usage:
python danpos.py <command> <wiggle_file_paths> [optional arguments]
positional arguments:
command set as 'profile'
wigfile_paths Path to file that contains protein occupancy data. Each path points to a wiggle format file. Can be multiple paths separated by ',', e.g. f.wig,file_b.wig,file_c.wig. For more information, please go to the page for input files.
optional arguments:
-h, --help show this help message and exit
--bed3file_paths Path to .bed format file that contain a set of genomic elements, such as the positions, peaks, or regions defined by DANPOS. Can be multiple paths separated by ',', e.g., peaks_a.bed,peaks_b.bed. Only the first three columns in bed format are required. For more information, please go to the page for input files. (default: None)
--genefile_paths Path to file that contain a set of genes. Can be multiple paths separated by ',', with each path point to one set of genes. For more information, please go to the page for input files. (default: None)
--genomic_sites the category of genomic site to be analyzed. Can be one or multiple categories chosen from:
TSS transcription start site
TTS transcription terminal site
CSS coding start site
CTS coding terminal site
ESS exon start site
ETS exon terminal site
center center of each element provided in bed file
region the whole region of each element provided in bed file
gene gene body
Names must be separated by ',', (default:TSS,TTS,CSS,CTS,ESS,ETS,gene,center,region)
--heatmap Set to 1 to calculate heatmap values, else set to 0 to cancel this analysis. (default: 0)
--periodicity Set to 1 to do power spectrum density (PSD) analysis, else set to 0 to cancel this analysis. This function checks the strength of periodicity in protein occupancy along DNA. (default: 0)
--wigfile_aliases name for each .wig file. Can be multiple names separated by ',' but must be arranged in the same order as the .wig files. (default: None)
--bed3file_aliases name for each .bed file. Can be multiple names separated by ',' but must be arranged in the same order as the .bed files. (default: None)
--genefile_aliases name for each gene file. Can be multiple names separated by ',' but must be arranged in the same order as the gene files. (default: None)
--name A name for the this run. (default: profile)
--vcal The method to calculate average plot value at each position relative to a given genomic site category (e.g. TSS or peak) in group of genes or genomic elements, could be 'median' or 'mean' (default: mean)
--excludeP Exclude the extremely low or high (outgroup) values by this percentage. useful to avoid the effects of repeat DNA or clonal reads. (default: 0)
--pos_neg The category of values in .wig file to be used in analysis, can be:
0 positive and negative values together
1 positive values only
-1 negative values only
2 positive and negative values separately
3 all kinds of analysis (together, positive, negative),
can be useful when we are analyze the differential signal between two samples. (default: 0)
--bin_size Bin size to be used for plotting, we suggest to set as the step or span size in the .wig files. (default: 10)
--flank_up How far to calculate from the up-stream of each category of genomic site (e.g., TSS). (default: 1500)
--flank_dn How far to calculate to the down-stream of each category of genomic site (e.g., TSS). (default: 1500)
--region_size when 'gene' or 'region' is included in the parameter --genomic_sites, normalize the length of each gene body or region (not include the flanking regions) to this size (default: 1500)
--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,darkgoldenrod)