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Inserting a variable in awk script

 
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Old 02-19-2016
Inserting a variable in awk script
I have file input.txt:
Code:
>TX1-1 Freq 55
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-2 Freq 19
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-3 Freq 17
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-4 Freq 6
cattctgatgaatatttgtcctttagttgttatttgt
>TX1-5 Freq 6
cattctgatgaatatttgtcctttagttgttatttgt

And I am using the following ChangeID script to modify the ID (>XXXXX)
Code:
#!/bin/bash
if [ -f $1 ]
then
	file=$1
fi
pattern=$2
awk 'FNR==1{n=$pattern} /^>/ {print ">" n "-" ++c, $3;next}1' $file > New$file

So, when I enter ChangeID Input.txt Pat3, I am expecting to use the second field (Pat 3) to replace the beginning of the ID (>Pat3-XXX). Thus, the desire output file would look like this:
Code:
>Pat3-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Pat-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Pat3-5 6
cattctgatgaatatttgtcctttagttgttatttgt

But that did not work obviously. I have tried changing the AWK part of my script to
Code:
awk 'FNR==1{n=$2} /^>/ {print ">" n "-" ++c, $3;next}1' $file > New$file

But the script, of course, uses the second field on the row (Freq), outputting the following file:
Code:
>Freq-1 55
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-2 19
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-3 17
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-4 6
cattctgatgaatatttgtcctttagttgttatttgt
>Freq-5 6
cattctgatgaatatttgtcctttagttgttatttgt

Any help will be greatly appreciated
 
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