How to use --stream with hybrid-min ?

2 replies [Last post]
Axel
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Joined: 03/24/2013

Hello Everybody,

I'm new to UNAFold and have a simple question how to use the --stream option with hybrid-min. How do I pipe the two required input files into hybrid-min ?
With hybrid-ss-min it is clear, because it only needs one input file (cat A.seq | hybrid-ss-min --stream), but how can I do it with hybrid-min ?

Many thanks,
Axel

zukerm
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Joined: 11/12/2010
--stream option in hybrid-min

Suppose I have two sequences, A and B. A is CCCCCCCC and B is GGGGGGGG and I want to run hybrid-min with the stream option. The trick is to add a semi-colon to the end of the first sequence (or to both). The semi-colon is the sequence separator. Let's run with default options (RNA at 37 °C).

    Options
  1. echo "CCCCCCCC; GGGGGGGG" | hybrid-min --stream
  2. Place both sequences into a single file, say AB.seq, making sure that they are separated by a semi-colon. Then run
    hybrid-min --stream < AB.seq
pascal
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Joined: 12/17/2016
I also would be interested in

I also would be interested in how to use the stream option. Any suggestions?