def run(self, edit, query):
## get the contents of the tab that is the focus in sublime
allcontent = sublime.Region(0, self.view.size())
## convert to string
allcontent = self.view.substr(allcontent)
## get a unique string for use in the tmp files
unique_filename = str(uuid.uuid4())
## open db and query files in /tmp and write allcontent (i.e. the 'page' open, with the sublime console at the bottom)
db_handle = '/tmp/%s.sublime_blast.tmp_db.fa' % unique_filename
with open(db_handle, 'w') as fo:
fo.write(allcontent)
query_handle = '/tmp/%s.sublime_blast.tmp_query.fa' % unique_filename
with open(query_handle, 'w') as fo:
fo.write('>query\n%s\n' % query)
## make a blastdb of the page open in sublime
subprocess.call(['/usr/local/bin/makeblastdb', '-dbtype', 'nucl', '-in', '%s' % db_handle])
## run blast, taking the query as what is input in the console
blast_output = subprocess.getoutput(['/usr/local/bin/blastn -db {0} -query {1} -outfmt 6'.format(db_handle, query_handle)])
## add the headers and the blast output to the end of the window of focus
## self.view.size() is where you want to insert the text, in this case, at the end of the file so we use self.view.size() which is the total size
## edit is a token which classes the insert as a single edit which can e.g. be undone with one 'undo'
self.view.insert(edit, self.view.size(), '\nqseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n')
self.view.insert(edit, self.view.size(), blast_output)
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