
svist4get (version 1.3): a simple visualization tool for genomic tracks from sequencing experiments.

COMMAND-LINE PARAMETERS
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[POST-INSTALL EXAMPLE DATA]

--sampledata
	Creates the 'svist4get' folder in the current working directory.
	The folder will contain sample data sets and adjustable
	configuration file templates.
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[MANDATORY ARGUMENTS]
-t <id>	
	Visualization of the genomic window of a particular
	transcript (using GTF transcript_id)
  OR
-g <id>
	Visualization of the genomic window of a particular
	gene (using GTF gene_id)
  OR
-t <id> -w tss|tis <upstream> <downstream>
	Visualization of the genomic window centered on a transcription start
	site|translation initiation site of a particular transcript
        (using GFF transcript_id) with a fixed offsets upstream and downstream
  OR 
-w <contig> <start> <end>
	Visualization an arbitrary genomic window using genomic coordinates

-fa <file.fa>
	Path to the genome assembly multifasta for the sequence track
	NOTE: the multifasta file must contain all contigs in a single file.

-gtf <file.gtf>
	Path to the gtf file with the transcript annotation
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[OPTIONAL ARGUMENTS]
-bg <file1.bedGraph> [<file2.bedGraph>...]
	Paths to bedGraph files for genomic signal tracks

-pbg <file1A.bedGraph file1A.bedGraph> [ -pbg <file2A.bedGraph file2B.bedGrap>...]
	Paths to 2 bedGraph files to be used for the paired genomic signal track
        (e.g. to plot signals for + and - DNA strands together). Positive and negative range
	of the Y-axis will be used for the first and second file, respectively
	(or vice versa if the reverse complementary transformation using -rc parameter is requested)
	The track will use absolute values from each bedGraph.
	Multiple paired tracks can be generated by using multiple '-pbg' parameters.
	For this track, the signs of values in each bedGraph will be ignored

-c <path> |A4_p1|A4_p2|A4_l 
	Path to a configuration file or name of the premade config file
	(can be A4_p1, A4_p2, A4_l)

-o <name> 
	Output file name. Generates a pdf (vector) or png (raster) file based on
	the provided extension. Both png and pdf will be generated if the extension is not specified.

-hi
	Hide intronic segments (default: false)

-rc
	Reverse-complement transformation of the genomic window (default: off)

-bgb mean|median|max|min|none
	This parameter sets the function to aggregate bedGraph signal values for a single bar of the bedGraph tracks.
  	Default: 'mean'. Alternatives: 'median', 'max', 'min'. 'none' forces plotting the raw signal at 1nt resolution.

-bg_log 
	Logarithmic (log2) scale for the each bedGraph (Y-axis).

-nts
	Show reference genomic sequence with single-nucleotide resolution
	(default: hide)

-aas auto|tics|codons
	Style of the aminoacid sequence track: tics (suitable for long regions e.g. > 160 nts,
 	shows only start and stop codons with colored tics) or codons (show each aminoacid as labeled block)
	(default: auto)

-it <text>
	Image title

-xs <N>
	X axis tics step (nt) (default: auto)

-lb <N1> [<N2>..]
	Y axis tics levels for a bedGraph track, a space-separated list
	of values, a separate value for each bedGraph track (default: auto)

-ys <N1> [<N2>...]
	Step between axis tics a the bedgraph track Y-axis, a space-separated
	list of values, a separate value for each bedGraph track (default: auto)

-bul <N1> <N2>... | max
 	Upper limit for a bedGraph track Y-axis, can be:
	1. a space-separated list of values: a separate axis limit for each
	   bedGraph track;
	2. max: a maximum reachable value across all visible tracks.
	Default: reachable maximum for each track separately.

-bll <N1> <N2>... | min
 	Lower limit for a bedGraph track Y-axis, can be:
	1. a space-separated list of values: a separate axis limit for each
	   bedGraph track;
	2. min: a minimum reachable value across all visible tracks.
	Paired bedGraph uses absolute values for both signal tracks,
	since the negative Y-axis range is used to display the 2nd track.
	
-bl <tex1t> <text2> 
	Text labels for the bedGraph tracks, space-separated list of values,
	a separate value required for each bedGraph track
	(default: names of the bedGraph files)
-blp left|center|right 
	Text label position for the bedGraph tracks (default: center)

-bgc <color1>[color2>..]
	Space-separated list of colors for bedGraph tracks. The colors should be specified
 	by names listed in the palette file (default: internal palette or palettes/palette.txt).
 	The list will be cycled through if shorter than the number of bedGraph tracks.
 	Paired and basic bedGraph tracks use joint color list.

-gi <s-e> [<s1-e1>...]
	Additional track showing selected genomic intervals as segments,
	space-separated list of start-end pairs

-gil <tex1t> <text2>...
	Labels for genomic intervals, space-separated list of strings,
	a separate value required for each gemomic intervals track

-gic <color1>[<color2>..]
	Space-separated list of colors for genomic intervals tracks, uses the same logic as -bgc parameter
	
-st <transcript_id1> <transcript_id2>...
	A complete list of transcript IDs to show (others will be hidden,
	applicable to -w and -g modes) 

-tl <transcript_id> <label>
	Allows to replace the default <transcript_id> label with an arbitrary text <label>.
	For re-labeling several transcripts, several '-tl' keys can be used.

-tls auto|both|id|name|gene_id|none 
	Transcript label style. Can be 'none' (hide the transcript label),
	'name','id' or gene_id (show annotated transcript_name, transcript_id or
	gene_id respectively as a transcript_label), 
	'both' (show annotated transcript_name and transcript_id)
	and 'auto' (hide name if it is included in the ID)
	
-hrf <N> 
	Highlight a particular reading frame (+0, +1 or +2) 
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[MISCELLANEOUS ARGUMENTS]
-h, --help
	Show this help message and exit

-v, --version
	Show program version
--debug
	Provide detailed stack trace for debugging purposes
--verbose 
	Show all progress messages

-hf <x1> <x2> <label>
	Highlight and label a given segment of the genomic window
	(global coordinates on the selected contig)

-hc <NtNtNt>
 	Highlight selected codon on the aminoacid sequence track, e.g. -hc TGA
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[SIMPLE EXAMPLE WITH MINIMAL ARGUMENTS]
svist4get -gtf svist4get_data/S.cerevisiae.gtf -fa svist4get_data/S.cerevisiae.dna.fa -bg svist4get_data/RiboCov_cut.bedGraph -t YFL031W
