From ed537af0fa953d03f8d77a6af809b50b17adfd48 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Wed, 10 May 2017 11:54:00 +0200
Subject: [PATCH] build step implemented

---
 detector.py | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 62 insertions(+), 3 deletions(-)

diff --git a/detector.py b/detector.py
index 8e71208..4ec5c6a 100644
--- a/detector.py
+++ b/detector.py
@@ -1,5 +1,16 @@
 import click
 
+import os
+import tempfile
+
+import subprocess
+import shlex
+
+
+BLAST_MODULE = 'biotools/ncbi-blast-2.3.0+'
+
+BUILD_DB_CMD = 'makeblastdb -dbtype prot -in %s -out %s'
+
 
 @click.group()
 def cli():
@@ -18,13 +29,61 @@ def cli():
 
 @cli.command()
 @click.argument('path', type=click.Path())
-def build(path):
+@click.argument('db', type=click.Path())
+def build(path, db):
     """
     Builds the blast database.
 
-    usage: detector build PATH (the directory with .fasta files to build the database)
+    usage: detector build PATH DB
+
+    Fasta files in PATH should have the extension .fasta !
 
+    The output from makeblastdb will be written to DB.
     """
-    click.echo("Building the database ... ")
+    click.echo("Building the database from FASTA files... ")
     click.echo("Input path: %s" % path)
 
+    full_fasta = tempfile.mktemp()
+    fasta_count = 0
+
+    # find fasta files and concatenate them to a temporary file
+    with open(full_fasta, 'w') as f_out:
+        for file in os.listdir(path):
+            if file.lower().endswith('.fasta'):
+                click.echo("\tFound file: %s" % file)
+                fasta_count += 1
+                with (open(os.path.join(path, file), 'r')) as f_in:
+                    for line in f_in:
+                        f_out.write(line)
+
+    click.echo("Concatenated %d fasta files in temporary file %s" % (fasta_count, full_fasta))
+    click.echo("\nCreating Blast database")
+
+    cmd = BUILD_DB_CMD % (full_fasta, db)
+    click.echo("Executing command: %s" % cmd)
+    subprocess.call(shlex.split(cmd))
+
+    # delete temporary file
+    os.remove(full_fasta)
+
+    # done
+    click.echo("All done!")
+
+
+@cli.command()
+@click.argument('db', type=click.Path())
+@click.argument('output', type=click.Path())
+def blast(db, output):
+    """
+    Runs Blast
+    """
+    pass
+
+
+@cli.command()
+@click.argument('input', type=click.Path())
+def analyze(intput):
+    """
+    Analyzes blast output
+    """
+    pass