perl -reading from 2 files and merge them

[robelb4]

Hi All,

I just want read 2 files and write their result (3 lines from each file at time) in another file, how do i do it in perl?? thanks

example:
file1.txt content file2.txt content

> zzzzzzzzzzzzzzz >aaaaaaaaaaaaaa
xxxxxxxxxxxxxxxxx bbbbbbbbbbbbb
vvvvvvvvvvvvvv cccccccccccccc
> sssssssssssssss > 1111111111111
mmmmmmmmmm 2222222222222
nnnnnnnnnnnnnn 3333333333333

output.txt content should be

> zzzzzzzzzzzzzzz
xxxxxxxxxxxxxxxxx
vvvvvvvvvvvvvv
>aaaaaaaaaaaaaa
bbbbbbbbbbbbb
cccccccccccccc
> sssssssssssssss
mmmmmmmmmm
nnnnnnnnnnnnnn
> 1111111111111
222222222222222
33333333333333

[robelb4]

by the way the 2 files i put side by side is just two show they're the same format.

thanks

[damiankao]

do you just want to merge two fasta files together? you can just use the 'cat' linux command for that. So something like this:

cat fastaA.fa fastaB.fa > mergedFasta.fa

[robelb4]

do you just want to merge two fasta files together? you can just use the 'cat' linux command for that. So something like this:

cat fastaA.fa fastaB.fa > mergedFasta.fa

Not like that, it should be 3 lines at a time, as I said it above

[EHC]

use paste

PASTE(1) BSD General Commands Manual PASTE(1)

NAME
paste -- merge corresponding or subsequent lines of files

SYNOPSIS
paste [-s] [-d list] file ...

DESCRIPTION
The paste utility concatenates the corresponding lines of the given input files, replacing all but the last file's newline characters with a single tab character, and writes the
resulting lines to standard output. If end-of-file is reached on an input file while other input files still contain data, the file is treated as if it were an endless source of
empty lines.

The options are as follows:

[kmcarr]

Hi All,

I just want read 2 files and write their result (3 lines from each file at time) in another file, how do i do it in perl?? thanks

example:

file1.txt content              file2.txt content

> zzzzzzzzzzzzzzz                     >aaaaaaaaaaaaaa
xxxxxxxxxxxxxxxxx                     bbbbbbbbbbbbb
vvvvvvvvvvvvvv                        cccccccccccccc
> sssssssssssssss                     > 1111111111111
mmmmmmmmmm                            2222222222222
nnnnnnnnnnnnnn                        3333333333333
 
output.txt content should be

> zzzzzzzzzzzzzzz
xxxxxxxxxxxxxxxxx
vvvvvvvvvvvvvv 
>aaaaaaaaaaaaaa
bbbbbbbbbbbbb
cccccccccccccc
> sssssssssssssss 
mmmmmmmmmm  
nnnnnnnnnnnnnn  
> 1111111111111
222222222222222
33333333333333

(Using CODE tags around text you want to present in a formatted manner helps with readability.)

A few questions:

Are the two files you want to merge FASTA files? I'm guessing because of the ">" at the beginning of each block of text. Also, are there really spaces between the ">" and the character following it?

Can you be absolutely positive that every block is exactly 3 lines long?

Can you be absolutely positive that there are exactly the same number of text blocks in each file?