use yacman; close databio#156

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

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

requirements/reqs-ngstk.txt

@@ -1,4 +1,4 @@
 numpy
 pandas
 pysam
-pyyaml
+yacman

requirements/reqs-pypiper.txt

@@ -1,4 +1,4 @@
 attmap>=0.12.5
-pyyaml>=5
 psutil
-pandas
+pandas
+yacman