source $CA_VERSION_DATA
if * ]
then
echo "CA_RELESE $CA_RELEASE is invalid"
exit -1
fi
+ source /etc/ncgl/ca_version_data
++ CA_PRODUCT_ID=samxts
++ CA_RELEASE=6
++ CA_WEEK_NO=7
++... (3 Replies)
Dear All,
I am trying to sort an array of numbers to retrieve the mimimum and maximum values of numbers in that array, by printing the first and last elements of the sorted array. My code is @sorted_numbers = sort (@numbers);
print "@sorted_numbers\n";
print "$sorted_numbers,... (0 Replies)
Hello All,
I'm trying to extract the lines between two consecutive elements of an array from a file.
My array looks like:
problem_arr=(PRS111 PRS213 PRS234)
j=0
while } ]
do
k=`expr $j + 1`
sed -n "/${problem_arr}/,/${problem_arr}/p" problemid.txt
---some operation goes... (11 Replies)
hi All ,
I am having a large file with lots of modules as shown below
###############################################
module KKK
kksd
kskks
jsn;lsm
jsnlsn;
Ring
jjsjsj
kskmsm
jjs
endmodule
module llll
1kksd11
k232skks
j33sn;l55sm (6 Replies)
Discussion started by: kshitij
6 Replies
LEARN ABOUT V7
vp
VP(4) Kernel Interfaces Manual VP(4)NAME
vp - Versatec printer-plotter
DESCRIPTION
Vp0 is the interface to a Versatec D1200A printer-plotter with a Versatec C-PDP11(DMA) controller. Ordinarily bytes written on it are
interpreted as ASCII characters and printed. As a printer, it writes 64 lines of 132 characters each on 11 by 8.5 inch paper. Only some
of the ASCII control characters are interpreted.
NL performs the usual new-line function, i.e. spaces up the paper and resets to the left margin. It is ignored however following a CR
which ends a non-empty line.
CR is ignored if the current line is empty but is otherwise like NL.
FF resets to the left margin and then to the top of the next page.
EOT resets to the left margin, advances 8 inches, and then performs a FF.
The ioctl(2) system call may be used to change the mode of the device. Only the first word of the 3-word argument structure is used. The
bits mean:
0400 Enter simultaneous print/plot mode.
0200 Enter plot mode.
0100 Enter print mode (default on open).
040 Send remote terminate.
020 Send remote form-feed.
010 Send remote EOT.
04 Send remote clear.
02 Send remote reset.
On open a reset, clear, and form-feed are performed automatically. Notice that the mode bits are not encoded, so that it is required that
exactly one be set.
In plot mode each byte is interpreted as 8 bits of which the high-order is plotted to the left; a `1' leaves a visible dot. A full line of
dots is produced by 264 bytes; lines are terminated only by count or by a remote terminate function. There are 200 dots per inch both ver-
tically and horizontally.
When simultaneous print-plot mode is entered exactly one line of characters, terminated by NL, CR, or the remote terminate function, should
be written. Then the device enters plot mode and at least 20 lines of plotting bytes should be sent. As the line of characters (which is
20 dots high) is printed, the plotting bytes overlay the characters. Notice that it is impossible to print characters on baselines that
differ by fewer than 20 dot-lines.
In print mode lines may be terminated either with an appropriate ASCII character or by using the remote terminate function.
FILES
/dev/vp0
SEE ALSO opr(1)VP(4)
04-28-2011
