<filename>bin/create-newick-relabeling-output.py
#!/usr/bin/env python

from __future__ import print_function

import sys
import argparse

from dark.reads import addFASTACommandLineOptions, parseFASTACommandLineOptions


parser = argparse.ArgumentParser(
    formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    description=('Find sequences that have a specific property (as detected '
                 'by the "relabel" function in the file specified by '
                 '--relabelFunctionFile) and print a TAB-separated list of '
                 'renamings to standard output.'))

parser.add_argument(
    '--relabelFunctionFile', required=True,
    help=('A file containing a Python function named "relabel" that takes a '
          'list of reads and returns a dictionary of renamings.'))

addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTACommandLineOptions(args)

relabel = origRelabel = object()

try:
    exec(open(args.relabelFunctionFile).read())
except Exception as e:
    print('Could not execute Python in %s: %s' % (args.relabelFunctionFile, e),
          file=sys.stderr)
    sys.exit(1)

if relabel is origRelabel:
    print('The Python file %s did not define a function called "relabel".' %
          args.relabelFunctionFile, file=sys.stderr)
    sys.exit(2)

for old, new in relabel(reads).items():
    print('%s\t%s' % (old, new))

<filename>bin/create-newick-relabeling-output.py
#!/usr/bin/env python

from __future__ import print_function

import sys
import argparse

from dark.reads import addFASTACommandLineOptions, parseFASTACommandLineOptions


parser = argparse.ArgumentParser(
    formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    description=('Find sequences that have a specific property (as detected '
                 'by the "relabel" function in the file specified by '
                 '--relabelFunctionFile) and print a TAB-separated list of '
                 'renamings to standard output.'))

parser.add_argument(
    '--relabelFunctionFile', required=True,
    help=('A file containing a Python function named "relabel" that takes a '
          'list of reads and returns a dictionary of renamings.'))

addFASTACommandLineOptions(parser)
args = parser.parse_args()
reads = parseFASTACommandLineOptions(args)

relabel = origRelabel = object()

try:
    exec(open(args.relabelFunctionFile).read())
except Exception as e:
    print('Could not execute Python in %s: %s' % (args.relabelFunctionFile, e),
          file=sys.stderr)
    sys.exit(1)

if relabel is origRelabel:
    print('The Python file %s did not define a function called "relabel".' %
          args.relabelFunctionFile, file=sys.stderr)
    sys.exit(2)

for old, new in relabel(reads).items():
    print('%s\t%s' % (old, new))

#!/usr/bin/env python