edit names in phylogenetic tree in newick format

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I have a phylogenetic tree in newick format, and I would like to remove some fragments of the name of the taxa, 



1_[genus_specie_1]_characters:0.2654682758,(((((((((((((((2_[genus_specie_2]_characters:0.0379334280,54_[genus_specie_2]_characters:0.0605802067)/1/100:0.0121248674,(3_[genus_specie_3]_characters:0.0206432295,4_[genus_specie_4]_characters:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,30_[genus_specie_5]_characters


I would like to remove the fragments out of the square brackets, for example



genus_specie_1:0.2654682758,(((((((((((((((genus_specie_2:0.0379334280,genus_specie_2:0.0605802067)/1/100:0.0121248674,(genus_specie_3:0.0206432295,genus_specie_4:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,genus_specie_5
perl -i -pe 'y///d' file.nwk



and I have also tried whit the next sed command 



sed 's/[[:alnum:]_]*[([[:alnum:]_]*)][[:alnum:]_]*/1/g'


but it doesn't work






linux shell sed perl






share







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    up vote
    0
    down vote

    favorite












    I have a phylogenetic tree in newick format, and I would like to remove some fragments of the name of the taxa, 



    1_[genus_specie_1]_characters:0.2654682758,(((((((((((((((2_[genus_specie_2]_characters:0.0379334280,54_[genus_specie_2]_characters:0.0605802067)/1/100:0.0121248674,(3_[genus_specie_3]_characters:0.0206432295,4_[genus_specie_4]_characters:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,30_[genus_specie_5]_characters


    I would like to remove the fragments out of the square brackets, for example



    genus_specie_1:0.2654682758,(((((((((((((((genus_specie_2:0.0379334280,genus_specie_2:0.0605802067)/1/100:0.0121248674,(genus_specie_3:0.0206432295,genus_specie_4:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,genus_specie_5
    perl -i -pe 'y///d' file.nwk



    and I have also tried whit the next sed command 



    sed 's/[[:alnum:]_]*[([[:alnum:]_]*)][[:alnum:]_]*/1/g'


    but it doesn't work






    linux shell sed perl






    share







    New contributor




    erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
    Check out our Code of Conduct.





















      up vote
      0
      down vote

      favorite









      up vote
      0
      down vote

      favorite











      I have a phylogenetic tree in newick format, and I would like to remove some fragments of the name of the taxa, 



      1_[genus_specie_1]_characters:0.2654682758,(((((((((((((((2_[genus_specie_2]_characters:0.0379334280,54_[genus_specie_2]_characters:0.0605802067)/1/100:0.0121248674,(3_[genus_specie_3]_characters:0.0206432295,4_[genus_specie_4]_characters:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,30_[genus_specie_5]_characters


      I would like to remove the fragments out of the square brackets, for example



      genus_specie_1:0.2654682758,(((((((((((((((genus_specie_2:0.0379334280,genus_specie_2:0.0605802067)/1/100:0.0121248674,(genus_specie_3:0.0206432295,genus_specie_4:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,genus_specie_5
      perl -i -pe 'y///d' file.nwk



      and I have also tried whit the next sed command 



      sed 's/[[:alnum:]_]*[([[:alnum:]_]*)][[:alnum:]_]*/1/g'


      but it doesn't work






      linux shell sed perl






      share







      New contributor




      erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.











      I have a phylogenetic tree in newick format, and I would like to remove some fragments of the name of the taxa, 



      1_[genus_specie_1]_characters:0.2654682758,(((((((((((((((2_[genus_specie_2]_characters:0.0379334280,54_[genus_specie_2]_characters:0.0605802067)/1/100:0.0121248674,(3_[genus_specie_3]_characters:0.0206432295,4_[genus_specie_4]_characters:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,30_[genus_specie_5]_characters


      I would like to remove the fragments out of the square brackets, for example



      genus_specie_1:0.2654682758,(((((((((((((((genus_specie_2:0.0379334280,genus_specie_2:0.0605802067)/1/100:0.0121248674,(genus_specie_3:0.0206432295,genus_specie_4:0.0141250479)/1/100:0.0647820408)/1/100:0.0235327264,genus_specie_5
      perl -i -pe 'y///d' file.nwk



      and I have also tried whit the next sed command 



      sed 's/[[:alnum:]_]*[([[:alnum:]_]*)][[:alnum:]_]*/1/g'


      but it doesn't work






      linux shell sed perl




      linux shell sed perl





      share







      New contributor




      erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.










      share







      New contributor




      erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.








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      erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.









      asked 1 min ago









      erick rodriguez

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      erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
      Check out our Code of Conduct.






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      Check out our Code of Conduct.

























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