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5,776
Posted By @man
SBATCH trinity for multiple files and rename/move the output files
Hey guys,
I have wrote the following script to apply a module named "trinity" on my files. (it takes two input files and spit a trinity.fasta as output)
#!/bin/bash -l
#SBATCH -p node
#SBATCH -A...
1,761
Posted By @man
I still get the same... tr -d '\015'...
I still get the same...
tr -d '\015' <file1.txt > file1_new.txt
tr -d '\015' <file2.txt > file2_new.txt

file1_new.txt 21.50
file1.txt 21.50
file2_new.txt 1515.00
file2.txt 1515.00

I'm...
1,761
Posted By @man
cat -vet file2.txt chr2L^I10^I230^M$ ...
cat -vet file2.txt
chr2L^I10^I230^M$
chr2L^I20^I20^M$
chr2L^I35^I1.5^M$
chr2L^I36^I1000^M$
chr3R^I12^I100^M$
chr3R^I20^I300^M$
chrX^I10^I15^M$
chrX^I26^I1500

I am so thankful for your...
1,761
Posted By @man
I don't think I have more than 7 digits. I tried...
I don't think I have more than 7 digits. I tried it with two following sample files:
file1.txt
chr2L 10 23
chr2L 20 20
chr2L 35 15
chr2L 36 10
chr3R 12 10
chrX 10 15

file2.txt...
1,761
Posted By @man
Thanks for your reply vgersh99! It has some...
Thanks for your reply vgersh99!

It has some problems
First of all it does not do the sorting properly. Here is what I got for top 0.1% for example:
258
2575
257
2553
255
251
25
......
1,761
Posted By @man
Calculate average of top n% of values - UNIX
Hey guys,

I have several huge tab delimited files which look like this:
a 1 20
a 3 15
a 5 10
b 2 15
b 6 10
c 3 23

what I am interested is to calculate the average of top n% of data in...
1,045
Posted By @man
Dear alister, I appreciate that you try not to...
Dear alister,
I appreciate that you try not to give a fish! ;)
I should have replied much earlier... but then I managed to write the script and didn't update the thread.

you have always...
1,045
Posted By @man
Re-scaling values - perl
Hey folks

I have a big tab delimited file with 3 columns looks like this:

chr2L 552 0.85
chr2R 135 1.06
chr3L 820 2.89
chr3R 581 3.93
chr4 585 0.94
chrX 605 1.93

All I want to do is...
1,546
Posted By @man
balajesuri!! OMG! when I saw all your comment I...
balajesuri!! OMG! when I saw all your comment I was stunned! Man I appreciate what you do! Big one!
And I ran it for the sample inout file and it works perfectly. I am pretty sure it works for the...
1,546
Posted By @man
Make Separated files from a single matrix - Perl
Hey Masters,

Here is my input:

fragmentID chromosome start end HEL25E TRIP1
r5GATC2L00037 chr2L 5301 6026 0.03 0.036
r5GATC2L00038 chr2L 6023 6882 -0.025 -0.041...
1,206
Posted By @man
I am sorry for not being clear... I have...
I am sorry for not being clear...

I have attached one of my several files.
And the reference file.
and based on those the desired output File.
It's OK if you don't have time to make it. But...
1,206
Posted By @man
Thanks Pamu for your time. here are two...
Thanks Pamu for your time.

here are two problems! :|
1. I have several files. instead of writing the names manually can I use something like *.txt ?

2. I am more dumb than what I thought!...
1,206
Posted By @man
Match columns several files
Hey fellas!

Here come my problem. I appreciate if you have a look at it.

I have several files with following structure:

file_1:1 21
4 45

file_2:2 31
4 153
6 341

and so on...
...
4,723
Posted By @man
my lines are like this: ...
my lines are like this:
chr2L Center=128181;Length=461

I want this at output for each line:
chr2L 128181

I tried this:
awk '{print $1 "\t" substr($2,8)}'...
4,723
Posted By @man
awk substr
Hello life savers!!

Is there any way to use substr in awk command for returning one part of a string from declared start and stop point?

I mean I know we have this:
substr(string, start,...
2,213
Posted By @man
thank you Yoda and alister. As you said...
thank you Yoda and alister.

As you said shorter is not always better! :) I was not sure if what I used does the matching strictly or not. Now I'm
once again thanks to both of you.

Cheers!
2,213
Posted By @man
awk regular expression
Hello,

I have big files which I wanna filter them based on first column.

first column should be one of these strings: chr2L || chr2R || chr3L || chr3R || chr4 || chrX
and something like...
2,282
Posted By @man
Thanks bartus11! now that I have this 2...
Thanks bartus11!

now that I have this 2 dimensional array I would like to do this afterward:

I want to fill an empty matrix with these letters in this array. The reason for creating random...
2,282
Posted By @man
Store in a 2 dimensional array - Perl
Hey guyz.

Here is my sample input file following by first part of my code:

* A B C D E
reg1 1 0 1 1 0
reg2 0 1 0 0 1
reg3 1 0 0 1 0
reg4 0 0 1 0 1
reg5 1 1 0 0 1


use strict;
use...
1,788
Posted By @man
Help with Perl
You are damn right Jim! :) I like how you described it... cool!! ;)
I found an algorithm how to randomize my -rather complex to explain- data.

I explain it here:

Suppose I have the...
1,788
Posted By @man
@Rudic: The actual input data that I have is much...
@Rudic: The actual input data that I have is much bigger than this! It might be possible to have 1000 permutations.
Actually my worries is if it's possible to do this simulation and repeat it...
1,788
Posted By @man
Randomize a matrix
--please have a look at my third post in this thread! there I explained it more clearly--

Hey guys.

I posted a complex problem few days back. No reply! :|
Here is simplified question:

I...
1,064
Posted By @man
Randomization a matrix - perl / Shell
Hello all,

I have a tricky question! (at least for me it is!). I'll try to explain it carefully here. Hope you can help me solving the whole or even parts of it! Here it is:

I have a big...
2,524
Posted By @man
It works man! For some reason it is space...
It works man! For some reason it is space delimited which I used this command line to convert space to tabs:

awk -v OFS="\t" '$1=$1' filename

Thanks elixir_sinari! A friend was right that he...
2,524
Posted By @man
elixir_sinari I gonna check it now. I'll let you...
elixir_sinari I gonna check it now. I'll let you know. Thanks one more time.

pamu as I mentioned before in some lines there are duplicates for some factors, which we have to take the maximum...
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