implemented blast

detector.py

@@ -10,6 +10,7 @@
 BLAST_MODULE = 'biotools/ncbi-blast-2.3.0+'
 
 BUILD_DB_CMD = 'makeblastdb -dbtype prot -in %s -out %s'
+RUN_BLAST_CMD = 'blastp -query %s -db %s -out %s -outfmt 6'
 
 
 @click.group()
@@ -71,18 +72,31 @@ def build(path, db):
 
 
 @cli.command()
-@click.argument('db', type=click.Path())
+@click.argument('fasta', type=click.Path())
+@click.argument('db')
 @click.argument('output', type=click.Path())
-def blast(db, output):
+def blast(fasta, db, output):
     """
     Runs Blast
+
+    usage: detector blast FASTA DB OUTPUT
+
+    Blasts (blastp) the file defined by FASTA against a database DB and stores the output in OUTPUT
     """
-    pass
+
+    click.secho("Running BLASTP... ", fg='green', bold=True)
+
+    cmd = BUILD_DB_CMD % (fasta, db, output)
+    click.echo("Executing command: %s" % cmd)
+    subprocess.call(shlex.split(cmd))
+
+    # done
+    click.secho("All done!", fg='green', bold=True)
 
 
 @cli.command()
 @click.argument('input', type=click.Path())
-def analyze(intput):
+def analyze(input):
     """
     Analyzes blast output
     """