Utility to fetch the nucleotide sequence of two consecutive genes from Entrez
This was specifically hacked together to allow the user to input one Entrez Accession ID and get back the nucleotide sequence of the specified gene, the next downstream gene (depending on which strand the specified gene is on), and the interstitial region.
While this behavior is certainly a niche, the underlying functions are a decent reference for how to use the Entrez E-Utilities API's with Python. I specifically did not use the Requests library here because I wanted maximum portability to bare Python installations. I'm sure the code could be much cleaner with Requests.
Written (and tested) in Python 3.3.x
Good reference on the Entrez E-utilities API: http://www.ncbi.nlm.nih.gov/books/NBK25499/
python3 seqFetch.py YP_XXXXXXXXX.X
This will write 3 files in the working directory:
- The full Entrez gene record for the requested accession ID
- The full Entrez gene record for the next gene
- The fasta file of the sequence
As of this writing, Entrez Gene is displaying an odd behavior where the nucleotide indices bounding the sequence are off by one in the positive direction. This results in the output sequence having an extra base, i.e. len(seq) % 3 != 0, that isn't actually part of the sequence.
The XPath queries used are very generic and could easily break if the returned XML is in a different order. During testing the API always returned in the same order (as it should), but it could change in the future.
If the script is used multiple times in a row, genes in the same organism will have the same filename for the fasta sequence output, i.e the first result will be overwritten by the second set of results.