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I would like to share with you the sequence of how perl extracts genes from the evolutionary tree. I believe most people don't know much about it, so share this article for your reference. I hope you can learn a lot after reading this article. Let's learn about it together.

The sequence of genes extracted from the evolutionary tree

There is a sequence of genes in the evolutionary tree, and sometimes we need to use this gene list. If we do it manually, it will be troublesome. Is there any quick way?

In fact, there is a sequence of genes in the nwk file of the evolutionary tree:

(chicken, (mouse,rat), (chimp,human)

We can find that the order of the branches in the figure is the order in the nwk file, so we only need to extract this order. Here I wrote a script, as follows:

Usage:

Perl nwk_geneid.pl-I in.nwk-o out.txt

In.nwk is the input nwk file, and out.txt is the exported gene ID file.

Script code

Use Getopt::Long;use strict;my% opts;GetOptions (\% opts, "iShares", "oforms", "h"); open (IN, "$opts {I}") | | die "open $opts {I} failed\ n"; open (OUT, "> $opts {o}") | | die "open $opts {o} failed\ n"; while () {chomp;my $str = $_; $str = ~ s /\ d\.\ dhoptThere is GTHR = ~ s /\ (/ / Gintintstr = ~ s /\) / g $str = ~ s print OUT join perl GMT * I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!

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