Question: Linearizing Mixed Fasta
0
gravatar for PoGibas
6.2 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

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.

fasta linux • 1.4k views
ADD COMMENTlink modified 6.2 years ago by Andreas2.4k • written 6.2 years ago by PoGibas4.8k

this post was closed. Please, keep it open to redirect the future queries.

ADD REPLYlink written 6.2 years ago by Pierre Lindenbaum121k
1
gravatar for Martin A Hansen
6.2 years ago by
Martin A Hansen3.0k
Denmark
Martin A Hansen3.0k wrote:

With Biopieces www.biopieces.org):

read_fasta -i in.fna | write_tab -o out.tab -x
ADD COMMENTlink written 6.2 years ago by Martin A Hansen3.0k
1
gravatar for Andreas
6.2 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

Concatenated fasta is sometimes also called vienna format. Here's an awk script to convert it.

Andreas

ADD COMMENTlink written 6.2 years ago by Andreas2.4k
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