Closed tyleraland closed 9 years ago
I made "email" a required argument. Biopython produces some warning messages (stderr) if it isn't explicitly provided and I'm not sure how to catch it.
Here is the header and an example line from seqinfo (comma-separated values manually split into separate lines). I'm open to suggestions.
seqid,gi,gb,taxid,fullname
gi|310601|gb|L19300.1|, 310601, L19300.1, 1280, "Staphylococcus aureus DNA sequence encoding three ORFs, complete cds; prophage phi-11 sequence homology, 5' flank"
The ">" is markup in the fasta file, and should not be part of the sequence name. Put another way, the first column of the seq_info file must be identical to the value of seq.id, where 'seq' is the corresponding sequence object.
blast: support for remote (ncbi) blast
ncbi_fetch (new): Given list of seqids (gi or accession numbers) fetch their corresponding sequences from ncbi