Latest commit 6d8ffca Aug 16, 2016 @gregcaporaso gregcaporaso committed on GitHub Merge pull request #2151 from iugrina/doc_fix
improve doc for filter_fasta (--valid_states)
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add_alpha_to_mapping_file.py REL: updated for 1.9.1-dev May 22, 2015
add_qiime_labels.py REL: updated for 1.9.1-dev May 22, 2015
adjust_seq_orientation.py REL: updated for 1.9.1-dev May 22, 2015
align_seqs.py REL: updated for 1.9.1-dev May 22, 2015
alpha_diversity.py REL: updated for 1.9.1-dev May 22, 2015
alpha_rarefaction.py REL: updated for 1.9.1-dev May 22, 2015
ampliconnoise.py REL: updated for 1.9.1-dev May 22, 2015
assign_taxonomy.py REL: updated for 1.9.1-dev May 22, 2015
beta_diversity.py REL: updated for 1.9.1-dev May 22, 2015
beta_diversity_through_plots.py REL: updated for 1.9.1-dev May 22, 2015
beta_significance.py REL: updated for 1.9.1-dev May 22, 2015
blast_wrapper.py REL: updated for 1.9.1-dev May 22, 2015
categorized_dist_scatterplot.py REL: updated for 1.9.1-dev May 22, 2015
check_id_map.py REL: updated for 1.9.1-dev May 22, 2015
clean_raxml_parsimony_tree.py REL: updated for 1.9.1-dev May 22, 2015
cluster_quality.py REL: updated for 1.9.1-dev May 22, 2015
collapse_samples.py REL: updated for 1.9.1-dev May 22, 2015
collate_alpha.py REL: updated for 1.9.1-dev May 22, 2015
compare_alpha_diversity.py REL: updated for 1.9.1-dev May 22, 2015
compare_categories.py REL: updated for 1.9.1-dev May 22, 2015
compare_distance_matrices.py REL: updated for 1.9.1-dev May 22, 2015
compare_taxa_summaries.py REL: updated for 1.9.1-dev May 22, 2015
compare_trajectories.py REL: updated for 1.9.1-dev May 22, 2015
compute_core_microbiome.py MNT: use pyplot instead of pylab for imports Apr 26, 2016
compute_taxonomy_ratios.py BUG: Change taxa in compute_taxonomy_ratios.py Dec 9, 2015
conditional_uncovered_probability.py REL: updated for 1.9.1-dev May 22, 2015
consensus_tree.py REL: updated for 1.9.1-dev May 22, 2015
convert_fastaqual_fastq.py REL: updated for 1.9.1-dev May 22, 2015
convert_unifrac_sample_mapping_to_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
core_diversity_analyses.py REL: updated for 1.9.1-dev May 22, 2015
count_seqs.py REL: updated for 1.9.1-dev May 22, 2015
demultiplex_fasta.py REL: updated for 1.9.1-dev May 22, 2015
denoise_wrapper.py REL: updated for 1.9.1-dev May 22, 2015
denoiser.py REL: updated for 1.9.1-dev May 22, 2015
denoiser_preprocess.py REL: updated for 1.9.1-dev May 22, 2015
denoiser_worker.py REL: updated for 1.9.1-dev May 22, 2015
detrend.py REL: updated for 1.9.1-dev May 22, 2015
differential_abundance.py REL: updated for 1.9.1-dev May 22, 2015
dissimilarity_mtx_stats.py REL: updated for 1.9.1-dev May 22, 2015
distance_matrix_from_mapping.py REL: updated for 1.9.1-dev May 22, 2015
estimate_observation_richness.py REL: updated for 1.9.1-dev May 22, 2015
exclude_seqs_by_blast.py REL: updated for 1.9.1-dev May 22, 2015
extract_barcodes.py REL: updated for 1.9.1-dev May 22, 2015
extract_reads_from_interleaved_file.py REL: updated for 1.9.1-dev May 22, 2015
extract_seqs_by_sample_id.py REL: updated for 1.9.1-dev May 22, 2015
filter_alignment.py REL: updated for 1.9.1-dev May 22, 2015
filter_distance_matrix.py REL: updated for 1.9.1-dev May 22, 2015
filter_fasta.py improve doc for filter_fasta (--valid_states) May 25, 2016
filter_otus_by_sample.py REL: updated for 1.9.1-dev May 22, 2015
