Resolved issue #577 (mostly); most scripts output filenames written to at end of main

	modified:   scripts/abundance-dist-single.py
	modified:   scripts/abundance-dist.py
	modified:   scripts/count-median.py
	modified:   scripts/count-overlap.py
	modified:   scripts/extract-long-sequences.py
	modified:   scripts/extract-paired-reads.py
	modified:   scripts/fastq-to-fasta.py
	modified:   scripts/filter-abund-single.py
	modified:   scripts/interleave-reads.py
	modified:   scripts/load-graph.py
	modified:   scripts/load-into-counting.py
	modified:   scripts/make-initial-stoptags.py
	modified:   scripts/merge-partitions.py
	modified:   scripts/partition-graph.py
	modified:   scripts/split-paired-reads.py

scripts that WERE updated && notes:

	abundance-dist			already does earlier in script
	abundance-dist-single		already does earlier in script
	count-overlap
	extract-long-sequences
	extract-paried-reads 		explicitly two output files; listed on one line:
					print('wrote to: ' + outfile + '.se' + ' and ' + outfile + '.pe')
	fastq-to-fasta			file output optional; either outputs 'wrote to' message or 'did not write output to file'
	filter-abund-single		already does earlier in script
	interleave-reads		file output optional; either outputs 'wrote to' message or 'did not write output to file'
	load-graph
	load-into-counting		creates various partway files, messages for them already exists.
					'wrote to: ' message only prints on successful program end to ensure being printed
					at the end of output.
	make-initial-stoptags		uncertain how output is written since script uses "htable.save_stop_tags()" instead
					of explicit file write object. 'wrote out: ' message added anyway.
	merge-partitions		No API entry exists for this script!
					Already messages earlier in script
	partition-graph			threading is confusing; potentially multiple files
	split-paired-reads		explicitly two output files; message is:
					"'wrote to: ' + out1 + ' and ' + out2"

scripts that were NOT updated && notes on why:

	annotate-partitions 		already does, multiple files
	count-median 			already does
	do-partition 			already does, multiple files
	extract-paritions		already does, multiple files
	filter-abund			already does, multiple files
	filter-stoptags			already does, multiple files
	find-knots			already does (mostly), multiple files, renames some things without outputting message
	normalize-by-median		personally uncertain about logic flow && script appears to warn on output anyway
	sample-reads-randomly		already does, multiple files
On Tue, Sep 16, 2014 at 08:04:49AM -0700, bocajnotnef wrote:
> > @@ -67,6 +67,11 @@ def main():
> >  
> >      else:
> >          print >> sys.stderr, 'No lines dropped from file.'
> > +    
> > +    if args.output:
> > +        print('wrote to: ' + args.output)
> > +    else:
> > +        print('did not write output to file')
> 
> Hmm. Cannot push to this fork on the ged repository--access denied for me. Expected?

You should be pushing to your own fork, which is at 

https://github.com/bocajnotnef/khmer

and to the branch 

lowhangingfruit/script-output-file-listing

-- take another look through the docs,

http://khmer.readthedocs.org/en/latest/dev/getting-started.html

--titus
-- 
C. Titus Brown, ctb@msu.edu