Contplot

CONTPLOT

version 2.0

Contig Generation tool

Installation procedure

In order to install contplot, the following files should be present in the same bin directory, inside the conplot package:

File Description
contplot
contplot executable
gnuplot
gnuplot executable
VeraBd.ttf
font file used to generate the images
prologue.ps
prologue and epilogue file used to generate eps files

Usage instructions

To generate a distinct contig, the star spectra file, the abruijn graph file and the sps_seqs file are needed. Also, the contig needs to be specified. For example:

$ ./contplot --abruijn  component_info.bin --star stars.pklbin --seqs sps_seqs.pklbin --contig 1

Will generate the associated representation in a 'png' file format of the first contig found. 

Different output formats such as 'eps' can be specified with the '--format' command-line option.  Here is a summary of relevant options:

Parameter Value Default Required Description
--abruijn FILE   YES Abruijn graph file.
--star FILE   YES Stars file.
--seqs FILE   YES Seqs file.
--font-dir DIRECTORY origin   Font files location in the file system.
--renderer-dir DIRECTORY origin   Renderer location in the file system.
--contig INDEX   YES Contig (X) 1-based
--reverse   N/A   Reverse contig.
--reference SEQUENCE     Reference sequence.
--homolog SEQUENCE     Homolog sequence.
--denovo SEQUENCE     Denovo sequence.
--user SEQUENCE     User sequence.
--mass-reference VALUE LIST     Reference sequence mass intervals, separated by the ' | ' character
--mass-homolog VALUE LIST     Homolog sequence mass intervals, separated by the ' | ' character
--offset-reference VALUE     Reference sequence mass offset
--offset-homolog VALUE     Homolog sequence mass offset
--offset-user VALUE     User sequence mass offset
--peakmasstol VALUE     Amino acid peak mass tolerance
--individual-peakmasstol       If specified, individual peak mass tolerance is used
--individual-peakmasstol   N/A   If specified, individual peak mass tolerance is used.
--parentmasstol VALUE     Parent mass tolerance
--annotation-style-inspect   N/A   Set annotation style to INSPECT.
--notitle   N/A   Disables title generation
--title STRING     Specifies title
--zoom VALUE 1.0   Zoom factor
--image-width NUMBER 800   Image width, in pixels.
--image-height NUMBER 600   Image height, in pixels.
--image-stretch-width NUMBER -1   Image width limit, in pixels. -1 for unlimited stretch.
--image-stretch-height NUMBER -1   Image height limit, in pixels. -1 for unlimited stretch.
--format STRING eps   Image output format (png or eps)
--outdir DIRECTORY .   Output directory
--outfile FILE file.png   Output filename
--target STRING file   Output target (file, cout, internal)
--encoding STRING none   Output encoding (uu64, default is no encoding)
--eps-correction   N/A   Use shift correction for eps files.
--minimum-intensity   N/A   Use minimum intensity values to draw the peaks.
--peak-thickness NUMBER 4   Specify peak line thickness (Default is 4).
--request-id       No effect. Used to allow the generation of different request (browser string) in order to avoid browser caching.

In the above list, "origin" refers to the location of the executed contplot binary. By default, both the renderer and the fonts file are expected to be in the same directory as the contplot binary.

In case the reference or homolog mass intervals are omitted and the corresponding sequences are present, the mass intervals are calculated from the sequence using default amino acid mass values, as well as mass gaps defined in the sequence.

Additional usage examples

./contplot --star ./spectra/stars.pklbin --abruijn ./assembly/component_info.bin --seqs ./assembly/sps_seqs.pklbin --contig 5 --mass-reference "18.0|360.2|447.2|576.3|689.4|899.5|1030.5|1167.6|1410.6|1596.7|1709.8|1823.8|1880.9|2008.9" --mass-homolog "18.0|360.2|447.2|576.3|689.4|899.5|1030.5|1167.6|1410.6|1596.7|1709.8|1823.8|1880.9|2008.9" --offset-reference -18.01 --offset-homolog -18.01 --reverse --target cout --encoding uu64 --notitle --zoom 0.4 --homolog "(RSV)SEL(PI)MH(QD)WLNGK" --denovo "[342.196]SEI[210.13]MH[243.077]WINGQ[294.12]" --image-stretch-width 300 --image-stretch-height -1 --aa ../../../bin/AA_cys_nipia.txt --request-id 9 --outdir /tmp --outfile Contig5.png
./contplot --star ./spectra/stars.pklbin --abruijn ./assembly/component_info.bin --seqs ./assembly/sps_seqs.pklbin --title "Contig 1" --contig 1 --mass-reference "0.0|99.1|186.1|344.2|472.3|573.3|674.3|771.4|955.5|1054.5|1217.6|1427.7|1498.7|1810.9|1881.9|2010.0|2225.1" --mass-homolog "0.0|99.1|186.1|344.2|472.3|573.3|674.3|771.4|955.5|1054.5|1217.6|1427.7|1498.7|1810.9|1881.9|2010.0|2225.1" --offset-reference -0.00 --offset-homolog -0.00 --target cout --encoding uu64 --homolog "VS(SA)KTTP(PS)VY(PL)A(PGSA)AQ(TN)" --denovo "VS[158.062]QTTP[184.075]VY[210.131]A[312.124]AQ[215.101]" --image-stretch-width -1 --image-stretch-height -1 --aa ../../../bin/AA_cys_nipia.txt --outdir /tmp --outfile Contig1.png

Known issues

GnuPlot has some issues related to EPS file generation. There seems to exist a bug related to loss of precision in coordinate translation which introduces differences and gaps when dealing with large files. As a result, a correction was introduced to compensate for the experienced gaps. The user may use the correction through the parameter --eps-correction.

References

http://www.gnuplot.info/

http://people.duke.edu/~hpgavin/gnuplot.html

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