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1、个人整理的 QIIME 脚本命令用法大全By peterrjpadd_alpha_to_mapping_file.py Add alpha diversity data to a metadata mapping fileDescription: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
2、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 optionsInput Arguments:REQUIRED-i, -alpha_fpsAlpha diversity data
3、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_fpMapping file to modify by addi
4、ng the alpha diversity dataOPTIONAL-o, -output_mapping_fpFilepath for the modified mapping file default: mapping_file_with_alpha.txt-b, -number_of_binsNumber of bins default: 4.-x, -missing_value_nameBin prefix name for the sample identifiers that exist in the mapping file (mapping_fp) but not in th
5、e alpha diversity file (alpha_fp) default: N/A.-binning_methodSelect 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 nu
6、mber_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.-depthSelect the rarefaction depth to use when the alpha_fps refers to collated
7、 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 value default: highest depth available.-collated_inputUse to specify that the -i option is composed of collated alpha diversity data.Output:The result of r
8、unning this script is a metadata mapping file that will include 3 new columns per alpha diversity metric included in the alpha diversity file. For example, with an alpha diversity file with only PD_whole_tree, the new columns will PD_whole_tree_alpha, PD_whole_tree_normalized and PD_whole_tree_bin.A
9、dding alpha diversity data:Add the alpha diversity values to a mapping file and classify the normalized values into 4 bins, where the limits will be 0 FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_ AACAGATTAGACCAGATTAAGCCGAGATTTACCCGAand in the output combined fasta file
10、would be written like this Sample.1_0 FLP3FBN01ELBSX length=250 xy=1766_0111 region=1 run=R_2008_12_09_13_51_01_ AACAGATTAGACCAGATTAAGCCGAGATTTACCCGANo changes are made to the sequences.Usage: add_qiime_labels.py optionsInput Arguments:REQUIRED-m, -mapping_fpSampleID to fasta file name mapping file
11、filepath-i, -fasta_dirDirectory of fasta files to combine and label.-c, -filename_columnSpecify column used in metadata mapping file for fasta file names.OPTIONAL-o, -output_dirRequired output directory for log file and corrected mapping file, log file, and html file. default: .-n, -count_startSpeci
12、fy the number to start enumerating sequence labels with. default: 0Output:A combined_seqs.fasta file will be created in the output directory, with the sequences assigned to the SampleID given in the metadata mapping file.Example:Specify fasta_dir as the input directory of fasta files, use the metada
13、ta mapping file example_mapping.txt, with the metadata fasta file name column specified as InputFileName, start enumerating with 1000000, and output the data to the directory combined_fastaadd_qiime_labels.py -i fasta_dir -m example_mapping.txt -c InputFileName -n 1000000 -o combined_fastaadjust_seq
14、_orientation.py Get the reverse complement of all sequencesDescription:Write the reverse complement of all seqs in seqs.fasta (-i) to seqs_rc.fasta (default, change output_fp with -o). Each sequence description line will have RC appended to the end of it (default, leave sequence description lines un
15、touched by passing -r):Usage: adjust_seq_orientation.py optionsInput Arguments:REQUIRED-i, -input_fasta_fpPath to the input fasta fileOPTIONAL-o, -output_fpThe output filepath-r, -retain_seq_idLeave seq description lines untouched default: append ” RC” to seq description linesOutput:Example:Reverse
16、complement all sequences in seqs.fna and write result to seqs_rc.fnaadjust_seq_orientation.py -i seqs.fnaalign_seqs.py Align sequences using a variety of alignment methodsDescription:This script aligns the sequences in a FASTA file to each other or to a template sequence alignment, depending on the method chosen. Currently, there are three methods which can be used by the user:1. PyNAST (Caporaso et al., 2009) - T
