Cat files situation

Shell Programming and Scripting
1

Hello,
I am PhD student (Biomedical sciences) and very new to Linux. I need some help with the following task :

I have files in the following format for their names :

An_A1_nnn_R1.txt;  An_A1_nnm_R1.txt;  An_A1_nnoo_R1.txt
An_A2_nnn_R1.txt;  An_A2_nnm_R1.txt;  An_A2_nno_R1.txt

..................
An_A900_nnn_R1.txt;  An_A900_nnm_R1.txt;  An_A900_nno_R1.txt

Between An_A(1..900) and R1 the string can be anything.

I need to do this:

cat An_A1_nnn_R1.txt  An_A1_nnmm_R1.txt   An_A1_nnoo_R1.txt > An_A1.R1.txt
```[/i]


obviously I can do 900 times a cat command but I am sure there should be and easy way using a for loop or something like that. 

any ideas?

Thanks in advance

Julio
2

If you have them all in one directory, you can easily do something like this:

cat *.txt >> your_big_file.text
1 Like
3

thanks Neo, maybe I did not explain it correctly..
what you suggest will cat all files in the directory...but I need to cat them depending on the number after "An_A" . So, since the name of the file go from An_A1* to An_A900* I finally will have 900 cat results..

---------- Post updated at 05:18 PM ---------- Previous update was at 04:56 PM ----------

I thought on doing something like this:

-----------------------------------

for i in {1..900}
       do 
                 cat *A$i*R1.txt > A$i.R1.txt
      done

--------------------------------------------

but it does not work...

4

You should append instead:

cat *A${i}*R1.txt >> A${i}.R1.txt
1 Like
5

*A$i*R1.txt would include A$i.R1.txt so A$i.R1.txt would be both read from and written to..

So instead try:

for i in {1..900}
do 
  cat *_A$i_*_R1.txt >> A$i.R1.txt
done

or

for i in {1..900}
do 
  cat *_A$i_*_R1.txt > A$i.R1.txt
done

if you want to empty the target files first..

1 Like
6

actually , using "trial and error" I just found that all these 3 cat codes do the job

----------------------

#!/bin/bash

for i in {1..900}
 do 

    #cat *A"$i"*R1* > A"$i".R1.txt
    #cat *A"$i"*R1* >> A"$i".R1.txt
    cat *A${i}*R1.txt >> A${i}.R1.txt

done

---------------------

thanks again Yoda and Neo

7

Hi Julio, I still see this as problematic. If you repeat the command then the second time the target files will exist and match the pattern, so they will be cat onto themselves.. I did a short test and I ended up with a very big file...

8

thanks ,
I guess if I change the target name to something like : A"$i".R1.fastq.txt
it should work since since the string fastq is not present in any of the files to be merge with cat? what do you think?

9

Yes that should work too, as long as the output file names do no match the input file patterns..

1 Like