# wonderfetch

The Entrez Direct service is sometimes nonfunctional. We wrote a very
simple replacement script that can fetch data in case `efetch` does not work.

### Install wonderfetch

    mkdir -p ~/bin
    curl http://data.biostarhandbook.com/scripts/wonderfetch.sh > ~/bin/wonderfetch
    chmod +x ~/bin/wonderfetch

### Using wonderfetch

    wonderfetch database accession format

for example:

    wonderfetch nucleotide AF086833 fasta

# wonderdump

As it happens the internal implementation of `fastq-dump`
precludes it from working on Bash for Windows. Use a helper script that we have created
to bypass this limitation. We call it the `wonderdump`:

### Install wonderdump

    curl http://data.biostarhandbook.com/scripts/wonderdump.sh > ~/bin/wonderdump
    chmod +x ~/bin/wonderdump

### Using wonderdump

Then enjoy access to the SRA files where instead of writing:

    fastq-dump -X 10000 --split-files $SRR

you'll need to write:

     wonderdump SRR1972739 -X 10000 --split-files

There is a catch though! Note how the SRR number must be the first parameter instead of last!

To download batches of SRA ids put them into a file then run:

    cat samples.txt | xargs -n 1 echo wonderdump | bash

# geodata

A simple script to fetch information from the Gene Expression Omnibus

### Install geodata.sh

    curl http://data.biostarhandbook.com/scripts/geodata.sh > ~/bin/geodata
    chmod +x ~/bin/geodata

### Usage

    geodata GSE78711