analyze_mode.html

有趣的模拟进化的程序 由国外一生物学家开发 十分有趣

    	Print the genotypes from the current batch as individual files (one
        genotype per file) in the directory given.  The files will be named
        by the genotype name, with a ".gen" appended to them.
<tr><td><b>TRACE [<font color="#008800">dir="genebank/"</font>] </b><br>
    	Trace all of the genotypes and print a listing of their execution.
	This will show step-by-step the status of all of the CPU components
	and the genome during the course of the execution.  The filename used
	for each trace will be the genotype's name with a ".trace" appended.
<tr><td><b>PRINT_TASKS [<font color="#008800">file="tasks.dat"</font>] </b><br>
    	This will print out the tasks doable by each genotype, one per line
	in the output file specified.  Note that this information must either
	have been loaded in, or a RECALCULATE must have been run to collect
	it.
<tr><td><b>DETAIL [<font color="#008800">file="detail.dat"</font>] [<font color="#008800">format ...</font>]</b><br>
    	Print out all of the stats for each genotype, one per line.  The
	format indicates the layout of columns in the file.  If the filename
	specified ends in ".html", html formatting will be used instead of
	plain text.  For the format, see the section on "Output Formats"
	below.
</table>

<p>
And at last, we have the actual analysis commands that perform tests on
the data and output the results.

<p align=center><b>Table 6: <font color="#008800">Analysis Commands</font></b>
<table cellpadding=6>
<tr><td><b>LANDSCAPE [<font color="#008800">file="landscape.dat"</font>]
	[<font color="#008800">dist=1</font>]</b><br>
    	For each genotype in the current batch, test all possible mutations
	(or combinations of mutations if dist > 1) and summarize the results,
	one per line in the specified file.
<tr><td><b>MAP_TASKS [<font color="#008800">dir="phenotype/"</font>]
	[<font color="#008800">flags ...</font>]
	[<font color="#008800">format ...</font>] </b><br>
    	Construct a genotype-phenotype array for each genotype in the
	current batch.  The format is the list of stats that you want
	to include as columns in the array.  Additionally you can have
	special format flags; the possible flags are "html" to print output
	in HTML format, and "link_maps" to create html links between
	consecutive genotypes in a lineage.
<tr><td><b>MAP_MUTATIONS [<font color="#008800">dir="mutations/"</font>]
	[<font color="#008800">flags ...</font>] </b><br>
    	Construct a genome-mutation array for each genotype in the
	current batch.  The format has each line in the genome as a row
        in the chart, and all available instructions representing the columns.
        The cells in the chart indicate the fitness were a mutation to
        occur at the position in the matrix, to the listed instruction.
        If the "html" flag is used, the charts will be output in HTML format.
<tr><td><b>HAMMING [<font color="#008800">file="hamming.dat"</font>]
	[<font color="#008800">b1=current</font>]
	[<font color="#008800">b2=b1</font>] </b><br>
    	Calculate the hamming distance between batches b1 and b2.  If only
	one batch is given, calculations are on all pairs within that batch.
<tr><td><b>LEVENSTEIN [<font color="#008800">file="lev.dat"</font>]
	[<font color="#008800">b1=current</font>]
	[<font color="#008800">b2=b1</font>]</b><br>
    	Calculate the levenstein distance (edit distance) between batches b1
	and b2.  This metric is similar to hamming distance, but calculates
	the minimum number of single insertions, deletions, and mutations to
	move from one sequence to the other.
<tr><td><b>SPECIES [<font color="#008800">file="species.dat"</font>]
	[<font color="#008800">b1=current</font>]
	[<font color="#008800">b2=b1</font>]</b><br>
    	Again this is similar to hamming distance, but calculates if genotypes
	would be considered the same species.
	Output:  Batch1Name  Batch2Name  AveDistance  Count  FailCount
</table>

<h3>Output Formats</h3>

<p>
 Several commands (such as DETAIL and MAP) require format parameters
 to specify what genotypic features should be output.  Before the
 such commands are used, other collection functions may need to be
 run.

