toolbucket

A collection of utility scripts

ena_downloader.py

Download metadata and fastqs from the European Nucleotide Archive using aspera or wget

python3 ena_downloader.py -h

usage: ena_downloader.py [-h] -s STUDY [-i IDS [IDS ...]] [-d DOWNLOADER]
                         [-p PROG_PATH] [-k SSHKEY] [-o OUTPUTDIR]
                         [-m METADATAFILE]

Utility to download fastqs from European Nucleotide Archive

optional arguments:
  -h, --help            show this help message and exit
  -s STUDY, --study STUDY
                        Study accessions numbers(ERP, SRP, DRP, PRJ prefixes)
                        e.g. SRX017289 or PRJNA342320
  -i IDS [IDS ...], --ids IDS [IDS ...]
                        Specific fastqs to download, defaults to all fastqs in
                        study
  -d DOWNLOADER, --downloader DOWNLOADER
                        either 'ascp' or 'wget' (default)
  -p PROG_PATH, --prog_path PROG_PATH
                        path to downloader binary, defaults to name of
                        program, i.e. 'ascp', 'wget' 
  -k SSHKEY, --sshkey SSHKEY
                        path to aspera openssh key file (i.e something like
                        ".aspera/connect/etc/asperaweb_id_dsa.openssh")
  -o OUTPUTDIR, --outputdir OUTPUTDIR
                        output directory to place fastqs, defaults to '.'
  -m METADATAFILE, --metadatafile METADATAFILE
                        filename for log file containing metadata downloaded
                        for study. defaults to study name + "_metadata.txt" in
                        outdir

find_and_install_dependencies.R

Simple R script that will scan a directory and try to install any packages that are referenced in R code.

bed_to_vcf.py

$ python bed_to_vcf.py -h
usage: bed_to_vcf.py [-h] -b BED -f FAI [-o OUTPUT]

Utility to convert bed-like file with alleles to a simple VCF

optional arguments:
  -h, --help            show this help message and exit
  -b BED, --bed BED     bed file to convert to vcf must have chrom, start,
                        end, ref, and alt columns
  -f FAI, --fai FAI     fasta index file generated by samtools faidx
  -o OUTPUT, --output OUTPUT
                        , output file name, prints to standard out if not
                        supplied