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editing headers

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Top Forums Shell Programming and Scripting editing headers
# 8  
Old 08-10-2011
The above awk comment worked but only for certain cases. It didn't work if the last line characters length were less than 6.
Code:
>AGT
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCGACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCGTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGT
>BGT
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCCACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCTTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAAGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGT
>CGT
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCATTCAATGCGCTTTTAAAA
ACCTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCTCATAAG
ATCCCACCTACAATCATTTCACGTTGTCAGCGCTTTGAATTCCGAAAAATATCAGTGAAT
GATATTGTTGAGAGATTATCAACGGTCGTGACAAATGAAGGTACGCAAGTGGAAGGTGAA
GCATTACAAATTGTTGCGCGTGCTGCCGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCTATATCTTATAGTGATGAGATTGTTACGACAGAAGATGTATTGGCCGTAACA
GGA
>DGT
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAACCGCCAGGACATGTCATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATTATTTCGCGTTGCCAACGTTTCGAATTTCGAAAGATATCAGTAAAT
GATATTGTTGAGAGATTATCGACAGTTGTAAACAATGAAGGTACGCAAGTAGAAGATGAA
GCGTTACAAATCGTTGCACGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCAATATCTTATAGTGATGAGACTGTTACGACAGAAGATGTATTAGCTGTAACA
GGG

when apply this code
Code:
awk 'NR==1{$0=$0" 1"}length<6&&NR>1{$0=">"$0}1' 1.fasta

Code:
>AGT
 GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
 ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
 ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
 GATATTGTTGAGAGATTGTCGACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
 GCGTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
 GATCAGGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
 >GGT
 >BGT
 GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
 ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
 ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
 GATATTGTTGAGAGATTGTCCACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
 GCTTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
 GATCAAGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
 >GGT
 >CGT
 GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCATTCAATGCGCTTTTAAAA
 ACCTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCTCATAAG
 ATCCCACCTACAATCATTTCACGTTGTCAGCGCTTTGAATTCCGAAAAATATCAGTGAAT
 GATATTGTTGAGAGATTATCAACGGTCGTGACAAATGAAGGTACGCAAGTGGAAGGTGAA
 GCATTACAAATTGTTGCGCGTGCTGCCGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
 GATCAGGCTATATCTTATAGTGATGAGATTGTTACGACAGAAGATGTATTGGCCGTAACA
 >GGA
 >DGT
 GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
 ACGTTAGAAGAACCGCCAGGACATGTCATCTTTATTTTGGCGACAACAGAACCGCATAAG
 ATACCGCCTACAATTATTTCGCGTTGCCAACGTTTCGAATTTCGAAAGATATCAGTAAAT
 GATATTGTTGAGAGATTATCGACAGTTGTAAACAATGAAGGTACGCAAGTAGAAGATGAA
 GCGTTACAAATCGTTGCACGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
 GATCAGGCAATATCTTATAGTGATGAGACTGTTACGACAGAAGATGTATTAGCTGTAACA
 >GGG

Please let me know how to solve this problem

---------- Post updated at 01:29 PM ---------- Previous update was at 12:56 PM ----------

I would like to give one more hint. In my real case data the header begins only with either B/b or G(capital G). Beyond the header, rest of the charcters will be either A or C or T or G (all capitals)
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