filter_otus_from_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
filter_samples_from_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
filter_taxa_from_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
filter_tree.py REL: updated for 1.9.1-dev May 22, 2015
fix_arb_fasta.py REL: updated for 1.9.1-dev May 22, 2015
group_significance.py REL: updated for 1.9.1-dev May 22, 2015
identify_chimeric_seqs.py REL: updated for 1.9.1-dev May 22, 2015
identify_missing_files.py REL: updated for 1.9.1-dev May 22, 2015
identify_paired_differences.py REL: updated for 1.9.1-dev May 22, 2015
inflate_denoiser_output.py REL: updated for 1.9.1-dev May 22, 2015
jackknifed_beta_diversity.py REL: updated for 1.9.1-dev May 22, 2015
join_paired_ends.py Update join_paired_ends.py Jul 29, 2016
load_remote_mapping_file.py REL: updated for 1.9.1-dev May 22, 2015
make_2d_plots.py REL: updated for 1.9.1-dev May 22, 2015
make_bipartite_network.py REL: updated for 1.9.1-dev May 22, 2015
make_bootstrapped_tree.py REL: updated for 1.9.1-dev May 22, 2015
make_distance_boxplots.py REL: updated for 1.9.1-dev May 22, 2015
make_distance_comparison_plots.py REL: updated for 1.9.1-dev May 22, 2015
make_fastq.py REL: updated for 1.9.1-dev May 22, 2015
make_library_id_lists.py REL: updated for 1.9.1-dev May 22, 2015
make_otu_heatmap.py REL: updated for 1.9.1-dev May 22, 2015
make_otu_heatmap_html.py make even with biocore Dec 22, 2014
make_otu_network.py REL: updated for 1.9.1-dev May 22, 2015
make_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
make_per_library_sff.py REL: updated for 1.9.1-dev May 22, 2015
make_phylogeny.py REL: updated for 1.9.1-dev May 22, 2015
make_prefs_file.py REL: updated for 1.9.1-dev May 22, 2015
make_qiime_py_file.py REL: updated for 1.9.1-dev May 22, 2015
make_rarefaction_plots.py REL: updated for 1.9.1-dev May 22, 2015
make_tep.py REL: updated for 1.9.1-dev May 22, 2015
map_reads_to_reference.py REL: updated for 1.9.1-dev May 22, 2015
merge_mapping_files.py REL: updated for 1.9.1-dev May 22, 2015
merge_otu_maps.py REL: updated for 1.9.1-dev May 22, 2015
merge_otu_tables.py REL: updated for 1.9.1-dev May 22, 2015
multiple_extract_barcodes.py REL: updated for 1.9.1-dev May 22, 2015
multiple_join_paired_ends.py REL: updated for 1.9.1-dev May 22, 2015
multiple_rarefactions.py REL: updated for 1.9.1-dev May 22, 2015
multiple_rarefactions_even_depth.py REL: updated for 1.9.1-dev May 22, 2015
multiple_split_libraries_fastq.py Modified usage scripts to fix script test failures, added text for cl… May 3, 2016
neighbor_joining.py REL: updated for 1.9.1-dev May 22, 2015
nmds.py REL: updated for 1.9.1-dev May 22, 2015
normalize_table.py REL: updated for 1.9.1-dev May 22, 2015
observation_metadata_correlation.py REL: updated for 1.9.1-dev May 22, 2015
otu_category_significance.py REL: updated for 1.9.1-dev May 22, 2015
parallel_align_seqs_pynast.py REL: updated for 1.9.1-dev May 22, 2015
parallel_alpha_diversity.py REL: updated for 1.9.1-dev May 22, 2015
parallel_assign_taxonomy_blast.py REL: updated for 1.9.1-dev May 22, 2015
parallel_assign_taxonomy_rdp.py REL: updated for 1.9.1-dev May 22, 2015
parallel_assign_taxonomy_uclust.py REL: updated for 1.9.1-dev May 22, 2015
parallel_beta_diversity.py REL: updated for 1.9.1-dev May 22, 2015
parallel_blast.py REL: updated for 1.9.1-dev May 22, 2015
parallel_identify_chimeric_seqs.py REL: updated for 1.9.1-dev May 22, 2015
parallel_map_reads_to_reference.py REL: updated for 1.9.1-dev May 22, 2015
