Question: Remove accession numbers form nexus tree files
0
gravatar for AB
16 months ago by
AB0
AB0 wrote:

Hi,

I'm relatively new to bioinformatics and am trying to work out how to remove the accession numbers from a Nexus formatted tree.

e.g.

#NEXUS
BEGIN TREES;
    TREE 1 = (CY116033b|A/swine/England/195852/1992,(((CY038004b|A/swine/En$
END;

I want to remove every accession number between the ( and | as this is causing issues with downstream programs.

I've tried sed (commands such as sed -e 's/.*\([A-Z][A-Z][0-9][0-9][0-9][0-9][0-9][0-9]\).*/\1/g' but can't seem to get it to work.

Does anyone know how to do this?

Any help would be much appreciated!

AB

nexus accession numbers • 319 views
ADD COMMENTlink modified 14 months ago by Pierre Lindenbaum121k • written 16 months ago by AB0
0
gravatar for Pierre Lindenbaum
14 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:
 sed -r  's/\([A-Za-z0-9]+\|/(/g'

?

ADD COMMENTlink written 14 months ago by Pierre Lindenbaum121k
0
gravatar for cpad0112
14 months ago by
cpad011211k
India
cpad011211k wrote:
$ echo "(CY116033b|A/swine/England/195852/1992,(((CY038004b|A/swine/En" | sed 's/(\w\+|//g' 
A/swine/England/195852/1992,((A/swine/En
ADD COMMENTlink modified 14 months ago • written 14 months ago by cpad011211k
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