个人整理的qiime命令用法大全

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1、个人整理的QIIME脚本命令用法大全Bypeterrjpadd_alpha_to_mapping_file.py –AddalphadiversitydatatoametadatamappingfileDescription:AddalphadiversitydatatoamappingfileforusewithotherQIIMEscripts,i.e. make_3d_plots.py.Theresultingmappingfilewillcontainthreenewcolumnspermetricin

2、thealphadiversitydata;thefirstcolumnbeingtherawvalue,thesecondbeinganormalizedrawvalueandthethirdonealabelclassifyingthebinwherethisvaluefitsbasedonthenormalizedvalue.Usage: add_alpha_to_mapping_file.py [options]InputArguments:[REQUIRED]-i, --alpha_fpsAlphad

3、iversitydatawithoneormultiplemetricsi.e.theoutputof alpha_diversity.py.Thiscanalsobeacomma-separatedlistofcollatedalphadiversityfilepathsi.e.theoutputof collate_alpha.py,whenusingcollatedalphadiversitydatathe–depthoptionisrequired-m, --mapping_fpMappingfilet

4、omodifybyaddingthealphadiversitydata[OPTIONAL]-o, --output_mapping_fpFilepathforthemodifiedmappingfile[default:mapping_file_with_alpha.txt]-b, --number_of_binsNumberofbins[default:4].-x, --missing_value_nameBinprefixnameforthesampleidentifiersthatexistinthem

5、appingfile(mapping_fp)butnotinthealphadiversityfile(alpha_fp)[default:N/A].--binning_methodSelectthemethodnametocreatethebins,theoptionsare‘equal’and‘quantile’.Bothmethodsworkoverthenormalizedalphadiversityvalues.Ontheonehand‘equal’willassignthebinsonequally

6、spacedlimits,dependingonthevalueof–number_of_binsi.e.ifyouselect4thelimitswillbe[0.25,0.50,0.75].Ontheotherhand‘quantile’willselectthelimitsbasedonthe–number_of_binsi.e.thelimitswillbethequartilesif4isselected[default:equal].--depthSelecttherarefactiondeptht

7、ousewhenthealpha_fpsreferstocollatedalphadiversityfile(s)i.e.theoutputof collate_alpha.py.Alltheiterationscontainedatthisdepthwillbeaveragedtoformasinglemeanvalue[default:highestdepthavailable].--collated_inputUsetospecifythatthe-ioptioniscomposedofcollateda

8、lphadiversitydata.Output:Theresultofrunningthisscriptisametadatamappingfilethatwillinclude3newcolumnsperalphadiversitymetricincludedinthealphadiversityfile.Forexample,withanalphadiversityfilewit