[...]
My bash file is complete and working like a charm but I am interested in learning better ways to use awk and/or perl to improve my script [...]
I am going to take your word for it. I took a look at your script and and run it against the Example.txt. It processes just one entry in pykA-Example.txt. You are opening and closing files quite a bit and overwriting them.
Anyway, for whatever is worth, here's an easy to understand Perl snippet that it produces the same output without the calling of external programs and continually opening and close files. The output gets send to your stdout instead of multiple files, so you may want to redirect.
Instead of hard coding gene, bait, primers and fwd, I created an extra setting file that contains these gene entries and patterns, which it does get read before hand.
Here's the look of it:
Here's the code that pulls it:
Save as xterra.pl
Run as perl xterra.pl patterns.txt Example.txt > results.output.
It is trivial to add the functionality of outputting a different file for each gene, if necessary.
Here's a resource link to learn more about Perl and Bioinformatics in case that it might be usable.
Last edited by Aia; 03-24-2016 at 12:27 AM..
Reason: Corrects wrong indentation.
Thanks! I will analyze your script. I know perl is great. However, at this point I am trying to learn more about SED and awk. Once I am really familiar with both, I am planning to start with perl
Hello,
Opearting System Environment : HP Unix B.11.31 U
I look for script to
On specific folders list
On specific filelist
Search for given string
For Example :
r48_buildlib.txt contains
wpr480.0_20161027
wpr480.0_20161114
wpr481.0_20161208
wpr482.0_20161222... (4 Replies)
Hello,
I want to search two strings in a file and print the same in the new file using perl script.
Can anyone suggest me how to do this...
The file looks like below:
<UML:ModelElement.requirement>
<UML:Dependency name="Row_MainColumn_FW_0009"> <UML:ModelElement.taggedValue>... (3 Replies)
Hi,
Need some help...
I want to execute sequence commands, like below
test1.sh
test2.sh
...etc
test1.sh file will generate log file, we need to search for 'complete' string on test1.sh file, once that condition success and then it should go to test2.sh file, each .sh scripts will take... (5 Replies)
Hello All,
Im a Hardware engineer, I have written this script to automate my job. I got stuck in the following location.
CODE:
..
..
...
foreach $key(keys %arr_hash) {
my ($loc,$ind,$add) = split /,/, $arr_hash{$key};
&create_verilog($key, $loc, $ind ,$add);
}
sub create_verilog{... (2 Replies)
Hi All
I want to search a string from an array in Perl. If a match occurs, assign that string to a variable else assign 'No match'. I tried writing the script as follows but it's in vain. Please help me..
#!/usr/bin/perl
use strict;
my $NER;
my @text=("ORG","PER");
... (4 Replies)
ok so what I am trying to do is search through 200k files that have ext .000 or .702. for *@yahoo.com.tw and if it finds that in the file. then remove the file. this is my code... what am i doing wrong. it seams it will only find asdflkajsdf@yahoo.com.tw as a string and not *@yahoo.com.tw so it... (5 Replies)
Hi,
I have a line where i need to get certain part of it.. example..
text txt tt: 1909
thats how exactly it looks and all spaces are to be counted.. i need to retrieve 1909..
Thanks (11 Replies)
Hi All,
I have a file that I need to be able to find a pattern match on a line, search that line for a text pattern, and replace that text.
An example of 4 lines in my file is:
1. MatchText_randomNumberOfText moreData ReplaceMe moreData
2. MatchText_randomNumberOfText moreData moreData... (4 Replies)
Hi All,
I have a file that I need to be able to find a pattern match on one line then parse data on the next or subsequent lines - I will know which line needs to be parsed beforehand.
This is what I currently have:
while (<COMMAND_OUT>) {
if ($_ =~ m/TEST/) {
... (4 Replies)