added --evalue parameter

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3110 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified to allow the user to specify the field to be used for the otu id from the usearch output. for functional assignment, we want this to be the entry that represents the reference sequence in the database.


git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3111 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modifications to the functional assignment code - this is still _very much_ in progress

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3112 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
cleaned up the functional assignment code as I'm writing a parallel wrapper

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3113 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
add log file to functional assignment code

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3114 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Generalized convert_fastaqual_to_fastq.py to handle conversions both ways (fasta/qual to fastq, fastq to fasta/qual), committing code generated by Abhisaar Yadav, reviewed by myself.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3115 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated the get_split_libraries_fastq_params_and_file_types function to allow 13 bases in fastq file while mapping only has 12



git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3116 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
solved, issue in test_make_3d_plots.py

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3117 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
changed the naming of the inputs for summarize_otu_by_cat.py to be in line with the rest of qiime

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3118 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Fixed citation string that had an invalid ASCII character that made python complain.

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3119 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
reverted a change because it broke something

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3120 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
actually reverting

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3121 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
finally fixing the problems i recently caused by uploading personal untested code

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3122 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
finally fixing the problems i recently caused by uploading personal untested code

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3123 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
centralized code for timing out tests

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3124 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
Added .fas extension to valid fasta files that will be checked for add_qiime_labels.py

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3125 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
integrated test timeout/alarm code that was moved to test.py

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3126 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
updated parameters based on basic evaluation on muegge mammals vs m5nr. full parameter sweep is in order

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3127 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
modified functional assignment code for easier testing and added basic test

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3128 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a
expanded the test template

git-svn-id: https://qiime.svn.sourceforge.net/svnroot/qiime/trunk@3129 b0fff984-a1a5-4f5a-893b-b8b2c7becc1a