From 43fb8ae768b174114b227aa0c0639eaa73bcc0b6 Mon Sep 17 00:00:00 2001
From: Kevin Bonham <kevbonham@gmail.com>
Date: Sat, 28 May 2016 12:17:32 -0400
Subject: [PATCH] Add status updates (#17)

* Added status for multi-species GenBank files

* added status for blast import

* More progress indicators, bug fix in run.analyze()
---
 run.py                     |  4 ++--
 src/Analysis/output.py     |  2 ++
 src/DataImport/gb_parse.py |  8 ++++++--
 src/FindHGT/run_blast.py   | 14 +++++++++-----
 4 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/run.py b/run.py
index 91e32d8..45e88c7 100644
--- a/run.py
+++ b/run.py
@@ -37,8 +37,8 @@ def blast():
 def analyze(minimum_identity, minimum_length=500, dist_between_hits=5000):
     groups = output.hgt_groups(minimum_identity, minimum_length, dist_between_hits)
     output.output_groups(
-        groups, MONGODB.name, os.path.join(
-            OUTPUT, "{}-{}-{}-groups.csv".format(
+        groups, os.path.join(
+            OUTPUT, MONGODB.name, "{}-{}-{}-groups.csv".format(
                 int((minimum_identity)*100), minimum_length, dist_between_hits
                 )
             )
diff --git a/src/Analysis/output.py b/src/Analysis/output.py
index a53e234..cf37258 100644
--- a/src/Analysis/output.py
+++ b/src/Analysis/output.py
@@ -63,6 +63,7 @@ def get_hits_from_species(hits_list):
 
     """
     for species in db['genes'].distinct('species'):
+        print("---> Getting blast hits for {}".format(species))
         yield [record['_id'] for record in db['genes'].find({'species': species, 'type': 'CDS', '_id': {'$in': hits_list}})]
 
 
@@ -181,4 +182,5 @@ def output_groups(groups_list, output_file, min_group_size=2):
                     name=db_handle['species']
                 )
                 df=df.append(series)
+    print("Creating file at {}".format(output_file))
     df.to_csv(output_file, columns=df_index)
diff --git a/src/DataImport/gb_parse.py b/src/DataImport/gb_parse.py
index fcaba90..1fa6945 100644
--- a/src/DataImport/gb_parse.py
+++ b/src/DataImport/gb_parse.py
@@ -40,7 +40,7 @@ def add_contig_data(records, genbank_file):
     contig_counter = 0
     contig_ids = []
 
-
+    current_species = None
     for contig in records:
         contig_counter += 1
         try:
@@ -49,6 +49,10 @@ def add_contig_data(records, genbank_file):
             # uses filename (without extension) as species name
             species = os.path.splitext(os.path.basename(genbank_file)[0])
 
+        if not species == current_species:
+            print("Importing {}".format(species))
+            current_species = species
+
         if contig.id in contig_ids: # in case the id field is present but not unique
             contig.id = "{}_{}".format(contig.id, contig_counter)
         else:
@@ -114,4 +118,4 @@ def add_features(contig, species):
                 'contig': contig.id},
         }
 
-        yield feature_record
\ No newline at end of file
+        yield feature_record
diff --git a/src/FindHGT/run_blast.py b/src/FindHGT/run_blast.py
index bf1550b..ee1a654 100644
--- a/src/FindHGT/run_blast.py
+++ b/src/FindHGT/run_blast.py
@@ -1,5 +1,5 @@
 from tempfile import NamedTemporaryFile
-from subprocess import Popen
+from subprocess import Popen, PIPE
 from DataImport.mongo_import import mongo_import_record
 from bson.objectid import ObjectId
 from Bio.Blast import NCBIXML
@@ -14,13 +14,14 @@ def blast_all(query_fasta, blast_db):
     """
     tmp_results = NamedTemporaryFile()
 
-    Popen(
+    print(Popen(
         ['blastn',
          '-query', query_fasta.name,
          '-db', blast_db,
          '-out', tmp_results.name,
-         '-outfmt', '5']  # xml output
-    ).wait()  # waits for return code before proceeding
+         '-outfmt', '5'],
+         stdout=PIPE  # xml output
+    ).wait())  # waits for return code before proceeding
 
     return tmp_results
 
@@ -30,9 +31,10 @@ def parse_blast_results_xml(results_file):
 
     :param results_file: blast results in xml format
     """
-
+    counter = 0
     results_file.seek(0)
     for blast_record in NCBIXML.parse(results_file):
+        counter += 1
         query_id = blast_record.query
 
         for alignment in blast_record.alignments:
@@ -55,6 +57,8 @@ def parse_blast_results_xml(results_file):
                         },
                         "blast_results"
                     )
+        if counter % 500 == 0:
+            print("---> {} blast records imported".format(counter))
 
 
 def check_blast_pair(query, subject):