added python code

[biopieces.git] / code_python / Cjung / Args.py

diff --git a/code_python/Cjung/Args.py b/code_python/Cjung/Args.py
new file mode 100644 (file)
index 0000000..52027cc
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+++ b/code_python/Cjung/Args.py
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+"""
+Handling of arguments: options, arguments, file(s) content iterator
+
+For small scripts that:
+- read some command line options
+- read some command line positional arguments
+- iterate over all lines of some files given on the command line, or stdin if none given
+- give usage message if positional arguments are missing
+- give usage message if input files are missing and stdin is not redirected
+"""
+
+__author__ = 'Peter Kleiweg'
+__version__ = '0.2'
+__date__ = '2004/08/28'
+
+import os, sys, getopt
+
+class Args:
+       """
+       Perform common tasks on command line arguments
+       
+       Instance data:
+       progname (string) -- name of program
+       opt (dictionary) -- options with values
+       infile (string) -- name of current file being processed
+       lineno (int) -- line number of last line read in current file
+       linesum (int) -- total of lines read
+       """
+
+       def __init__(self, usage='Usage: %(progname)s [opt...] [file...]'):
+               "init, usage string: embed program name as %(progname)s"
+               self.progname = os.path.basename(sys.argv[0])
+               self.opt = {}
+               self.infile = None
+               self.lineno = 0
+               self.linesum = 0
+               self._argv = sys.argv[1:]
+               self._usage = usage
+
+       def __iter__(self):
+               "iterator: set-up"
+               if self._argv:
+                       self.infile = self._argv.pop(0)
+                       self._in = open(self.infile, 'r')
+                       self._stdin = False
+               else:
+                       if sys.stdin.isatty():
+                               print "### USAGE in __iter__"
+                               #self.usage()  # Doesn't return
+                               return None
+                       self.infile = '<stdin>'
+                       self._in = sys.stdin
+                       self._stdin = True
+               return self
+
+       def next(self):
+               "iterator: get next line, possibly from next file"
+               while True:
+                       line = self._in.readline()
+                       if line:
+                               self.lineno += 1
+                               self.linesum += 1
+                               return line
+
+                       if self._stdin:
+                               break
+
+                       self._in.close()
+                       try:
+                               self.infile = self._argv.pop(0)
+                       except IndexError:
+                               break
+                       self.lineno = 0
+                       self._in = open(self.infile, 'r')
+
+               self.lineno = -1
+               self.infile = None
+               raise StopIteration
+
+       def getopt(self, shortopts, longopts=[]):
+               "get options and merge into dict 'opt'"
+               try:
+                       options, self._argv = getopt.getopt(self._argv, shortopts, longopts)
+               except getopt.GetoptError:
+                       print "### USAGE in getopt"
+                       #self.usage()
+                       return None
+               self.opt.update(dict(options))
+
+       def shift(self):
+               "pop first of remaining arguments (shift)"
+               try:
+                       return self._argv.pop(0)
+               except IndexError:
+                       #print "### USAGE in shift"
+                       #self.usage()
+                       return None
+
+
+       def pop(self):
+               "pop last of remaining arguments"
+               try:
+                       return self._argv.pop()
+               except IndexError:
+                       print "### USAGE in pop"
+                       #self.usage()
+                       return None
+
+       def warning(self, text):
+               "print warning message to stderr, possibly with filename and lineno"
+               if self.lineno > 0:
+                       print >> sys.stderr, '%s:%i: warning: %s' % (self.infile, self.lineno, text)
+               else:
+                       print >> sys.stderr, '\nWarning %s: %s\n' % (self.progname, text)
+
+       def error(self, text):
+               "print error message to stderr, possibly with filename and lineno, and exit"
+               if self.lineno > 0:
+                       print >> sys.stderr, '%s:%i: %s' % (self.infile, self.lineno, text)
+               else:
+                       print >> sys.stderr, '\nError %s: %s\n' % (self.progname, text)
+               sys.exit(1)
+
+       def usage(self):
+               "print usage message, and exit"
+               print >> sys.stderr
+               print >> sys.stderr, self._usage % {'progname': self.progname}
+               print >> sys.stderr        
+               #sys.exit(1)
+
+
+if __name__ == '__main__':
+
+       a = Args('Usage: %(progname)s [-a value] [-b value] [-c] word [file...]')
+
+       a.opt['-a'] = 'option a'    # set some default option values
+       a.opt['-b'] = 'option b'    #
+       a.getopt('a:b:c')           # get user supplied option values
+
+       word = a.shift()            # get the first of the remaining arguments
+                                                               # use a.pop() to get the last instead
+
+       for line in a:              # iterate over the contents of all remaining arguments (file names)
+               if a.lineno == 1:
+                       print 'starting new file:', a.infile
+               a.warning(line.rstrip())
+
+       print 'Options:', a.opt
+       print 'Word:', word
+       print 'Total number of lines:', a.linesum
+
+       print 'Command line:', sys.argv     # unchanged
+
+       a.warning('warn 1')         # print a warning
+       a.error('error')            # print an error message and exit
+       a.warning('warn 2')         # this won't show
+