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Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l .nh .SH "NAME" filter.pl \- filters output from murasaki based on various filters .SH "SYNOPSIS" .IX Header "SYNOPSIS" filter.pl [options] [output file] .SH "OPTIONS" .IX Header "OPTIONS" .Vb 11 \& Filtering options: \&Filtering can be performed on "length", "hits", "tfidf", or "score". \&You can filter by either setting either a "min" or "max". \&For example: "\-\-minlength 50" filters out any anchors with an average \&length shorter than 50. (average length is used because an anchor \&may be different sizes on different sequences). \&Filters can also use the average(x), standard deviation(s), \&variance(v), or anchor count(a) in an expression to set a filter. \&For example: "\-\-minscore=2x" sets the minimum score threshold to \&twice the average score. "\-\-minlength=x+s/2" sets the minimum length \&threshold to the average length plus half a standard deviation. \& \& Input modification: \& "\-\-widen=500" => extends each anchor 500 bases in both directions \& "\-\-randomwiden=500" => extends each anchor 500 bases _at random_ \& (ie: to compare to \-\-widen) \& \& Output options: \& "\-\-statdump" => dump all available stats into 1 file with a header row \& "\-\-dumpstats tfidf,length" => dumps stats tfidf and length to separate files \& one line per anchor \& "\-\-dumpstats" => assumes "\-\-dumpstats all" \& \& Plot options: \&filter.pl can plot any or all of the statistics gathered by using \&the "\-\-plot" option. \& Examples: \& "\-\-plot hits,length" => plots both hits and length \& "\-\-plot" => assumes "\-\-plot all" \& \& "\-\-plotopts" allows setting of various gnuplot and special plot options. \&Different statistics can be targeted separately by prefixing the setting \&name with the statistic(s) of your choice followed by a "." \&For example: \& "\-\-plotopts hits,length.flatx" => disables the log scale on the x axis \& of the hits and length plots only \& "\-\-plotopts with=points" => uses points instead of bars on all plots \& "\-\-plotopts =" => can be used to set arbitrary \& gnuplot options of the form "set " \& \& "\-\-bins" can be used to specify the number of bins. \& "\-\-nobins" turns off binning and plots a raw (likely bumpy) histogram \& "\-\-showall=crop" sends all data to gnuplot even on logscale plots (by \& default for logscale plots values <=1 at the extreme right end are \& chopped off because they don\*(Aqt show up in gnuplot (1 is the baseline) \& but they do affect the visible range, and thus causes some scrunching. \& "\-\-showall=scale" manually sets to the X and Y ranges to the range of the \& data (so 1\*(Aqs are visibly different from 0\*(Aqs). \& "\-\-showall=" disables scaling/cropping .Ve .PP The Gnuplot commands for generating the plots are also dumped to ..plot and can be run interactively in gnuplot by typing: load \*(L"..plot\*(R" .PP .Vb 10 \& Statistical Options: \& "\-\-all/\-\-quick" => standard deviation calculations require a second \& pass through the data, and as histogram plots are generally much \& more useful than a standard deviation statistic (especially considering \& not all of these statistics may be gaussian), so unless one of your \& constraints calls for standard deviation, this calculation is skipped. \& It can be forced by applying \-\-all. (\-\-quick is the default) \& "\-\-nodetails" => disables reconstruction of term indicies (this will \& disable tfidf stats). \& "\-\-tags" => enables reading of annotation. \& This produces "good, miss, shuffle" stats (which can also be plotted) \& and specificity/sensitivity information \& "\-\-notags" => disables reading of annotation (by default) \& \& COG/KOG Statistics: \& At any rate: \& "\-\-kogfile=path/to/kog" => enables kog\-based alignment \& "\-\-kogmap 3=hsa" => forces sequence 3 (note: sequences are 0 indexed) to \& be assigned to the "hsa" kog. If the file name includes one of the \& kog species abbreviations, it is assumed to belong to that kog. \& \& Debugging: \& "\-\-linear" => forces linear scans for CDS\*(Aqs instead of binary searches \& (if this returns different results, it means something is very wrong) \& \& [output file]: \&If the input filename is of the form .anchors.details, then the \&[output file] defaults to .filtered. .Ve .PP Incidentally, if you don't provide a .anchors.details file, it probably won't work anyway... .SH "DESCRIPTION" .IX Header "DESCRIPTION" Filters murasaki alignments based on various statistics. Various statistics can be plotted using \-\-plot. Annotation data is processed from input files using BioPerl. .PP \&\s-1ROC\s0 data can be calculated using \s-1KOG\s0 data (which is much more reliable than just gene names). To do so you need to specify a \s-1KOG\s0 data file which can be downloaded from the \s-1COG\s0 database at: http://www.ncbi.nlm.nih.gov/COG/ You'll be looking for either the \*(L"whog\*(R" file for COGs or the \*(L"kog\*(R" file on the \s-1KOG\s0 side. \s-1KOG\s0 locus naming sometimes differs from \s-1GBK\s0 file to file, and locus names are sometimes missing, so \s-1KOG\s0 based assessment is currently best effort (capitalization is ignored, locii which don't appear in the annotation are ignored, and domain-specific _x endings are ignored).