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editing headers

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# 1  
Old 07-21-2011
editing headers
Hi,
I have a folder that contains many (multiple) files

1.fasta
2.fasta
3.fasta
4.fasta
5.fasta
.
.
100's of files

Each such file have data in the following format
for example:
vi 1.fasta

Code:
  58    390
A
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCGACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCGTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
B
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCCACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCTTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAAGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
C
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCATTCAATGCGCTTTTAAAA
ACCTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCTCATAAG
ATCCCACCTACAATCATTTCACGTTGTCAGCGCTTTGAATTCCGAAAAATATCAGTGAAT
GATATTGTTGAGAGATTATCAACGGTCGTGACAAATGAAGGTACGCAAGTGGAAGGTGAA
GCATTACAAATTGTTGCGCGTGCTGCCGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCTATATCTTATAGTGATGAGATTGTTACGACAGAAGATGTATTGGCCGTAACA
GGACGTGATATGTTCCGTAAGTTGAGTGAA
D
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAACCGCCAGGACATGTCATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATTATTTCGCGTTGCCAACGTTTCGAATTTCGAAAGATATCAGTAAAT
GATATTGTTGAGAGATTATCGACAGTTGTAAACAATGAAGGTACGCAAGTAGAAGATGAA
GCGTTACAAATCGTTGCACGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCAATATCTTATAGTGATGAGACTGTTACGACAGAAGATGTATTAGCTGTAACA
GGGCGTGATATGTTCCGAATGTTAAGTGAA

I need to edit the above files by adding two separate things into each of the file.
1. add 1 (number one) on the first line of each file ( 58 390 1).
2. add > inthe beginning of each of the headers ( >A >B >C >D.
Basically edit the above file and get the output as below:

Code:
  58    390 1
>A
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCGACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCGTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
>B
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCCACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCTTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAAGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
>C
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCATTCAATGCGCTTTTAAAA
ACCTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCTCATAAG
ATCCCACCTACAATCATTTCACGTTGTCAGCGCTTTGAATTCCGAAAAATATCAGTGAAT
GATATTGTTGAGAGATTATCAACGGTCGTGACAAATGAAGGTACGCAAGTGGAAGGTGAA
GCATTACAAATTGTTGCGCGTGCTGCCGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCTATATCTTATAGTGATGAGATTGTTACGACAGAAGATGTATTGGCCGTAACA
GGACGTGATATGTTCCGTAAGTTGAGTGAA
>D
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAACCGCCAGGACATGTCATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATTATTTCGCGTTGCCAACGTTTCGAATTTCGAAAGATATCAGTAAAT
GATATTGTTGAGAGATTATCGACAGTTGTAAACAATGAAGGTACGCAAGTAGAAGATGAA
GCGTTACAAATCGTTGCACGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCAATATCTTATAGTGATGAGACTGTTACGACAGAAGATGTATTAGCTGTAACA
GGGCGTGATATGTTCCGAATGTTAAGTGAA

Please let me know the best way to do this either using awk or sed.
LA
# 2  
Old 07-21-2011
Try:
Code:
awk 'NR==1{$0=$0" 1"}length==1{$0=">"$0}1' 1.fasta

# 3  
Old 07-21-2011
The first part worked (adding 1 in the first line) but the second part didn't work (adding > before the header)

---------- Post updated at 04:53 PM ---------- Previous update was at 04:51 PM ----------

also the headers not always have single letters. There are headers with more than 2 letters.
# 4  
Old 07-21-2011
Post examples of those headers.
# 5  
Old 07-21-2011
ADC8_
BC
ACR4
TYUI
# 6  
Old 07-21-2011
So they are always less than 6 characters? If so, then this might work:
Code:
awk 'NR==1{$0=$0" 1"}length<6&&NR>1{$0=">"$0}1' 1.fasta

# 7  
Old 07-22-2011
With the help od sed:

$ sed -e 's/58 390/58 390 1/' -e 's/^\(.\)$/\>&/' <filename>

58 390 1
>A
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCGACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCGTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
>B
GTATACATTATTGATGAAGTCCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATCATTTCGCGTTGCCAACGTTTCGAATTTCGAAAAATATCAGTAAAT
GATATTGTTGAGAGATTGTCCACGGTTGTGACTAATGAAGGTACGCAAGTAGAAGATGAG
GCTTTACAAATTGTTGCGCGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAAGCGATATCTTATAGTGATGAGAGGGTTACGACAGAAGATGTATTAGCTGTAACG
GGTCGTGATATGTTCCGTATGTTAAGTGAA
>C
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCATTCAATGCGCTTTTAAAA
ACCTTAGAAGAGCCGCCAGGACATGTTATCTTTATTTTGGCGACAACAGAACCTCATAAG
ATCCCACCTACAATCATTTCACGTTGTCAGCGCTTTGAATTCCGAAAAATATCAGTGAAT
GATATTGTTGAGAGATTATCAACGGTCGTGACAAATGAAGGTACGCAAGTGGAAGGTGAA
GCATTACAAATTGTTGCGCGTGCTGCCGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCTATATCTTATAGTGATGAGATTGTTACGACAGAAGATGTATTGGCCGTAACA
GGACGTGATATGTTCCGTAAGTTGAGTGAA
>D
GTATACATTATTGATGAAGTTCACATGCTTTCTATGGGTGCCTTCAATGCGCTTTTAAAA
ACGTTAGAAGAACCGCCAGGACATGTCATCTTTATTTTGGCGACAACAGAACCGCATAAG
ATACCGCCTACAATTATTTCGCGTTGCCAACGTTTCGAATTTCGAAAGATATCAGTAAAT
GATATTGTTGAGAGATTATCGACAGTTGTAAACAATGAAGGTACGCAAGTAGAAGATGAA
GCGTTACAAATCGTTGCACGTGCCGCTGAAGGTGGTATGCGTGATGCGCTTAGTCTTATT
GATCAGGCAATATCTTATAGTGATGAGACTGTTACGACAGAAGATGTATTAGCTGTAACA
GGGCGTGATATGTTCCGAATGTTAAGTGAA
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