htsworkflow/util/ucsc.py

   1 """Wrap ucsc command line utilities
   2 """
   3
   4 import logging
   5 import os
   6 from subprocess import Popen, PIPE
   7
   8 LOGGER = logging.getLogger(__name__)
   9
  10 def parseNumber(number):
  11     buffer = []
  12     isFloat = False
  13     for n in number:
  14         if n == ',':
  15             continue
  16         if n == '.':
  17             isFloat = True
  18             buffer.append(n)
  19         else:
  20             buffer.append(n)
  21     if isFloat:
  22         return float(''.join(buffer))
  23     else:
  24         return int(''.join(buffer))
  25
  26 def parseBoolean(value):
  27     if value.lower() in ('yes', '1', 'true'):
  28         return True
  29     elif value.lower() in ('no', '0', 'false'):
  30         return False
  31
  32 class bigWigInfo:
  33     def __init__(self, filename=None):
  34         self.version = None
  35         self.isCompressed = None
  36         self.isSwapped = None
  37         self.primaryDataSize = None
  38         self.primaryIndexSize = None
  39         self.zoomLevels = None
  40         self.chromCount = None
  41         self.basesCovered = None
  42         self.mean = None
  43         self.min = None
  44         self.max = None
  45         self.std = None
  46         self.filename = None
  47         if filename:
  48             self.scan_file(filename)
  49             self.filename = filename
  50
  51     def scan_file(self, filename):
  52         cmd = ['bigWigInfo',
  53                filename]
  54         p = Popen(cmd, stdout=PIPE)
  55         stdout, _ = p.communicate()
  56         for line in stdout.split(os.linesep):
  57             if len(line) > 0:
  58                 term, value = line.split(': ')
  59                 if term in ('isCompressed', 'isSwapped'):
  60                     value = parseBoolean(value)
  61                 else:
  62                     value = parseNumber(value)
  63                 LOGGER.debug('%s: %s', term, str(value))
  64                 setattr(self, term, value)
  65
  66
  67