network

Introduction

cctk network performs pairwise comparisons of CRISPR arrays and represents their spacer-sharing relationships in as a network. This functionality is included in both cctk minced and cctk blast which output Array_network.txt. This network creation functionality is provided separately in cctk network to allow the creation of networks in, for example, the following situations:

When analyzing CRISPR arrays that were not identified by CCTK tools.
To generate a network of a the relationships between a subset of arrays.
To generate a network of arrays that have been modified after their identification by cctk minced or cctk blast (e.g. following manual curation).

Before you run

CCTK is built around the Array_IDs.txt file (or Array_seqs.txt if you prefer) and that file is the only required input for cctk network. If you identified CRISPR arrays using a non-CCTK tool then you will need to format your arrays into the format of the Array_IDs.txt file. That format is composed of two tab-delimited columns containing the following information:

A unique identifier for the array. This can be any string of characters including numbers, letters, and symbols.
A space-delimited list of identifiers for the spacers in this array. Spacer identifiers can also be any string of characters including numbers, letters, and symbols. The only requirement is that the identifier used for a spacer is the same between arrays in which it is contained.

N.B. While cctk minced and cctk blast output Array_IDs.txt in the format

<Array ID>\t<spacer> <spacer>...

with a tab betewen the two columns, this file can be successfully read with any whitespace delimiters. Array ID must come before the first whitespace character and the spacers must be separated by whitespace, but tabs and spaces will work equally well in all locations. You can use all tabs or all spaces when generating this file if it is easier.

Basic usage

The minimal command for cctk network requirs only an Array_IDs.txt or Array_seqs.txt file as input. cctk network will write a file called Array_network.txt to the directory specified using -o which is your currently directory (./) by default.

cctk network -i <Array file>

This produces a version of the Array_network.txt file produced by ctk minced and cctk blast that contains only the first 4 columns.

Array_A Array_B Shared_spacers  Jaccard_similarity
     2       2       0.2
     3       5       0.5
     4       8       0.8

See Advanced Usage for information about producing a file including the remaining columns.

An Array_clusters.txt file like that produced by ctk minced and cctk blast is also output.

Advanced Usage

With the command described in the Basic usage, the output file will contain only the first 4 columns contained in the Array_network.txt files produced by cctk minced and cctk blast. This is because cctk network does not attempt to infer CRISPR type information from your array file. If you want columns describing the CRISPR type of arrays in the network, you need to provide that information as a separate file using -t.

Array types file

The array types file contains two columns. The first is the Array ID used in Array_IDs.txt or Array_seqs.txt, the second is the CRISPR type that you would like written to your Array_network.txt file and can be any string of characters you wish (it does not need to correspond to any other information and could, in fact, be any kind of annotation as long as it contains no whitespace characters).

     1F
     Type_I_Subtype_F
     I-E
     Other_annotation

If you are simply making a network from a subset of arrays in an existing Array_IDs.txt file then you can quickly and easily produce the array types file using grep and sed:

$ cat Array_IDs.txt

1       1F_42 1F_18 1F_153 1F_53 1F_82
2       1F_90 1F_56 1F_166 1F_26
3       1F_56 1F_166 1F_26 1F_141
4       1F_156 1F_19 1F_26 1F_141
...

$ sed 's/_.*//' Array_IDs.txt | grep -Ew "^1|^2|^3|^4|..." > Array_types.txt

$ cat Array_types.txt

1       1F
2       1F
3       1F
4       1F
...

Complete command

We can then use the Array types file to annotate edges in the output network with information about the connected arrays with the following command (also including output directory specification for completeness):

cctk network -i <Array file> -t <array types file> -o <output dir>

If we used the example file described in the :ref`network-array-types` section, then this would result in the following output file:

Array_A Array_B Shared_spacers  Jaccard_similarity      Array_A_type    Array_B_type
     2       2       0.2     1F      Type_I_Subtype_F
     3       5       0.5     1F      I-E
     4       8       0.8     1F      Other_annotation