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Replace names in a file

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# 1  
Old 10-01-2013
Replace names in a file
Hi, I have a file like this:
Code:
>Contig1
TTTTCATCAGCAATAGGTGCCTTCAACAAGTTTGAGAATTTTTTACACATGACTACAGGG
CACGTGCACAATGTTTTGAGCACTGCCAATGTCGTCTTTTCTTCCCTGCTGATTCTATTT
AGCTAGATTCACTTTGTTTCCAAAAAACGACAACAAATTCCAAGGTGTACCAAGGTGTAT
>Contig2
CCCGTAGTAAAGATCAAAACTATCCCCTGCTGTATTCTCAACCAAATCCAACAAACTCTC
GTACCCTTTTGTATTGATTGGCGTAGACTCCAATTTCAACGTCTCCAACACTCTCCCAAC
AGTATGTGTAATAAACTGTGATCCTGCTGCATACTTATCTTGGTCTTGACAACTCATTTC
CAACATTTTACATCCCTCTCTAGCAAAAATATCAAGAAATCTTTTACACCTATCAATTCT
TGATTTCTCTTTGCCAATTCTAACATTCTCATACACAAATTGGAGATCATCCCATCCAAG
ATTGGCACTTTGAGGAC
....
>Contig34172
AAAAATTTTGAATTTTCATTTATTTAAGTAAAGCTGTGTCAAATAGTTAATATCTTGACA
CCTTCAATATATAATTAATCCAAGATATAAGATTAAAGAAATTACAAGAACGCTGAAAAT
TTGGTGGATATAACAATGACCAAATATTATTTAAGGTAACCACTGCTCTTTCTTGAAAAA
GCAGCCTCCATTTTCATAGGATTTCTTGAGGAAACGCCGTCTCTCTGGAATTGCATTGCA
GACGACAGCATTTCCATTTTCAACATTGAAACCCAT
>contig00002  length=24  numreads=36  gene=isogroup00001  status=it_thresh
TGTATACCTTCCTAAAGGCCTCAA
>contig00004  length=30  numreads=51  gene=isogroup00001  status=it_thresh
TATTGTGTATCCAAATGATGCTTATGATGA
>contig00013  length=37  numreads=25  gene=isogroup00001  status=it_thresh
TGAAGCTCTCTGCCTGTTTTGCAAGCATGCCTTCAAG
.....

How could i replace the name from ">contig00002 length=24 numreads=36 gene=isogroup00001 status=it_thresh" to ">Contig34173". Same for the later "contigs"....

Thanks,
Vivi
# 2  
Old 10-01-2013
For the sample you provided, this should work:
Code:
awk '/^>Contig/ {i=$1; sub (/>Contig/,"", i)} /^>contig/ {print ">CONTIG"++i; next} 1' file

# 3  
Old 10-01-2013
Rudic, Thanks!!!

If i want to replace
Code:
contig00002 length=24 ...

to
Code:
contig00002_newbler

,
Code:
contig00004 length=30 ...

to
Code:
contig00004_newbler

, and so on.

What should i do??
# 4  
Old 10-02-2013
Change
Code:
/^>contig/ {print ">CONTIG"++i; next}

to
Code:
/^contig/ {$1=$1"_newbler"}

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