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    <p><em>Note: See the information regarding Graphviz below.</em></p> <p>This should give you a starting point:</p> <p><strong>Edit:</strong> This version handles genes that are described by more than one character.</p> <pre><code>awk ' BEGIN { regdelim = "|" } { delim="" if ($2 == "+") { if (plus[$1]) delim=regdelim plus[$1]=plus[$1] delim $3 } else if ($2 == "-") { if (minus[$1]) delim=regdelim minus[$1]=minus[$1] delim $3 } } END { for (root in plus) { split(plus[root],regs,regdelim) for (reg in regs) { if (plus[regs[reg]] &amp;&amp; plus[root] ~ plus[regs[reg]]) { print "Match: ", root, "+", regs[reg], "+", plus[regs[reg]] } } } } ' inputfile </code></pre> <p>In the <code>BEGIN</code> clause, set <code>regdelim</code> to a character that doesn't appear in your data.</p> <p>I've omitted the processing code for the minus data.</p> <p>Output:</p> <pre><code>Match: a + b + c Match: f + g + h </code></pre> <p><strong>Edit 2:</strong></p> <p>The version below allows you to search for arbitrary combinations. It generalizes the technique used in the original version so no code needs to be duplicated. It also fixes a couple of other <s>bugs</s><i>limitations</i>.</p> <pre><code>#!/bin/bash # written by Dennis Williamson - 2010-11-12 # for http://stackoverflow.com/questions/4161001/counting-the-occurrence-of-a-sub-graph-in-a-graph # A (AB) B, A (AC) C, B (BC) C - where "(XY)" represents a + or a - # provided by the positional parameters $1, $2 and $3 # $4 carries the data file name and is referenced at the end of the script awk -v AB=$1 -v AC=$2 -v BC=$3 ' BEGIN { regdelim = "|" } { if ($2 == AB) { if (regAB[$1]) delim=regdelim; else delim="" regAB[$1]=regAB[$1] delim $3 } if ($2 == AC) { if (regAC[$1]) delim=regdelim; else delim="" regAC[$1]=regAC[$1] delim $3 } if ($2 == BC) { if (regBC[$1]) delim=regdelim; else delim="" regBC[$1]=regBC[$1] delim $3 } } END { for (root in regAB) { split(regAB[root],ABarray,regdelim) for (ABindex in ABarray) { split(regAC[root],ACarray,regdelim) for (ACindex in ACarray) { split(regBC[ABarray[ABindex]],BCarray,regdelim) for (BCindex in BCarray) { if (ACarray[ACindex] == BCarray[BCindex]) { print " Match:", root, AB, ABarray[ABindex] ",", root, AC, ACarray[ACindex] ",", ABarray[ABindex], BC, BCarray[BCindex] } } } } } } ' "$4" </code></pre> <p>This can be called like this to do an exhaustive search:</p> <pre><code>for ab in + -; do for ac in + -; do for bc in + -; do echo "Searching: $ab$ac$bc"; ./searchgraph $ab $ac $bc inputfile; done; done; done </code></pre> <p>For this data:</p> <pre><code>a - e a + b b + c c - f m - n b - d a + c b - e l - n f + g b + i g + h l + m f + h a + i a - j k - j a - k </code></pre> <p>The output of the shell loop calling the new version of the script would look like this:</p> <pre><code>Searching: +++ Match: a + b, a + c, b + c Match: a + b, a + i, b + i Match: f + g, f + h, g + h Searching: ++- Searching: +-+ Searching: +-- Match: l + m, l - n, m - n Match: a + b, a - e, b - e Searching: -++ Searching: -+- Searching: --+ Searching: --- Match: a - k, a - j, k - j </code></pre> <p><strong>Edit 3:</strong></p> <h3>Graphviz</h3> <p>Another approach would be to use <a href="http://www.graphviz.org/" rel="nofollow noreferrer">Graphviz</a>. The <a href="http://www.graphviz.org/doc/info/lang.html" rel="nofollow noreferrer">DOT language</a> can describe the graph and <a href="http://linux.die.net/man/1/gvpr" rel="nofollow noreferrer"><code>gvpr</code></a>, which is an "AWK-like"<sup>1</sup> programming language, can analyze and manipulate DOT files.</p> <p><a href="https://i.stack.imgur.com/zHJwM.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/zHJwM.png" width="300"></a></p> <p>Given the input data in the format as shown in the question, you can use the following AWK program to convert it to DOT:</p> <pre><code>#!/usr/bin/awk -f BEGIN { print "digraph G {" print " size=\"5,5\"" print " ratio=.85" print " node [fontsize=24 color=blue penwidth=3]" print " edge [fontsize=18 labeldistance=5 labelangle=-8 minlen=2 penwidth=3]" print " {rank=same; f l}" m = "-" # ASCII minus/hyphen as in the source data um = "−" # u2212 minus: − which looks better on the output graphic p = "+" } { if ($2 == m) { $2 = um; c = lbf = "red"; arr=" arrowhead = empty" } if ($2 == p) { c = lbf = "green3"; arr="" } print " " $1, "-&gt;", $3, "[taillabel = \"" $2 "\" color = \"" c "\" labelfontcolor = \"" lbf "\"" arr "]" } END { print "}" } </code></pre> <p>The command to run would be something like this:</p> <pre><code>$ ./dat2dot data.dat &gt; data.dot </code></pre> <p>You can then create the graphic above using:</p> <pre><code>$ dot -Tpng -o data.png data.dot </code></pre> <p>I used the extended data as given above in this answer.</p> <p>To do an exhaustive search for the type of subgraphs you specified, you can use the following <code>gvpr</code> program:</p> <pre><code>BEGIN { edge_t AB, BC, AC; } E { AB = $; BC = fstedge(AB.head); while (BC &amp;&amp; BC.head.name != AB.head.name) { AC = isEdge(AB.tail,BC.head,""); if (AC) { printf("%s %s %s, ", AB.tail.name, AB.taillabel, AB.head.name); printf("%s %s %s, ", AC.tail.name, AC.taillabel, AC.head.name); printf("%s %s %s\n", BC.tail.name, BC.taillabel, BC.head.name); } BC = nxtedge(BC, AB.head); } } </code></pre> <p>To run it, you could use:</p> <pre><code>$ gvpr -f groups.g data.dot | sort -k 2,2 -k 5,5 -k 8,8 </code></pre> <p>The output would be similar to that from the AWK/shell combination above (under "Edit 2"):</p> <pre><code>a + b, a + c, b + c a + b, a + i, b + i f + g, f + h, g + h a + b, a − e, b − e l + m, l − n, m − n a − k, a − j, k − j </code></pre> <hr> <p><sup><strong>1</strong></sup><sub> Loosely speaking.</sub></p>
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    1. COThanks for the script. This works perfectly fine if the nodes of the graph are characters (strings of length 1) but not for the strings which I need for my real application. What changes are required for it to work on strings.
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    2. CO@lovedynasty: I've updated the code to handle multi-character strings. See my edited answer.
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    3. COThanks for the script that works perfectly for strings as well :-). Matching a+b+c or a-b-c is now easy. But what modifications are necessary to match for example if a positively regulates b but negatively regulates c and b also negatively regulates c or such combinations. Apologies for repeated questions but I'm just a beginner in AWK. Thanks once again.
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