ncrf_cat.py

#!/usr/bin/env python
"""
Concatenate several output files from Noise Cancelling Repeat Finder.
"""

from sys   import argv,stdin,stdout,stderr,exit
from os    import path as os_path
from errno import EPIPE
from gzip  import open as gzip_open


def usage(s=None):
	message = """
usage: ncrf_cat <file1> [<file2> ...] [--markend]
  <file1>    an output file from Noise Cancelling Repeat Finder
  <file2>    another output file from Noise Cancelling Repeat Finder
  --markend  assume end-of-file markers are absent in the input, and add an
             end-of-file marker to the output
             (by default we require inputs to have proper end-of-file markers)

Concatenate several output files from Noise Cancelling Repeat Finder.  This
is little more than copying the files and adding a blank line between the
files.

It can also be used to verify that the input files contain end-of-file markers
i.e. that they were not truncated when created."""

	if (s == None): exit (message)
	else:           exit ("%s\n%s" % (s,message))


def main():

	# parse the command line

	requireEof    = True
	markEndOfFile = False
	filenames     = []

	for arg in argv[1:]:
		if (arg in ["--noendmark","--noeof","--nomark"]):   # (unadvertised)
			requireEof = False
		elif (arg in ["--markend]","--markeof"]):
			requireEof    = False
			markEndOfFile = True
		else:
			filenames += [arg]

	if (filenames == []):
		usage("you have to give me at least one file")

	# copy the files;  note that we don't bother (or care) to verify that they
	# are really output from ncrf

	for (ix,filename) in enumerate(filenames):
		if (ix > 0): print

		eofMarkerSeen = False

		if (filename.endswith(".gz")) or (filename.endswith(".gzip")):
			f = gzip_open(filename,"rt")
		else:
			f = file(filename,"rt")

		for line in f:
			line = line.rstrip("\n")
			if (eofMarkerSeen) and (line != ""):
				exit("%s: \"%s\" contains additional stuff after end marker (starting with \"%s\")"
				   % (os_path.basename(argv[0]),filename,line[:10]))
			if (line == "# ncrf end-of-file"):
				eofMarkerSeen = True
				markEndOfFile = True
				continue
			if (not eofMarkerSeen):
				try:
					print line
				except IOError,ex:
					# "Broken pipe" can happen when downstream tools reject
					# our output as their input
					if (ex.errno == EPIPE):
						exit("%s: [Errno %d] Broken pipe"
						   % (os_path.basename(argv[0]),ex.errno))

		f.close()

		if (requireEof) and (not eofMarkerSeen):
			exit("%s: \"%s\" may have been truncated (end marker is absent)"
			   % (os_path.basename(argv[0]),filename))

	if (markEndOfFile):
		print "# ncrf end-of-file"


if __name__ == "__main__": main()