From b894a8efe9f0620597ac8b9e63ecf1af86ade62a Mon Sep 17 00:00:00 2001
From: Vince <vince.reuter@gmail.com>
Date: Wed, 19 Jun 2019 22:16:42 -0400
Subject: [PATCH] use yacman; close #156

---
 pypiper/manager.py            |  8 ++------
 pypiper/ngstk.py              | 14 ++++----------
 requirements/reqs-ngstk.txt   |  2 +-
 requirements/reqs-pypiper.txt |  4 ++--
 4 files changed, 9 insertions(+), 19 deletions(-)

diff --git a/pypiper/manager.py b/pypiper/manager.py
index c60b1feb..25be0109 100644
--- a/pypiper/manager.py
+++ b/pypiper/manager.py
@@ -29,6 +29,7 @@
 
 from attmap import AttMapEcho
 from hashlib import md5
+from yacman import load_yaml
 from .exceptions import PipelineHalt, SubprocessError
 from .flags import *
 from .utils import \
@@ -315,12 +316,7 @@ def __init__(
         if config_to_load is not None:
             print("\nLoading config file: {}\n".format(config_to_load))
             with open(config_to_load, 'r') as conf:
-                # Set the args to the new config file, so it can be used
-                # later to pass to, for example, toolkits
-                import yaml
-                # An also use yaml.FullLoader for trusted input. . .
-                config = yaml.load(conf, Loader=yaml.SafeLoader)
-                self.config = AttMapEcho(config)
+                self.config = AttMapEcho(load_yaml(conf))
         else:
             print("No config file")
             self.config = None
diff --git a/pypiper/ngstk.py b/pypiper/ngstk.py
index be1ee191..d3bd3355 100755
--- a/pypiper/ngstk.py
+++ b/pypiper/ngstk.py
@@ -1,15 +1,15 @@
-#!/usr/env python
+""" Broadly applicable NGS processing/analysis functionality """
 
 import os
 import re
 import subprocess
 import errno
 from attmap import AttMapEcho
+from yacman import load_yaml
 from .exceptions import UnsupportedFiletypeException
 from .utils import is_fastq, is_gzipped_fastq, is_sam_or_bam
 
 
-
 class NGSTk(AttMapEcho):
     """
     Class to hold functions to build command strings used during pipeline runs.
@@ -42,14 +42,8 @@ class NGSTk(AttMapEcho):
     def __init__(self, config_file=None, pm=None):
         # parse yaml into the project's attributes
         # self.add_entries(**config)
-
-        if config_file is None:
-            super(NGSTk, self).__init__()
-        else:
-            import yaml
-            with open(config_file, 'r') as config_file:
-                config = yaml.load(config_file)
-            super(NGSTk, self).__init__(config)
+        super(NGSTk, self).__init__(
+            None if config_file is None else load_yaml(config_file))
 
         # Keep a link to the pipeline manager, if one is provided.
         # if None is provided, instantiate "tools" and "parameters" with empty AttMaps
diff --git a/requirements/reqs-ngstk.txt b/requirements/reqs-ngstk.txt
index 85b710ed..80184784 100644
--- a/requirements/reqs-ngstk.txt
+++ b/requirements/reqs-ngstk.txt
@@ -1,4 +1,4 @@
 numpy
 pandas
 pysam
-pyyaml
+yacman
diff --git a/requirements/reqs-pypiper.txt b/requirements/reqs-pypiper.txt
index 78ea834a..9ed3e149 100644
--- a/requirements/reqs-pypiper.txt
+++ b/requirements/reqs-pypiper.txt
@@ -1,4 +1,4 @@
 attmap>=0.12.5
-pyyaml>=5
 psutil
-pandas
\ No newline at end of file
+pandas
+yacman