Merge pull request #24 from ENCODE-DCC/dev0.2.2

Dev0.2.2

CHANGELOG.rst

@@ -0,0 +1,7 @@
+Changelog
+===========
+
+19.08.1 (20.8.2019)
+-------------------------
+- `QCMetric` can now be created from a dict-like only. The parsing needs to be done separately. This is a breaking change.
+- Change versioning into `CalVer <https://calver.org>`_. The format will be YY.MM.minor.

docs/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../CHANGELOG.rst

docs/index.rst

@@ -19,7 +19,7 @@ Getting Started
 Usage
 =======
 
-The basic pattern is to create ``QCMetric`` objects, and then add related ones to a ``QCMetricRecord``. ``QCMetric`` objects can be created directly from dicts, or from files. Supported parsers are for now for samtools flagstats and for STAR log. You can also write your own: provide a function that takes a filepath as input and returns a dict.
+The basic pattern is to create ``QCMetric`` objects, and then add related ones to a ``QCMetricRecord``. ``QCMetric`` objects can be created from dicts. Supported parsers are for now for samtools flagstats and for STAR log. You can also write your own: provide a function that takes a path to a file as input and returns a dict.
 
 Examples
 ---------
@@ -39,8 +39,9 @@ To create from a STAR log file in ``/path/to/star_Log.out``:
 
     from qc_utils import QCMetric, QCMetricRecord
     from qc_utils.parsers import parse_starlog
+    starlog = parse_starlog("/path/to/star_Log.out")
     record = QCMetricRecord()
-    log_qc_obj = QCMetric("starlogQC", "/path/to/star_Log.out", parser=parse_starlog)
+    log_qc_obj = QCMetric("starlogQC", starlog)
     record.add(log_qc_obj)
 
 To create from a samtools flagstats file in ``/path/to/flagstats.txt`` and write into a ``json``-object in ``/path/to/flagstats.json``:
@@ -49,7 +50,8 @@ To create from a samtools flagstats file in ``/path/to/flagstats.txt`` and write
     import json
     from qc_utils import QCMetric, QCMetricRecord
     from qc_utils.parsers import parse_flagstats
-    flagstat_qc_obj = QCMetric("flagstat", "/path/to/flagstats.txt", parser=parse_flagstats)
+    flagstats = parse_flagstats("/path/to/flagstats.txt")
+    flagstat_qc_obj = QCMetric("flagstat", flagstats)
     with open("/path/to/flagstats.json", "w") as fp:
         json.dump(flagstat_qc_obj.to_ordered_dict(), fp)
 
@@ -59,8 +61,10 @@ QCMetricRecord can also have a name, and can be written into ``json`` as follows
     import json
     from qc_utils import QCMetric, QCMetricRecord
     from qc_utils.parsers import parse_flagstats, parse_starlog
-    log_qc_obj = QCMetric("starlogQC", "/path/to/star_Log.out", parser=parse_starlog)
-    flagstat_qc_obj = QCMetric("flagstat", "/path/to/flagstats.txt", parser=parse_flagstats)
+    starlog = parse_starlog("/path/to/star_Log.out")
+    flagstats = parse_flagstats("/path/to/flagstats.txt")
+    log_qc_obj = QCMetric("starlogQC", starlog)
+    flagstat_qc_obj = QCMetric("flagstat", flagstats)
     record = QCMetricRecord([log_qc_obj, flagstat_qc_obj], name="alignment_qc")
     with open("/path/to/alignment_qc.json", "w") as fp:
         json.dump(record.to_ordered_dict(), fp)
@@ -86,6 +90,7 @@ Table of Contents
    :maxdepth: 2
 
    license
+   changelog
 
 Indices and tables
 ==================

qc_utils/__init__.py

@@ -1,7 +1,7 @@
 from qc_utils.qcmetric import QCMetric, QCMetricRecord
 
 __title__ = "qc-utils"
-__version__ = "0.2.1"
+__version__ = "19.08.1.dev0"
 __description__ = "Tool for representing ENCODE QC metrics"
 __url__ = "https://github.com/ENCODE-DCC/qc-utils"
 __uri__ = __url__

qc_utils/qcmetric.py

@@ -8,11 +8,8 @@ class QCMetric(object):
     instantiated from a regular dict.
     """
 
-    def __init__(self, qc_metric_name, qc_metric_content, parser=None):
-        if parser is not None:
-            qc_metric_dict = parser(qc_metric_content)
-        else:
-            qc_metric_dict = qc_metric_content
+    def __init__(self, qc_metric_name, qc_metric_content):
+        qc_metric_dict = qc_metric_content
         if not isinstance(qc_metric_dict, dict):
             raise TypeError("QCMetric data must be a dict.")
         self._name = qc_metric_name