Biotools is an integrated toolset for bioinformatics. It contains tools for formatting data, performing statistical analyses on bioinformatics data, handling phylogenetic trees, and more.
- Motivation
When manipulating a large phylogenetic tree, for example, one with thousands of leaf nodes, analyzing the relationships of each node becomes challenging when using GUI tools. Drawing this tree on printable paper is also problematic, as it may not be clear when printed on an A4-sized paper. Therefore, I developed these tools to address these issues.
-
phytree_setroot
For a tree(stored in newick format), which not set outgroup, and need to chose a node as outgruop node and root this tree. This tool is used doing this job, just give the tree file and name of outgroup node, the tool will output a tree file which is rooted. -
phytree_show
This tool is used to show tree, and to have quick look of tree and save the figure in pdf format file. -
phytree_statistic
Show tree information, for example leaf which have longest branch, the average branch length of leaf. those information is usful when clustering or collapse the tree. -
phytree_cluster
As showed in above figure, the tree node would be clustered into groups, and print the clusting result into file. Then those cluser can be used for downstream analysis. -
phytree_collapse
Same as phytree_cluster tool, and collapse node within a cluster into a new node(We called it a circle node), and generage a profile tree, which represent the circle node tree.
- python3 >= 3.7
- biobrary
-
Install requirements.
pip installl biobrary --user -
Install biotools
git clone https://github.com/benjaminfang/biotools
cd biobrary
./biobrary -hoptional: you can link biobrary to you PATH environment, in oreder to run this command without path prefix.
biotools -h
Tools for bioinformatics.
The flowing tools/subcommand was supported:
* format_fasta_head
* format_table_separater
* extra_table_raws
* statistic_assembly
* statistic_phytree
* find_updown_elements
* phytree_setroot
* phytree_show
* phytree_statistic
* phytree_cluster
* phytree_collapse
usage: biotools [-h] [-V] cmd_name [cmd_args [cmd_args ...]]
positional arguments:
cmd_name subcommand name.
cmd_args subcommand arguments.
optional arguments:
-h, --help show this help message and exit
-V, --version show program's version number and exit
usage: phytree_setroot [-h] [-TF TREE_FORMAT] [-OG OUT_GROUP] [-o OUT_FILE]
nwkfile
set root of tree.
positional arguments:
nwkfile tree file name in newick format.
optional arguments:
-h, --help show this help message and exit
-TF TREE_FORMAT, --tree_format TREE_FORMAT
newick tree format. default is 0.
-OG OUT_GROUP, --out_group OUT_GROUP
name of outgroup.
-o OUT_FILE, --out_file OUT_FILE
file name of output.
biotools phytree_show -h
usage: phytree_show [-h] [-TM {c,r}] [-SBL] [-SLN] [-SBP] [-SIN] [-AL] [-HI]
[-SP]
nwkfile
show phylogeneitc tree.
positional arguments:
nwkfile tree file name in newik format.
optional arguments:
-h, --help show this help message and exit
-TM {c,r}, --tree_mode {c,r}
tree style mode.
-SBL, --show_branch_length
show branch length
-SLN, --show_leaf_name
show leaf name.
-SBP, --show_branch_support
show branch support.
-SIN, --show_inner_name
show inner node name.
-AL, --align_leaf_name
align leaf name
-HI, --hide_inner_node
hide inner node point.
-SP, --save_plot save plot directly.
-o OUT_FILE, --out_file OUT_FILE
file name of saved pdf.
biobrary phytree_statistic -h
usage: phytree_statistic [-h] [-f_out F_OUT] tree_file
statistic phylogenetice tree.
positional arguments:
tree_file tree file name.
optional arguments:
-h, --help show this help message and exit
-f_out F_OUT out file name.
biotools phytree_cluster -h
usage: phytree_groups [-h] [-f_cluster_res F_CLUSTER_RES]
[-f_profile_tree F_PROFILE_TREE]
treefile edge_len_cutoff
This is a utility to cluster a tree's node according to length of edge.
positional arguments:
treefile file name of newike tree.
edge_len_cutoff cutoff of edge length to make a circlal cluster.
optional arguments:
-h, --help show this help message and exit
-f_cluster_res F_CLUSTER_RES
file name to output cluster result, default is
"cluster.fasta".