parallel_merge_otu_tables.py REL: updated for 1.9.1-dev May 22, 2015
parallel_multiple_rarefactions.py REL: updated for 1.9.1-dev May 22, 2015
parallel_pick_otus_blast.py REL: updated for 1.9.1-dev May 22, 2015
parallel_pick_otus_sortmerna.py REL: updated for 1.9.1-dev May 22, 2015
parallel_pick_otus_trie.py REL: updated for 1.9.1-dev May 22, 2015
parallel_pick_otus_uclust_ref.py REL: updated for 1.9.1-dev May 22, 2015
parallel_pick_otus_usearch61_ref.py REL: updated for 1.9.1-dev May 22, 2015
pick_closed_reference_otus.py REL: updated for 1.9.1-dev May 22, 2015
pick_de_novo_otus.py REL: updated for 1.9.1-dev May 22, 2015
pick_open_reference_otus.py REL: updated for 1.9.1-dev May 22, 2015
pick_otus.py REL: updated for 1.9.1-dev May 22, 2015
pick_rep_set.py REL: updated for 1.9.1-dev May 22, 2015
plot_rank_abundance_graph.py REL: updated for 1.9.1-dev May 22, 2015
plot_semivariogram.py MNT: use pyplot instead of pylab for imports Apr 26, 2016
plot_taxa_summary.py REL: updated for 1.9.1-dev May 22, 2015
poller.py REL: updated for 1.9.1-dev May 22, 2015
principal_coordinates.py REL: updated for 1.9.1-dev May 22, 2015
print_metadata_stats.py REL: updated for 1.9.1-dev May 22, 2015
print_qiime_config.py REL: updated for 1.9.1-dev May 22, 2015
process_iseq.py REL: updated for 1.9.1-dev May 22, 2015
process_qseq.py REL: updated for 1.9.1-dev May 22, 2015
process_sff.py REL: updated for 1.9.1-dev May 22, 2015
quality_scores_plot.py REL: updated for 1.9.1-dev May 22, 2015
relatedness.py REL: updated for 1.9.1-dev May 22, 2015
shared_phylotypes.py REL: updated for 1.9.1-dev May 22, 2015
simsam.py REL: updated for 1.9.1-dev May 22, 2015
single_rarefaction.py REL: updated for 1.9.1-dev May 22, 2015
sort_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
split_libraries.py REL: updated for 1.9.1-dev May 22, 2015
split_libraries_fastq.py ENH/DOC: Improve docs and pieces of code Aug 29, 2015
split_libraries_lea_seq.py REL: updated for 1.9.1-dev May 22, 2015
split_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
split_otu_table_by_taxonomy.py REL: updated for 1.9.1-dev May 22, 2015
split_sequence_file_on_sample_ids.py REL: updated for 1.9.1-dev May 22, 2015
start_parallel_jobs.py REL: updated for 1.9.1-dev May 22, 2015
start_parallel_jobs_sc.py REL: updated for 1.9.1-dev May 22, 2015
start_parallel_jobs_slurm.py fix bug in parameter Oct 14, 2015
start_parallel_jobs_torque.py REL: updated for 1.9.1-dev May 22, 2015
subsample_fasta.py REL: updated for 1.9.1-dev May 22, 2015
summarize_otu_by_cat.py make even with biocore Dec 22, 2014
summarize_taxa.py REL: updated for 1.9.1-dev May 22, 2015
summarize_taxa_through_plots.py REL: updated for 1.9.1-dev May 22, 2015
supervised_learning.py Merge pull request #2044 from ElDeveloper/sl-docs May 3, 2016
transform_coordinate_matrices.py REL: updated for 1.9.1-dev May 22, 2015
tree_compare.py REL: updated for 1.9.1-dev May 22, 2015
trflp_file_to_otu_table.py REL: updated for 1.9.1-dev May 22, 2015
trim_sff_primers.py REL: updated for 1.9.1-dev May 22, 2015
truncate_fasta_qual_files.py REL: updated for 1.9.1-dev May 22, 2015
truncate_reverse_primer.py REL: updated for 1.9.1-dev May 22, 2015
unweight_fasta.py REL: updated for 1.9.1-dev May 22, 2015
upgma_cluster.py REL: updated for 1.9.1-dev May 22, 2015
validate_demultiplexed_fasta.py fixes #2102 Nov 5, 2015
validate_mapping_file.py REL: updated for 1.9.1-dev May 22, 2015