个人整理的Qiime命令用法大全详解.doc

个人整理的QIIME脚本命令用法大全 By peterrjp add_alpha_to_mapping_file.py?– Add alpha diversity data to a metadata mapping file Description: Add alpha diversity data to a mapping file for use with other QIIME scripts, i. e.?make_3d_plots.py. The resulting mapping file will contain three new columns per metric in the alpha diversity data; the first column being the raw value, the second being a normalized raw value and the third one a label classifying the bin where this value fits based on the normalized value. Usage:?add_alpha_to_mapping_file.py?[options] Input Arguments: [REQUIRED] -i,?--alpha_fps Alpha diversity data with one or multiple metrics i. e. the output of?alpha_diversity.py. This can also be a comma-separated list of collated alpha diversity file paths i. e. the output of?collate_alpha.py, when using collated alpha diversity data the –depth option is required -m,?--mapping_fp Mapping file to modify by adding the alpha diversity data [OPTIONAL] -o,?--output_mapping_fp Filepath for the modified mapping file [default: mapping_file_with_alpha.txt] -b,?--number_of_bins Number of bins [default: 4]. -x,?--missing_value_name Bin prefix name for the sample identifiers that exist in the mapping file (mapping_fp) but not in the alpha diversity file (alpha_fp) [default: N/A]. --binning_method Select the method name to create the bins, the options are ‘equal’ and ‘quantile’. Both methods work over the normalized alpha diversity values. On the one hand ‘equal’ will assign the bins on equally spaced limits, depending on the value of –number_of_bins i. e. if you select 4 the limits will be [0.25, 0.50, 0.75]. On the other hand ‘quantile’ will select the limits based on the –number_of_bins i. e. the limits will be the quartiles if 4 is selected [default: equal]. --depth Select the rarefaction depth to use when the alpha_fps refers to collated alpha diversity file(s) i. e. the output of?collate_alpha.py. All the iterations contained at this depth will be averaged to form a single mean