10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
Input File:
>Seq1
ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD
>Seq2
SDASDAQEQWEQeqAdfaasd
>Seq3
ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG
......
Desired Output File
>Seq1
ASDADAFASF
ASFADGSDGF
SDFSDFSDFS
DFSDFSDFSD
FSDFSDFSDF
SD
>Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies
2. Shell Programming and Scripting
I am looking for help in processing of those options: '-n' or '-p'
I understand what they do and how to use them.
But, I would like to use them with more than one file (and without any shell-loop; loading the 'perl' once.)
I did try it and -n works on 2 files.
Question is:
- is it possible to... (6 Replies)
Discussion started by: alex_5161
6 Replies
3. Shell Programming and Scripting
Hi all,
I am having a slight issue updating a file using perl from the command line I need some help with.
The item is:
DATA_FILE_TYPE=FULL
When I run the below command
/usr/bin/perl -p -i -e "s/DATA_FILE_TYPE=/DATA_FILE_TYPE=APPEND/g" processfile.cfg
It looks to be... (2 Replies)
Discussion started by: kstevens67
2 Replies
4. Shell Programming and Scripting
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
Discussion started by: margarita
2 Replies
5. Shell Programming and Scripting
Hello,
I'm pretty stumped, and I don't know why I am not able to redirect the output to the 'graphme' file with the command below in Fedora 18.
tcpdump -l -n -t "tcp == 18" | perl -ane '($s,$j)=split(/,/,$F,2); print "$s\n";' > graphme
In case you're wondering, I was following the example... (2 Replies)
Discussion started by: ConcealedKnight
2 Replies
6. UNIX for Dummies Questions & Answers
Hi all !
I have a fasta file that looks like that:
>Sequence1
RTYIPLCASQHKLCPITFLAVK
(it's just an example, obviously in reality I have several pairs of lines like that)
Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 Replies)
Discussion started by: Cevin21
7 Replies
7. Shell Programming and Scripting
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies
8. Shell Programming and Scripting
Hello,
Im very new to PERL and as a project to work on developing my skills at PERL Im trying to parse poker hands.
Ive tried many methods however I cant get the last step.
$yourfile= 'FILENAME';#poker hands to parse
open (FILE, "$yourfile") or die $!;
@lines = <FILE>;
for (@lines) ... (1 Reply)
Discussion started by: Ek0
1 Replies
9. Shell Programming and Scripting
Hi,
My perl script takes few switches which i'm parsing through GetOpt::Long module.
My script looks like something :
myscript.pl --file="foo" --or --file="bar"
The --file switch takes 2 arguments foo and bar.
The 2 values of file are separated by --or switch. I want to ensure that... (1 Reply)
Discussion started by: obelix
1 Replies
10. UNIX for Dummies Questions & Answers
how to parse the command line argument to look for '@' sign and the following with '.'.
In my shell script one of the argument passed is email address. I want to parse this email address to look for correct format.
rmjoe123@hotmail.com has '@' sign and followed by a '.'
to be more... (1 Reply)
Discussion started by: rmjoe
1 Replies