stream_fastq_ftp.sh

#/bin/bash
# uber simple version
# inspired by http://nxn.se/post/146066712225/streaming-rna-seq-data-from-ena

# usage:
# $ ./stream_ena SRR3185782.fastq | head
# @SRR3185782.1 HWI-D00361:180:HJG3GADXX:2:1101:1460:2181/1
# AGTGTGTTCATCAGTGTGGATTTGCCAATGCCGGTCTCCCCCACACAGAG
# +
# BBBFFBFFFB<FFFFFBFF<FFFFFFFFFFFFFIIIIFFFFFFFFIFFFF
# @SRR3185782.2 HWI-D00361:180:HJG3GADXX:2:1101:1613:2218/1
# GCCAATTTTCTTAATGTAAGTGCTGACTTCCTTAACAATTTCCTCATATC
# +
# BBBFFFFFFFFFFIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
# @SRR3185782.3 HWI-D00361:180:HJG3GADXX:2:1101:2089:2243/1
# CGGGTTCTTGGACTTCAGCCAGTTGAGCAGGGCATCCTTGTTGAAGGCGG


fastq_url="$1"

curl --keepalive-time 4 -s $fastq_url | zcat