anatolydryga / cdd_cluster

custom annotation to cdd hits

Annotation of Viral and Phage CDD hits with Gene Types

At present PFAM IDs are annotated with phage function(gene type) information, e.g. Phage Regulation, Phage Capsid. See file pfam_function.tsv for complete list of annotated families. If there is no phage function annotation we call it "Other".

Usage

To create Figure with gene type annotation for CDD hits for several samples:

Rscript GeneTypes.R input_file.tsv

that script creates Gene_types_counts.pdf Figure and Gene_types_proportions.pdf Figure

Input file(input_file.tsv) format has header and data:

files   sample_names
file_name1  label1
file_name2  label2
file_name3  label3

where each file_name* is tab-separated file with 2 columns: contig name and cdd accession hit(see file DNAmod_sample_cdd.tsv as an example), label is used on Figure for that file. The file_name* can be produced by ContigAnnotation script.

How to Add Human-Readable Title to CDD Accession

Create the csv file where 1st column is cdd acession(e.g. pfam1234) and run the script:

cdd_description_addition.py file_with_no_description.csv file_with_description.csv

that would create a file with last column as title.

If cdd accesion is not in the 1st column the last argument specify index of the cdd column(1-based indexing):

cdd_description_addition.py file_with_no_description.csv file_with_description.csv 2

means that in file file_with_no_description.csv column with cdd accession number is column number 2.

Development

Read data:

• read_contig_cdd
• read_cdd_annotation

Process data:

• add_annotataion_to_cdd
• cdd_annotation_counts

cdd_cluster's Issues

fail if file does not exist

add tests for py script