PeterMulhair / DToL_insects

Collection of scripts and data useful for analyses of insect genomes

DToL insects

Collection of scripts and data useful for analyses of insect genomes produced by the Darwin Tree of Life project.

Download DToL genomes

get_genomes.py is a script to pull down DToL genomes for any desired insect order from ncbi using xml file from the ncbi project page using the Send to: File drop down in the top right of the page and selecting XML from the format list.

Requirements

-i, --input flag requires an xml file from ncbi DToL page with all species genome information (see data/ folder for example).

-g, --group flag requires name of insect groups you wish to download data eg. Insecta or Hemiptera, Hymenoptera, Diptera or Lepidoptera (NOTE if Insecta is used, there is no need to specify individual insect orders). This can also be a name of a file with a list of species of interest (see data/sp_list.txt as an example).

• If the -a, --annotation flag is used only genomes for species that have annotation data available will be downloaded - requires csv file from ensembl rapid release site (see data/ folder for example)

Output

The output is the genomes from the desired insect group in fasta format.

If the -i, --info flag is used, a summary tsv file called genome_summary.tsv is also produced which conatins info on insect Order, species name, shortened DToL species name, genome size and chromosome count (number of scaffolds assigned to chromosomes).

Full usage

usage: get_genomes.py [-h] -i INPUT -g GROUP [GROUP ...] [-a ANNOTATION] [-d]
                      [-t THREADS]
required arguments:
  -i INPUT, --input INPUT
  -g GROUP [GROUP ...], --group GROUP [GROUP ...]
                        list of insect orders to download - eg. Insect,
			Odonata, Ephemeroptera, Coleoptera, Hymenoptera,
	 		Lepidoptera... Or name of text file with species
			names eg. see data/sp_list.txt

optional arguments:
  -h, --help            show this help message and exit
  -a ANNOTATION, --annotation ANNOTATION
                        flag to only download genomes that have annotation
			data available, requires ensembl csv data
  -d, --info            flag to output information on genome data - eg. genome
                        size, chromosome count
  -t THREADS, --threads THREADS
                        number of threads to use i.e. number of genomes to
			download at once, default is 1

Download DToL gene annotation data

get_genes.py is a script to pull down DToL annotation data (proteins, cds, gff, gtf) for all available species. Requires xml file (assembly_result.xml) from the ncbi project page and csv file (Species.csv) from ensembl rapid release site (which is obtained using the Download whole table tab in the top right corner of the page).

Requirements

--genomes flag requires an xml file from ncbi with all species genome information (see data/ folder for example).

--genes flag requires a csv file from ensembl with all species genome information (see data/ folder for example).

Optional: --group flag takes a text file of species names you wish to download data for (see data/sp_list.txt folder for example).

Output

The output is four directories containing peptides, cds, gff and gtf files for each species.

Full usage

usage: get_genes.py [-h] --genomes GENOMES --genes GENES [--group sp_list.txt]

required arguments:
  --genomes GENOMES  ncbi xml file with genome info
  --genes GENES      ensembl csv file with gene annotation info

optional arguments:
  -h, --help         show this help message and exit
  --group            Name of text file with species names
                     to download eg. see data/sp_list.txt