<p>
 Allowable formats after a normal load (assuming these values were available
 from the input file to be loaded in) are:
<p>
<center>
<table width=95%>
<tr><td width=33%><b>id</b>           (Genome ID)
    <td width=33%><b>parent_id</b>    (Parent ID)
    <td width=33%><b>num_cpus</b>     (Number of CPUs)
<tr><td><b>total_cpus</b>   (Total CPUs Ever)
    <td><b>length</b>       (Genome Length)
    <td><b>update_born</b>  (Update Born)
<tr><td><b>update_dead</b>  (Update Dead)
    <td><b>depth</b>        (Tree Depth)
    <td><b>sequence</b>     (Genome Sequence)
</table>
</center>

<p>
 After a RECALCULATE, the additional formats become available:

<p>
<center>
<table width=95%>
<tr><td width=33%><b>viable</b> (Is Viable [0/1])
    <td width=33%><b>copy_length</b> (Copied Length)
    <td width=33%><b>exe_length</b> (Executed Length)
<tr><td><b>merit</b> (Merit)
    <td><b>comp_merit</b> (Computational Merit)
    <td><b>gest_time</b> (Gestation Time)
<tr><td><b>efficiency</b> (Replication Efficiency)
    <td><b>fitness</b> (Fitness)
    <td><b>div_type</b> (Divide type used; 1 is default)
</table>
</center>

<p>
 If a FIND_LINEAGE was done before the RECALCULATE, the parent
 genotype for each regular genotype will be available, enabling the
 additional formats:

<p>
<center>
<table width=95%>
<tr><td width=50%><b>parent_dist</b> (Parent Distance)
    <td width=50%><b>comp_merit_ratio</b>, (Computational Merit Ratio with parent)
<tr><td><b>efficiency_ratio</b> (Replication Efficiency Ratio with parent)
    <td><b>fitness_ratio</b> (Fitness Ratio with parent)
<tr><td><b>parent_muts</b> (Mutations from Parent)
    <td><b>html.sequence</b> (Genome Sequence in Color; html format)
</table>
</center>

<p>
 Finally, if an ALIGN is run, one additional format is available:
 <b>alignment</b> (Aligned Sequence)


<h3>Variables</h3>

<p>
 For the moment, all variables can only be a single character (letter or
 number) and begin with a $ whenever they need to be translated to their
 value.  Lowercase letters are global variables, capital letters are
 local to a function (described later), and numbers are arguments to a
 function.  A $$ will act as a single dollar sign, if needed.

<p align=center><b>Table 7: <font color="#008800">Variable-Related Commands</font></b>
<table cellpadding=6>
<tr><td><b>SET [<font color="#0000AA">variable</font>]
	[<font color="#0000AA">value</font>] </b><br>
    	Sets the variable to the value...
<tr><td><b>FOREACH [<font color="#0000AA">variable</font>]
	[<font color="#0000AA">value</font>]
	[<font color="#008800">value ...</font>] </b><br>
    	Set the variable to each of the values listed, and run the code that
        follows between here and the next END command once for each of
	those values.
<tr><td><b>FORRANGE [<font color="#0000AA">variable</font>]
	[<font color="#0000AA">min_value</font>]
	[<font color="#0000AA">max_value</font>]
	[<font color="#008800">step_value=1</font>]</b><br>
    	Set the variable to each of the values between min and max (at steps
	given), and run the code that follows between here and the next END
	command, once for each of those values.
</table>

<h3>Functions</h3>

<p>
 These functions are currently very primitive with fixed inputs of
 $0 through $9.  $0 is always the function name, and then there can be up
 to 9 other arguments passed through.  Once a function is created, it can
 be run just like any other command.

<p align=center><b>Table 8: <font color="#008800">Function-Related Commands</font></b>
<table cellpadding=6>
<tr><td><b>FUNCTION [<font color="#0000AA">name</font>]</b><br>
    	This will create a function of the given name, including in it all
	of the commands up until an END is found.  These commands will be
	bound to the function, but are not executed until the function is
	run as a command.  Inside the function, the variables $1 through $9
	can be used to access arguments passed in.
</table>

<p>
Currently there are no conditionals or mathematical commands in this
scripting language.  These are both planned for the future.