Shell Programming and Scripting

Hi, Franklin52.
The code that you suggestion:

Code:

awk -F_ 'a[$1]{print "fastq_to_fasta "a[$1]" "$0; next} {a[$1]=$0}' file

[/quote]
It facing a problem if my input is look the following:
01234_ABC_L1_CDE_PE1.fq
01234_ABC_L1_CDE_PE2.fq
01234_ABC_L2_CDE_PE1.fq
01234_ABC_L2_CDE_PE2.fq
01234_ABC_L3_CDE_PE1.fq
01234_ABC_L3_CDE_PE2.fq
05512_ABC_L1_CDE_PE1.fq
05512_ABC_L1_CDE_PE2.fq
05512_ABC_L2_CDE_PE1.fq
05512_ABC_L2_CDE_PE2.fq
05512_ABC_L3_CDE_PE1.fq
05512_ABC_L3_CDE_PE2.fq

The code can't give the desired output like:
fastq_to_fasta 01234_ABC_L1_CDE_PE1.fq 01234_ABC_L1_CDE_PE2.fq
fastq_to_fasta 01234_ABC_L2_CDE_PE1.fq 01234_ABC_L2_CDE_PE2.fq
fastq_to_fasta 01234_ABC_L3_CDE_PE1.fq 01234_ABC_L3_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L1_CDE_PE1.fq 01234_ABC_L1_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L2_CDE_PE1.fq 01234_ABC_L2_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L3_CDE_PE1.fq 01234_ABC_L3_CDE_PE2.fq

Unfortunately, the code give me another result
Franklin52, do you have any better idea to get my desired output result?
Actually I got try a way like this:

Code:

awk '/PE1/{print $_}' file_name > file_name.txt
awk '/PE2/{print $_}' file_name > file_name2.txt
paste -d ' ' file_name.txt file_name2.txt > file_name.output.txt

At last, I vi and add the "fastq_to_fasta" inside file_name.output.txt one line by one line
It seem like quite troublesome and wasting time
I think it should got faster way. Just I still can't get it
Franklin52, thanks again for your help and sorry if bring you any inconvenience.

Code:

awk '{a = $0; getline; print "fastq_to_fasta " a " " $0}' file

That's what you want ?

Code:

# cat file
01234_ABC_L1_CDE_PE1.fq
01234_ABC_L1_CDE_PE2.fq
01234_ABC_L2_CDE_PE1.fq
01234_ABC_L2_CDE_PE2.fq
01234_ABC_L3_CDE_PE1.fq
01234_ABC_L3_CDE_PE2.fq
05512_ABC_L1_CDE_PE1.fq
05512_ABC_L1_CDE_PE2.fq
05512_ABC_L2_CDE_PE1.fq
05512_ABC_L2_CDE_PE2.fq
05512_ABC_L3_CDE_PE1.fq
05512_ABC_L3_CDE_PE2.fq
# awk 'NR%2{printf "fastq_to_fasta" FS $0 FS;next}1' file
fastq_to_fasta 01234_ABC_L1_CDE_PE1.fq 01234_ABC_L1_CDE_PE2.fq
fastq_to_fasta 01234_ABC_L2_CDE_PE1.fq 01234_ABC_L2_CDE_PE2.fq
fastq_to_fasta 01234_ABC_L3_CDE_PE1.fq 01234_ABC_L3_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L1_CDE_PE1.fq 05512_ABC_L1_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L2_CDE_PE1.fq 05512_ABC_L2_CDE_PE2.fq
fastq_to_fasta 05512_ABC_L3_CDE_PE1.fq 05512_ABC_L3_CDE_PE2.fq

thanks a lot, danmero
Your code work excellent and solve my trouble nice.
Can you roughly explain the reason of your code?
Thanks again.