Linearizing Mixed Fasta
How can I linearize mixed fasta?
>Seq1
ACGT
>Seq2
CGTAGT
>Seq3
CGTAGTCGTAGT
CTA
>Seq4
ATGC
It should look something like this:
sed '/^G\|A\|C\|T/s/\n//g'
But it's not working and I don't know how to command sed not to substitute one line sequnces.
2 answers
With Biopieces:
read_fasta -i in.fna | write_tab -o out.tab -x
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Ram
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written
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Martin A Hansen
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written
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Martin A Hansen
Concatenated fasta is sometimes also called vienna format. Here's an awk script to convert it.
Andreas
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