I would like to load all of the sequences from that search into one fasta file. I know that the entrez utilities exist, but they are not installed on the server I am working in.
Also how does entrez output to a file? I know I would want something like the code below, but I don't want to flood the terminal if I do install this.
esearch -db est -query "txid6200[Organism:exp] " | \
efetch -format fasta
@Steve Do you mind posting some py code as your answer? I am personally quite interested to see the code, but more importantly I feel your code will benefit the greater community. And you yourself can point people to your answer if they have similar problem. I believe the key aspect about this and alike forums to seek answers and by posting your code you will enable others to find answers and/or provide starting point.
@Kirill, No problem, I edited in my code. It's a bit dirty - SeqIO overwrites the file each write, and a quick work around I thought of was to copy the contents of the working fasta to a final output fasta after each write. I'm sure there's a more efficient way to do this; it took a couple hours to download ~100,000 sequences.
Whoops sorry about that. I'm familiar with python, but is there any way to use biopython for the function i need without using entrez?
You can use biopython to access entrez direction:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc108