A collection of utility scripts
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
Simple R script that will scan a directory and try to install any packages that are referenced in R code.
$ 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