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Top Forums Shell Programming and Scripting Shorten header of protein sequences in fasta file Post 302881218 by alexypaul on Friday 27th of December 2013 07:51:00 AM
Old 12-27-2013
Hi,

It works perfectly. Thank you very much!
 

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GVMAP.SH(1)						      General Commands Manual						       GVMAP.SH(1)

NAME
gvmap.sh - pipeline for running gvmap SYNOPSIS
gvmap.sh [-vV?] [ options ] [ -o outfile ] [ files ] DESCRIPTION
gvmap.sh takes as input a graph in DOT format, performs a layout, runs the output through gvmap and renders the output. At some point, it is hoped to integrate all of these tasks into gvmap. OPTIONS
The following options are supported: -a k The integer k specifies the average number of artificial points added along the bounding box of the labels. Such artificial points are added to avoid a country boundary cutting through the boundary box of the labels. Computing time is proportional to k; hence, for large graphs, a small value of k is suggested. If k = -1, a suitable value of k is automatically selected based on the graph size. By default k = -1. -K layout specifies which program should be use for the initial layout. By default, sfdp is run. Also by default, the layout is passed the flag -Goverlap=prism. This can be overridden using a -g flag. -T format specifies the final output format. This works the same way as the -T flag for any Graphviz layout program. -N attr=val specifies the setting of a default node attribute during the rendering phase. This works the same way as the -N flag for any Graphviz layout program. -G attr=val specifies the setting of a graph attribute during the rendering phase. This works the same way as the -G flag for any Graphviz lay- out program. -E attr=val specifies the setting of a default edge attribute during the rendering phase. This works the same way as the -E flag for any Graphviz layout program. -n attr=val specifies the setting of a default node attribute during the layout phase. This works the same way as the -N flag for any Graphviz layout program. -g attr=val specifies the setting of a graph attribute during the layout phase. This works the same way as the -G flag for any Graphviz layout program. -e attr=val specifies the setting of a default edge attribute during the layout phase. This works the same way as the -E flag for any Graphviz layout program. -A flag specifies a flag to be passed to gvmap. For example, gvmap.sh -Ae -As3 causes gvmap -e -s3 to be run. -v Set verbose mode. -V Print version information and exit. -? Print usage information and exit. EXAMPLES
The following invocation creates a map with edges in semi-transparent light gray and nodes laid out using sfdp: gvmap.sh -Ae -Ecolor=#55555522 -Tpng foo.gv > foo.png It is equivalent to running the pipeline sfdp -Goverlap=prism foo.gv | gvmap -e | neato -n2 -Ecolor=#55555522 -Tpng > foo.png AUTHOR
Emden R. Gansner <erg@research.att.com> SEE ALSO
gvmap(1), sfdp(1), neato(1), gvpr(1) E. R. Gansner, Y. Hu, S. G. Kobourov, "GMap: Visualizing graphs and clusters as maps," Proc. Pacific Vis. 2010, pp. 201-208. 31 March 2011 GVMAP.SH(1)
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