added, average traces in make_3d_plots

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3090 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated some discussion of version information

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3091 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed issue where parameter values that included spaces were not being parsed correctly

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3092 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
moved some tests that were in the wrong class

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3093 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added qiime_blastx_seqs() as a baseline function for performing functional read assignment using translated BLAST

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3094 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified get_blast_hits to support blastx searches for functional read assignment

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3095 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added basic functionality for doing clustering and ultimately functional assignment of reads using blastx

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3096 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified so blast db files are written to qiime_temp_dir rather than the directory where the input file is located

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3097 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated for better handling of case where directory containing refseqs file is not writable

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3098 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added functionality to support quality filtering and 'demultiplexing' of non-barcoded data

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3099 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified to support quality filtering of non-demultiplexed data from the command line. see two new usage examples.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3100 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated quality_scores_plot.py to support fastq files and gzipped fastq/qual files

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3101 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
added function to view lines from a gzip file.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3102 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed repetitive call to abspath which would fail if refseqs_fp == None

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3103 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Adding default values to all file variables. Prevents variable referenced before assignment errors

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3104 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed error that was introduced -- input_fps needs to be a string, not existing_filespaths, so wildcard statements can be passed in

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3105 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
all_tests.py now returns a non-zero exit code if any of the unit, script, or script usage tests fail (unless these were suppressed), or if any application cannot be found. Modified run_script_usage_tests() to return the number of failures in addition to the results summary string.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3106 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated to allow user to override the phred offset -- this is useful in special cases

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3107 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
fixed bug that required refseqs to be specified as a full path

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3108 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Add the --no_single_ok_generic option to assign_taxonomy.py and rtax.py.  This controls whether to classify based on a single read, when its mate pair is too short or too highly conserved to be informative.  (Requires Rtax 0.982)

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3109 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a