Merge pull request #5 from hroest/tapir_branch

Tapir branch

pymzml/__init__.py

@@ -37,4 +37,4 @@
 import pymzml.spec
 import pymzml.obo
 import pymzml.minimum
-import pymzml.plot
+# import pymzml.plot

pymzml/obo.py

@@ -66,7 +66,7 @@
 from __future__ import print_function
 import sys
 import os
-
+import codecs
 
 class oboTranslator(object):
     def __init__(self, version=None):
@@ -138,7 +138,8 @@ def parseOBO(self):
 
         # Modify the root for cx_freeze
         if getattr(sys, 'frozen', False):
-            obo_root = os.path.dirname(sys.executable)
+            # obo_root = os.path.dirname(sys._MEIPASS)
+            obo_root = os.path.dirname(__file__)
         else:
             obo_root = os.path.dirname(__file__)
 
@@ -149,7 +150,7 @@ def parseOBO(self):
         )
 
         if os.path.exists(obo_file):
-            with open(obo_file) as obo:
+            with codecs.open( obo_file, 'r', encoding = 'utf-8' ) as obo:
                 collections = {}
                 collect = False
                 for line in obo:

pymzml/run.py

@@ -575,6 +575,13 @@ def __getitem__(self, value):
             if len(self.info['offsets']) == 0:
                 raise IOError("File does support random access: index list missing...")
 
+            # Check for conversion of str/int issues
+            if not value in self.info['offsets']:
+                try:
+                    value = int(value)
+                except Exception:
+                    pass
+
             if value in self.info['offsets']:
                 startPos = self.info['offsets'][value]
                 endPos_index = bisect.bisect_right(

pymzml/spec.py

@@ -829,13 +829,25 @@ def _decodeNumpress(self, inData, compression):
         coder = pyopenms.MSNumpressCoder()
         np_config = pyopenms.NumpressConfig()
         np_config.estimate_fixed_point = True
+        zlib_compression = False
         if compression == 'ms-np-linear':
             np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.LINEAR
         elif compression == 'ms-np-pic':
             np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.PIC
         elif compression == 'ms-np-slof':
             np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.SLOF
-        coder.decodeNP(inData, result, False, np_config)
+        elif compression == 'zlib-ms-np-linear':
+            np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.LINEAR
+            zlib_compression = True
+        elif compression == 'zlib-ms-np-pic':
+            np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.PIC
+            zlib_compression = True
+        elif compression == 'zlib-ms-np-slof':
+            np_config.np_compression = pyopenms.MSNumpressCoder.NumpressCompression.SLOF
+            zlib_compression = True
+
+        coder.decodeNP(inData, result, zlib_compression, np_config)
+
         return result
 
     def _decode(self):
@@ -885,6 +897,8 @@ def _decode(self):
                         decodedData = zlib.decompress(decodedData)
                     elif compression in ['ms-np-linear', 'ms-np-pic', 'ms-np-slof']:
                         unpackedData = self._decodeNumpress(base64Data, compression)
+                    elif compression in ['zlib-ms-np-linear', 'zlib-ms-np-pic', 'zlib-ms-np-slof']:
+                        unpackedData = self._decodeNumpress(base64Data, compression)
                     elif compression == 'no':
                         pass
                     else:
@@ -1448,6 +1462,15 @@ def readAccession(self, parElement):
             accession = element.get('accession')
             self.ms[accession] = element
             if element.tag.endswith('cvParam'):
+
+                # Combination of zlib + msnumpress
+                if accession == "MS:1002746":
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-linear'))
+                elif accession == "MS:1002747":
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-pic'))
+                elif accession == "MS:1002748":
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-slof'))
+
                 if accession in self.param['accessions']:
                     for mzmlTag in self.param['accessions'][accession]['valuesToExtract']:
                         try:
@@ -1493,6 +1516,15 @@ def readAccession(self, parElement):
                     elif self.param['accessions'][accession]['name'] == 'MS-Numpress short logged float compression':
                         self['BinaryArrayOrder'].append(('compression', 'ms-np-slof'))
 
+                    elif self.param['accessions'][accession]['name'] == 'MS-Numpress linear prediction compression followed by zlib compression':
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-linear'))
+
+                    elif self.param['accessions'][accession]['name'] == 'MS-Numpress positive integer compression followed by zlib compression':
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-pic'))
+
+                    elif self.param['accessions'][accession]['name'] == 'MS-Numpress short logged float compression followed by zlib compression':
+                        self['BinaryArrayOrder'].append(('compression', 'zlib-ms-np-slof'))
+
             elif element.tag.endswith('precursorList'):
                 # TODO remove this completely?
                 self['precursors'] = []

requirements.txt

@@ -0,0 +1,2 @@
+nose
+plotly

setup.py

@@ -2,7 +2,7 @@
 
 from distutils.core import setup
 setup(name='pymzml',
-      version='0.8.0',
+      version='0.8.1',
       packages = ['pymzml'],
       package_dir = {'pymzml': 'pymzml'},
       package_data={'pymzml': ['obo/*.obo']},