Hi everyone,

I have a large text file containing DNA sequences in fasta format as follows:

>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq 
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA
etc.

someseq   5   10
another seq   1   12
seq3450   3   10
etc.

>someseq 5 10
TTGAGA
>another seq
GGCATTTTTGTG
>seq3450   3   10
TTCCTGTT

 
while read a b c; do nawk -v pattern="$a" -v start="$b" -v end="$c" '$0~pattern{getline;print substr($0,start,end);exit}' largefile.txt; done < index.txt

Thanks. I don't have 'nawk' in my MAC-OSX. So replacing 'nawk' with 'awk' and with your code and the data files above I get the following output, which appears incorrect:
TTGAGATCCG
G
TTCCTGTTCA

While the rest of your problem description is to the point, a few points remain to be clarified:

Does the file really look like that (with the line breaks) or have you just broken the long lines for better readability? Because it will change a possible solution it is important how you answer this question.

Which shell are you using? What you need is, by and large, a substring-function and some shells have such a function built in, others haven't. Therefore a solution in, for instance, ksh93 (which has a substring-function) will be a lot easier and a lot faster than, say, a solution in Bourne shell or ksh88 (both of which lack such a device).

As it might happen that one of the tools used has some special feature in one OS and doesn't so in the other you might as well tell us which OS you are using.

In short: ask questions the smart way, please! How this is done you can read here in detail.

I hope this helps.

bakunin

Try...

$ head file[12]
==> file1 <==
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450
TTTTCCTGTTCACTGCTGCTTTTCTATAGACAGCA
GCAGCAAGCAGTAAGAGAAAGTA

==> file2 <==
someseq 5       10
another seq     1       12
seq3450 3       10

$ awk 'NR==FNR{if($0~/^>/){i=substr($0,2);getline};a[i]=a[i] $0;next}{print ">" $1 ORS substr(a[$1], $2, $3-$2+1)}' file1 FS=\\t file2
>someseq
TTGAGA
>another seq
GGCATTTTTGTG
>seq3450
TTCCTGTT

$