-f_profile_tree F_PROFILE_TREE
CircleNode Tree profile tree file. default is
"profile.nwk".
biotools phytree_collapse -h
usage: phytree_collapse cluster [-h] [-cluster_result CLUSTER_RESULT]
[-collapse_tree COLLAPSE_TREE]
[-LK LEAF_NAME_KEEP | -LR LEAF_NAME_REMOVE | -MC MANUALLY_CHOOSE]
treefile edge_len_cutoff
positional arguments:
treefile phylogenetic tree file name in newike format.
edge_len_cutoff edge length to cluster.
optional arguments:
-h, --help show this help message and exit
-cluster_result CLUSTER_RESULT
file name of cluster result. default is cluster.fasta
-collapse_tree COLLAPSE_TREE
file name of collapse tree. default is
collapse_tree.nwk
-LK LEAF_NAME_KEEP, --leaf_name_keep LEAF_NAME_KEEP
file list, leaf name that want keep, which can not
coexist with "leaf_name_remove".
-LR LEAF_NAME_REMOVE, --leaf_name_remove LEAF_NAME_REMOVE
file list, leaf name that want remove, which can not
coexist with "leaf_name_keep".
-MC MANUALLY_CHOOSE, --manually_choose MANUALLY_CHOOSE
file list, choose which leaf left maully.
- phytree_setroot
Using "Reference" as outgroup and rooted the tree, and save the result into tree_rooted.nwk. If no outgroup given, using tree midpoint as root.
biotools phytree_setroot -o tree_rooted.nwk -OG Reference test/unrooted_tree.nwk
- phytree_show
Show tree by retangle shap and show leave name and aligned the names and hide inner node.
biotools phytree_show -TM r -SLN -HI -AL test/test_tree.nwk
To save the plot using -SP argument and a file named "plot.pdf" will gerated.
- phytree_statistic
Print statistical information of tree.
biotools phytree_statistic test/test_tree.nwk
max_edge_len: (Tree node 'C3' (0x7fb01c378cd), 9.6)
max_topology_len: (Tree node 'C3' (0x7fb01c378cd), 5.0)
shortest_leaf: [['D4', 0.3]]
longest_leaf: [['B1', 3.0]]
leaf_ave_len: 0.7058823529411765
- phytree_cluster
According a cutoff(you can decide this value baseon leaf_ave_len oupted by phytree_statistic), phytreee_cluster would generated two file. one is "cluster.fasta", and another is "profile.nwk", by default.
./biotools phytree_cluster test/test_tree.nwk 1.5
cluster.fasta file,
>CircleNode_0
@:0;
>CircleNode_5
@((E1:0.5,(E2:0.5,E3:0.7)1:0.6)1:0.7,(E4:0.5)1:0.8);
E1
E2
E3
E4
>CircleNode_6
@((D1:0.5,D2:0.4)1:0.4,(D3:0.5,D4:0.3)1:0.5);
D1
D2
D3
D4
>CircleNode_1
@(((A1:0.8,A2:0.6)1:0.7,A3:0.7)1:0.9);
A1
A2
A3
>CircleNode_2
@:1.8;
>CircleNode_4
@B1:3;
B1
>CircleNode_3
@((C1:0.7,C2:0.7)1:1,((C3:0.5,C4:0.5)1:1,C5:0.6)1:1.1);
C1
C2
C3
C4
C5
cluseter.fasta:
This file is used to record culster information. Every culster start by ">" and following cluster name,and "@" following subtree of this cluter, and other line is leaf name this cluster contained.
profile.nwk:
This is a tree file, which profile how cluster node is look like.
- phytree_collapse
biotools phytree_collapse cluster test/test_tree.nwk 1.5
This will generate two files by default: "collapse_tree.nwk" and "cluster.fasta".
"cluster.fasta" is same as file generated by phytree_cluster.
"collapse_tree.nwk" is a collapse tree removed leaves.
There are three will to chose whose leaves keeped in collapsed tree.
- -LK, a leaf name list, which used to indicate cluster which contain leaf from this list will keep all leaves of this cluster.
For example, using following command,
biotools phytree_collapse cluster test/test_tree.nwk 1.5 -KL keep.list
keep.list:
A1
E1
Would generate a collapsed tree list this:
-
-LR, A leaf list which will substract from all leaf, and then do works a -LK.
-
-MC, A leaf list, if a leaf within this list will be keeped, else, removed.(new added, not test untill now)