awk help!


 
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# 1  
Old 04-04-2014
awk help!

Hi,
I've two list files and two corresponding data files which looks like:

list1.txt
Quote:
a_name_1
g_name_2
x_name_3
list1.data.txt
Quote:
>a_name_1
ACGATCAGCTAATCAGCTACA
>g_name_2
ATCAGCTACGATCAGCTACA
>x_name_3
ATCAGCTAACGATCAGCTACA
Similarly:
list2.txt
Quote:
c_name_1
z_name_2
p_name_3
list2.data.txt
Quote:
>c_name_1
TGTGACGATCAGCTAATCAGCTACA
>z_name_2
GTGATCAGCTACGATCAGCTACA
>p_name_3
AAAAATCAGCTAACGATCAGCTACA
What I need is merging two list files into one list file and two data files into one data file in an Interleaving manner. Expected output would be:
merged.list.txt
Quote:
a_name_1
c_name_1
g_name_2
z_name_2
x_name_3
p_name_3
merged.data.txt
Quote:
>a_name_1
ACGATCAGCTAATCAGCTACA
>c_name_1
TGTGACGATCAGCTAATCAGCTACA
>g_name_2
ATCAGCTACGATCAGCTACA
>z_name_2
GTGATCAGCTACGATCAGCTACA
>x_name_3
ATCAGCTAACGATCAGCTACA
>p_name_3
AAAAATCAGCTAACGATCAGCTACA
Many thanks for your help.
# 2  
Old 04-04-2014
Why awk? What have you tried?
# 3  
Old 04-07-2014
awk - because in some previous example I found it simple, easy to use and re usability in other similar problems.
what I naively tried e.g. 'list.data.txt' seems working ok.
Code:
 paste <(awk '/^>/ { printf("\n%s\t",$0);next;} {printf("%s",$0);} END {printf("\n");}' list1.data.txt ) \
 <(awk '/^>/ { printf("\n%s\t",$0);next;} {printf("%s",$0);} END {printf("\n");}' list2.data.txt ) | tr "\t" "\n"

However, problem with above awk code is:
If the data is not in the same order as in the 'list.txt' file then the output will be wrong.

So I am looking for some code that will actually read 'list.txt' file and will write the data in that order.

Last edited by vbe; 04-07-2014 at 05:29 AM..
# 4  
Old 04-07-2014
So you want it sorted by the last number? Can that have more than one digit? And, if equal numbers, the order doesn't seem to matter (x_name before p_name)?
 
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