ged-lab/khmer — pull request #596 by bocajnotnef (2014-09-12 16:43:29+00:00)
Title: 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