edit names in phylogenetic tree in newick format
Clash Royale CLAN TAG#URR8PPP
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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
asked 1 min ago
erick rodriguez
61
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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
asked 1 min ago
erick rodriguez
61
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.
add a comment |Â
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
asked 1 min ago
erick rodriguez
61
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
asked 1 min ago
erick rodriguez
61
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.
asked 1 min ago
erick rodriguez
61
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.
asked 1 min ago
erick rodriguez
61
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.
asked 1 min ago
erick rodriguez
61
asked 1 min ago
erick rodriguez
61
61
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.
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.
erick rodriguez is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.
add a comment |Â
add a comment |Â
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erick rodriguez is a new contributor. Be nice, and check out our Code of Conduct.
erick rodriguez is a new contributor. Be nice, and check out our Code of Conduct.
erick rodriguez is a new contributor. Be nice, and check out our Code of Conduct.
erick rodriguez is a new contributor. Be nice, and check out our Code of Conduct.
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