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Execution problem with repeat the same program with two set of same data

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# 1  
Old 10-09-2009
Execution problem with repeat the same program with two set of same data
I got a program named as "fastq_to_fasta".
I got a long list of file all named as AB1 and AB2.

My input file is :
Code:
071022_L1_AB1.fq
012121_L1_AB1.fq
021213_L1_AB1.fq
012153_L1_AB1.fq
071022_L1_AB2.fq
012121_L1_AB2.fq
021213_L1_AB2.fq
012153_L1_AB2.fq
.
.
.
.
.
.

My desired output is write a work script or a text file look like this:
Code:
fastq_to_fasta 071022_L1_AB1.fq 071022_L1_AB2.fq
fastq_to_fasta 012121_L1_AB1.fq 012121_L1_AB2.fq
fastq_to_fasta 021213_L1_AB1.fq 021213_L1_AB2.fq
fastq_to_fasta 012153_L1_AB1.fq 012153_L1_AB2.fq
.
.
.
.
.
.

Actually all the long list of file need to do the same program like:
Code:
fastq_to_fasta <XXXXAB1.fq> <XXXXAB2.fq>
Same XXXXAB1 must work with same XXXXAB2

Does anybody know by using awk command or any other programming language can easy for me to get my desired output result.

Thanks a lot.
Last edited by Franklin52; 10-09-2009 at 08:18 AM.. Reason: Please use code tags!
# 2  
Old 10-09-2009
Something like this?

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

# 3  
Old 10-09-2009
Hi Franklin52
I try your code just now.
Unfortunately, It can't work Smilie
Do you have any other idea?
Actually I just want to produce a long list of below (based on same XXX_AB1 with XXX_AB2):
Code:
fastq_to_fasta 071022_L1_AB1.fq 071022_L1_AB2.fq
fastq_to_fasta 012121_L1_AB1.fq 012121_L1_AB2.fq
fastq_to_fasta 021213_L1_AB1.fq 021213_L1_AB2.fq
fastq_to_fasta 012153_L1_AB1.fq 012153_L1_AB2.fq
.
.
.

.
.
.

Thanks a lot for your help.
Last edited by Franklin52; 10-09-2009 at 08:58 AM.. Reason: Use code tags please!!!!!!
# 4  
Old 10-09-2009
Quote:
Originally Posted by patrick87
Hi Franklin52
I try your code just now.
Unfortunately, It can't work Smilie
Do you have any other idea?
Your comment doesn't make any sense, I can't guess what's wrong.

This is my output with your input file:

Code:
$ cat file
071022_L1_AB1.fq
012121_L1_AB1.fq
021213_L1_AB1.fq
012153_L1_AB1.fq
071022_L1_AB2.fq
012121_L1_AB2.fq
021213_L1_AB2.fq
012153_L1_AB2.fq
$ awk -F_ 'a[$1]{print "fastq_to_fasta "a[$1]" "$0; next} {a[$1]=$0}' file
fastq_to_fasta 071022_L1_AB1.fq 071022_L1_AB2.fq
fastq_to_fasta 012121_L1_AB1.fq 012121_L1_AB2.fq
fastq_to_fasta 021213_L1_AB1.fq 021213_L1_AB2.fq
fastq_to_fasta 012153_L1_AB1.fq 012153_L1_AB2.fq
$

# 5  
Old 10-09-2009
Thanks a lot Frankin52 Smilie
I think I understand what you mean now.
Maybe I type some error and let you misunderstanding it.
Actually all the *_AB1.fq and *_AB2.fq all are long list of "file" not the list of "contents" in a file.
But it should be not a problem.
I just do
[code]
ls *.fq > file
cat file
awk -F_ 'a[$1]{print "fastq_to_fasta "a[$1]" "$0; next} {a[$1]=$0}' file
[code]

I believe it should be work nice.
Thanks a lot and again, Frankin52 Smilie
Code:
$ cat file
071022_L1_AB1.fq
012121_L1_AB1.fq
021213_L1_AB1.fq
012153_L1_AB1.fq
071022_L1_AB2.fq
012121_L1_AB2.fq
021213_L1_AB2.fq
012153_L1_AB2.fq
$ awk -F_ 'a[$1]{print "fastq_to_fasta "a[$1]" "$0; next} {a[$1]=$0}' file
fastq_to_fasta 071022_L1_AB1.fq 071022_L1_AB2.fq
fastq_to_fasta 012121_L1_AB1.fq 012121_L1_AB2.fq
fastq_to_fasta 021213_L1_AB1.fq 021213_L1_AB2.fq
fastq_to_fasta 012153_L1_AB1.fq 012153_L1_AB2.fq
$

[/quote]

---------- Post updated at 08:33 PM ---------- Previous update was at 07:35 PM ----------

Thanks again Franklin52.
Your suggestion code look cool Smilie
I will go and find out the reason why you write this code.
Thus able to edit it next time to solve another similar problem.
In between, can I roughly know the explanation of your code written?
Sorry if bring you any inconvenience.
Quote:
Originally Posted by Franklin52
Code:

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

Your code is fantastic and work fastSmilie
# 6  
Old 10-10-2009
Code:
awk -F_ 'a[$1]{print "fastq_to_fasta "a[$1]" "$0; next} {a[$1]=$0}' file

Explanation:

Code:
awk -F_

Change the default field separator

Code:
a[$1]{print "fastq_to_fasta "a[$1]" "$0; next}

If element a[$1] of array a has a value, print a[$1], a space and the current line. Read the next line

Code:
{a[$1]=$0}

a[$1] is empty on this line. Here the element is filled with the value of the current line
# 7  
Old 10-10-2009
Thanks a lot for your explanation, Franklin52Smilie
I feel more comfortable and understanding about the reason of your code now.
I really appreciate for your explanation.
Thanks again Smilie
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