Dantools Options

[Jared Taylor]

Hello all, I am not sure how many of you have looked into dantools yet... But I see it as a very powerful downstream tool to use in concert with danpos!

My colleagues and I have put together this basic 'options' document for everyone to use.

python dantools.py peakSelector <peakfile_paths>[optional arguments] positional arguments: command This tells dantools the job that is to be done, may be peakSelector, peaksAnalysis, or wigAnalysis peakfile_path a path to the peak file, should be in the default output format of DANPOS. See DANPOS documentation for more information. optional arguments: -h, --help show this help message and exit --selector a set of column names from the peak file, names are seperated by'&', each column name comes with a pair of lower end cutoff and higher end cutoff in the format name1:low1:high1,name2:low2:high2, e.g. promoter:-350:50&control_smt_val:0:1000 means selecting peaks that are in the promoter region from 350bp upstream to 50bp downstream and have control_smt_val values between 0 and 1000. (default: None) --peak_out An output file name for saving the selected peaks. (default: peakSelector.xls) --gene_file A reference gene set, required for when need to select nucleosomes on gene promoters. gene set file must at least contain the following columns ordered as : name,chrom,strand, txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,exonEnds, we suggest to downoad gene set from the UCSC tables at http://genome.ucsc.edu/cgi-bin/hgTables?command=start (default: None) --gene_out An output file name for saving the genes associated with selected nucleosome peaks on promoters (default: None) Kaifu Chen, et al. chen...@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine. @user:~/danpos/test/dantools$ python dantools.py wigAnalysis -h usage: python dantools.py wigAnalysis <wiggle_file_paths> <gene_file_paths>[optional arguments] positional arguments: command This tells dantools the job that is to be done, may be peakSelector,peaksAnalysis or wigAnalysis wigfile_paths Paths to MNaseSeq data sets. each path connect to a wiggle format file, paths must be seperated by comma ','. genefile_paths Paths to files each contains a gene sets. paths must be seperated by comma ','. gene set file must contain at least the following columns ordered as: name,chrom,stra nd,txStart,txEnd,cdsStart,cdsEnd,exonCount,exonStarts,e xonEnds, we suggest to downoad gene set from the UCSC tables at http://genome.ucsc.edu/cgi- bin/hgTables?command=start optional arguments: -h, --help show this help message and exit --wigfile_aliases a set of short alias for the wiggle paths. must be seperated by comma ','. Each wiggle file path will be replaced by its alias in the output files (default: None) --genefile_aliases a set of short alias for the gene files, must be seperated by comma ','. Each gene file path will be replaced by its alias in the out put files. (default: None) --name A name for the experiment. (default: wigAnalysis) --pos_neg set to 0,1,-1,2,3 if want to do analysis for positive and negative values together, positive values only, negative values only, positive and negative values seperately, or all kinds of analysis (together, positive, negative), this will be useful when we are analyze the differential signal between two samples. (default: 0) --bin_size bin size to be used, it is suggested to be the same as step or span size in the input wiggle files. (default: 10) --tss_flank_up how far to calculate from the up stream of TSS. (default: 1500) --tss_flank_dn how far to calculate to the down stream of TSS. (default: 3000) --plot_row number of rows to plot on each page. (default: 2) --plot_column number of columns to polt on each page. (default: 2) --plot_xmin minimal value on the x axis of each plot. (default: None) --plot_xmax maximal value on the x axis of each plot. (default: None) --plot_ymin minimal value on the y axis of each plot. (default: None) --plot_ymax maximal value on the y axis of each plot. (default: None) --plot_xlab the label on the x axis. (default: Relative distance) --plot_ylab the label on the y axis. (default: Average signal value) --plot_colors the colors to be used in the plot. (default:black,gray ,red,blue,orange,purple,skyblue,cyan,green,blue4,darkgo ldenrod) Kaifu Chen, et al. chen...@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine. @user:~/danpos/test/dantools$ python dantools.py peaksAnalysis -h usage: python dantools.py peaksAnalysis <peakfile_paths>[optional arguments] positional arguments: command This tells dantools the job that is to be done, may be peakSelector, peaksAnalysis or wigAnalysis peakfile_paths a path to the peaks_file, should be in the default output format of DANPOS: each file contains peaks from a control sample and a treat sample. See DANPOS documentation for mor information. peakfile_aliases a set of aliases for the peaks_files, each peakfile would have a pair of alias in the format a:b, 'a' represent the control peaks, 'b' represents the treat peaks, different pairs must be seperated by comma ','. optional arguments: -h, --help show this help message and exit --name A name for the experiment. (default: peaksAnalysis) --dis_min minimal distance between nucleosome dyads. (default: None) --dis_max maximal distance between nucleosome dyads. (default: None) --dis_step bin size or step used to calculate the distribution of nucleosome dyads distances. (default: None) --occ_min minimal occupancy value of nucleosome peaks. (default: None) --occ_max maximal occupancy value of nucleosome peaks. (default: None) --occ_step step or bin size used to calculate occupancy values distribution. (default: None) --fuz_min minimal fuzziness score of nucleosome peaks. (default: None) --fuz_max maximal fuzziness score of nucleosome peaks. (default: None) --fuz_step step or bin size used to calculate fuzziness scores distribution. (default: None) --plot_row number of rows to plot on each page. (default: 2) --plot_column number of columns to polt on each page. (default: 2) --plot_colors the colors to be used in the plot (default:black,gray,red,blue,orange,purple,skyblue,cyan,green,blue4,darkgoldenrod) Kaifu Chen, et al. chen...@gmail.com, Li lab, Biostatistics department, Dan L. Duncan cancer center, Baylor College of Medicine.

If any of this is wrong, please alert me.

[Jared Taylor]

Also, Kaifu updated dantools 0.1.0 beta without updating the name, so if you guys attempted to use it a while ago, redownload it and try again! 

[Chen, Kaifu]

Thank you, Jared, we appreciate it!

The beta version will keep changing as we are making improvement. We will start releasing stable versions once we finish a more formal documentation.

----------------------------------------------------------------------
Postdoctoral Associate,
Tel: 1-713-798-4640
Li Lab, Dan L. Duncan Cancer Center,
Molecular and Cellular Biology Department, BCM.
450A C2, Cullen Building, 1 Baylor Plaza, Houston, TX 77030.

________________________________________
From: dan...@googlegroups.com [dan...@googlegroups.com] On Behalf Of Jared Taylor [taylor....@gmail.com]
Sent: Thursday, February 07, 2013 11:55 AM
To: dan...@googlegroups.com
Subject: Dantools Options

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