Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first? So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the genome as a fasta file and then use pyfaidx to extract the sequences at the given positions. But now that I'm working with several species at once, I was wondering if there's any kind of tool in Python or R that can fetch your sequences of interest without downloading a bunch of large files. Thanks
using a http request.

if there is a DAS server, you can always use this protocol to download the xml -> fasta. see https://www.biostars.org/p/56/

$ curl -s "http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chrM:100,200"  | xmllint --xpath '/DASDNA/SEQUENCE/DNA/text()' - | tr -d '\n'
ggagccggagcaccctatgtcgcagtatctgtctttgattcctgcctcattctattatttatcgcacctacgttcaatattacaggcgaacatacctacta


or use the UCSC utility twoBitToFa which works with remote files.

If you have an NCBI accession number you can use the E-utilities with seq_start and seq_end.

$ wget -q  -O -  "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&amp;id=AE014134.1&amp;seq_start=100&amp;seq_stop=300&amp;rettype=fasta"
&gt;AE014134.1:100-300 Drosophila melanogaster chromosome 2L complete sequence
TGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGATGAACGAGATGATAATATA
TTCAAGTTGCCGCTAATCAGAAATAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATG
CGAGAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCG