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.\" ========================================================================
.\"
.IX Title "FILTER 1"
.TH FILTER 1 "2021-03-19" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
filter.pl \- filters output from murasaki based on various filters
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
filter.pl [options] <detailed murasaki ailgnment file> [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 <gnuplot option>=<value>" => can be used to set arbitrary
\&       gnuplot options of the form "set <gnuplot option> <value>"
\&
\& "\-\-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=<anything else>" disables scaling/cropping
.Ve
.PP
The Gnuplot commands for generating the plots are also dumped to
<something>.<stat\-type>.plot and can be run interactively in gnuplot
by typing: load \*(L"<something>.<stat\-type>.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 <something>.anchors.details, then the
\&[output file] defaults to <something>.filtered.
.Ve
.PP
Incidentally, if you don't provide a <something>.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).
