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Replace lines of two files by the corresponding line numbers.

 
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# 1  
Old 10-07-2013
Replace lines of two files by the corresponding line numbers.
I want to replace lines. The files 1 are (separated by \t)
Code:
Gm01    phytozome9_0    three_prime_UTR 70641   70759   .       -       .       ID=PAC:26323927.three_prime_UTR.1;Parent=PAC:26323927;pacid=26323927
Gm01    phytozome9_0    three_prime_UTR 90230   90692   .       -       .       ID=PAC:26324253.three_prime_UTR.1;Parent=PAC:26324253;pacid=26324253

Files 2 are
Code:
>?_Gm01_70641_70759_-
GTTAGATGAGCTGGAAAGTGTTTCCATTCTGTCAATGACCCTTGCATGGG
ATGAATTTTCCTTCTCTACTTTTCAAGAAGCCCATTATTCGCTTCAAGTT
TCTCTAGACCAGGTGCCTG
>?_Gm01_70206_70267_-
TGTTCATGCTGCCTCTGTAATGGAGCAGGTTAAAGAGTTCCATTAGAAGA
GATGGTTTTGAG


I want output
Code:
>?_Gm01_pacid=26323927
GTTAGATGAGCTGGAAAGTGTTTCCATTCTGTCAATGACCCTTGCATGGG
ATGAATTTTCCTTCTCTACTTTTCAAGAAGCCCATTATTCGCTTCAAGTT
TCTCTAGACCAGGTGCCTG
>?_Gm01_pacid=26324253
TGTTCATGCTGCCTCTGTAATGGAGCAGGTTAAAGAGTTCCATTAGAAGA
GATGGTTTTGAG


Because the file 2 are generated from 1, so the sequence are the same. The first sequence in file 2 is from the first line in file 1, correspondingly.

Thank you.
Moderator's Comments:
Mod Comment Moderators have added CODE tags to several of your previous posts; and you have shown that you know how to do so. Please use CODE tags for all sample input, output, and code samples.
Last edited by Don Cragun; 10-07-2013 at 08:44 PM.. Reason: Add code tags.
# 2  
Old 10-07-2013
If your samples are representative of your actual input files, the following seems to do what you requested:
Code:
awk -F ';' '
FNR == NR {
        p[FNR] = $NF
        next
}       
/^>/ {  printf(">?_Gm01_%s\n", p[++oc])
        next
}       
1' "Files 1" "Files 2"

I strongly suggest that you tell whoever is producing your input files that there will be fewer mistakes made if data file with names that DO NOT contain space characters are used.

If you want to try this on a Solaris/SunOS system, use /usr/xpg4/bin/awk, /usr/xpg6/bin/awk, or nawk rather than /bin/awk or /usr/bin/awk.
 
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