Script to BLAST spacers against host genome

Motivation

Research has suggested that there may be cases when CRISPR systems are used for something besides immunity to foreign DNA - perhaps they could be regulating the host genome, or they might simply be inactive. A clue that one of these things might be happening is if there are spacers that come from their own host genome. To this end, we need functions to (A) BLAST spacers against the host genome and (B) analyze the BLAST output. The first function is described in this issue. The second is described in issue #62.

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The Function

Input:

• List of spacers in the genome. Example files in data/spacers contain a list of all the CRISPR spacers identified for that organism. The organism is identified by an NCBI accession number, which is the name of the file.
• Accession number of organism (title of file containing list of spacers) - i.e. NC_000853.
• Optional time window t (in months) - if date downloaded is more than t months ago, re-download from NCBI. - moved to Issue #74
• Optional BLAST parameters - could be left as default for first iteration.

The function should do the following:

• Check if the genome of the organism has already been downloaded - i.e., is it in phageParser/data/prokaryote_genomes? - moved to Issue #74
• If it hasn’t been downloaded OR if it is more than t months out of date, fetch the genome from NCBI using acc2gb.py. - moved to Issue #74
• BLAST the list of spacers for that organism against the genome using BioPython’s standalone BLAST wrapper. Note: you will need to install BLAST+ locally. The script BLAST_loop.py could be used as a template for this process. The main difference between the two is that in this version the subject sequence is a single genome, not a database.

Output:

• XML file with BLAST output.

Note: The default parameters may need some fiddling - the defaults in BLAST_loop.py are a good start.

[mbonsma]

@lwgray will be taking a look at this issue!

[mbonsma]

blast.py (#201) is now a general-purpose blast script.