PB Rename ids

--rename_ids, -ri

Description

Replace some regex pattern in taxa IDs and node labels with some other string.

Arguments

Regular expression ( str )

If there are any special characters in the expression, ensure the string is enclosed in quotes.

Substitution ( str )

The matched regular expression will be replaced by this text. If you want to retain part of the regex match, use the '(...)' syntax, and then include escaped indices (e.g., '\1', '\2') in the substitution string (see example 2 below).

Examples

Input file: Mle_Panx.nwk

(('Mle-Panxα12':0.24785,(('Mle-Panxα7A':0.51324,('Mle-Panxα2':0.5425,('Mle-Panxα6':0.31957,('Mle-Panxα1':0.62588,'Mle-Panxα5':0.48557)0.450:0.04238)0.652:0.02277)0.938:0.06567)0.867:0.04265,('Mle-Panxα4':0.50524,'Mle-Panxα8':0.33085)0.913:0.07789)0.924:0.05363)0.910:0.0533,('Mle-Panxα9':0.00394,('Mle-Panxα10B':0.00144,'Mle-Panxα10A':0.01578)1.000:0.05152)1.000:0.30415,('Mle-Panxα11':0.27774,'Mle-Panxα3':0.39731)0.922:0.05673);

Input tree

         /---------------------------------------------------------- Mle-Panxα12
         |
         |                   /-------------------------------------- Mle-Panxα7A
         |         /---------+
/--------+         |         |        /----------------------------- Mle-Panxα2
|        |         |         \--------+
|        |         |                  |         /------------------- Mle-Panxα6
|        |         |                  \---------+
|        \---------+                            |         /--------- Mle-Panxα1
|                  |                            \---------+
|                  |                                      \--------- Mle-Panxα5
|                  |
|                  |                                      /--------- Mle-Panxα4
+                  \--------------------------------------+
|                                                         \--------- Mle-Panxα8
|
|                                               /------------------- Mle-Panxα9
|-----------------------------------------------+
|                                               |         /--------- Mle-Panxα10B
|                                               \---------+
|                                                         \--------- Mle-Panxα10A
|
|                                                         /--------- Mle-Panxα11
\---------------------------------------------------------+
                                                          \--------- Mle-Panxα3

Usage example 1

$: pb Mle_Panx.nwk -ri 'α' 'A'

Output

(('Mle-PanxA12':0.24785,(('Mle-PanxA7A':0.51324,('Mle-PanxA2':0.5425,('Mle-PanxA6':0.31957,('Mle-PanxA1':0.62588,'Mle-PanxA5':0.48557)0.450:0.04238)0.652:0.02277)0.938:0.06567)0.867:0.04265,('Mle-PanxA4':0.50524,'Mle-PanxA8':0.33085)0.913:0.07789)0.924:0.05363)0.910:0.0533,('Mle-PanxA9':0.00394,('Mle-PanxA10B':0.00144,'Mle-PanxA10A':0.01578)1.000:0.05152)1.000:0.30415,('Mle-PanxA11':0.27774,'Mle-PanxA3':0.39731)0.922:0.05673);

Output tree

         /---------------------------------------------------------- Mle-PanxA12
         |
         |                   /-------------------------------------- Mle-PanxA7A
         |         /---------+
/--------+         |         |        /----------------------------- Mle-PanxA2
|        |         |         \--------+
|        |         |                  |         /------------------- Mle-PanxA6
|        |         |                  \---------+
|        \---------+                            |         /--------- Mle-PanxA1
|                  |                            \---------+
|                  |                                      \--------- Mle-PanxA5
|                  |
|                  |                                      /--------- Mle-PanxA4
+                  \--------------------------------------+
|                                                         \--------- Mle-PanxA8
|
|                                               /------------------- Mle-PanxA9
|-----------------------------------------------+
|                                               |         /--------- Mle-PanxA10B
|                                               \---------+
|                                                         \--------- Mle-PanxA10A
|
|                                                         /--------- Mle-PanxA11
\---------------------------------------------------------+
                                                          \--------- Mle-PanxA3

Usage example 2 (note that part of the match is retained)

$: pb Mle_Panx.nwk -ri 'α([3-9])' 'A\1'

Output

(('Mle-Panxα12':0.24785,(('Mle-PanxA7A':0.51324,('Mle-Panxα2':0.5425,('Mle-PanxA6':0.31957,('Mle-Panxα1':0.62588,'Mle-PanxA5':0.48557)0.450:0.04238)0.652:0.02277)0.938:0.06567)0.867:0.04265,('Mle-PanxA4':0.50524,'Mle-PanxA8':0.33085)0.913:0.07789)0.924:0.05363)0.910:0.0533,('Mle-PanxA9':0.00394,('Mle-Panxα10B':0.00144,'Mle-Panxα10A':0.01578)1.000:0.05152)1.000:0.30415,('Mle-Panxα11':0.27774,'Mle-PanxA3':0.39731)0.922:0.05673);

Output tree

         /---------------------------------------------------------- Mle-Panxα12
         |
         |                   /-------------------------------------- Mle-PanxA7A
         |         /---------+
/--------+         |         |        /----------------------------- Mle-Panxα2
|        |         |         \--------+
|        |         |                  |         /------------------- Mle-PanxA6
|        |         |                  \---------+
|        \---------+                            |         /--------- Mle-Panxα1
|                  |                            \---------+
|                  |                                      \--------- Mle-PanxA5
|                  |
|                  |                                      /--------- Mle-PanxA4
+                  \--------------------------------------+
|                                                         \--------- Mle-PanxA8
|
|                                               /------------------- Mle-PanxA9
|-----------------------------------------------+
|                                               |         /--------- Mle-Panxα10B
|                                               \---------+
|                                                         \--------- Mle-Panxα10A
|
|                                                         /--------- Mle-Panxα11
\---------------------------------------------------------+
                                                          \--------- Mle-PanxA3