File: traitCmd.html

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lamarc 2.1.10.1%2Bdfsg-3
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<HTML>
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<pre>
&ltlamarc-converter-cmd&gt
    &ltlamarc-header-comment&gttraitExample: generated with theta=0.1 rec=0.1 trait at position 906&lt/lamarc-header-comment&gt
    &ltoutfile&gtlamarc-trait-input.xml&lt/outfile&gt
    &lttraits&gt
        &lttrait-info&gt
            &ltname&gtfunny-nose&lt/name&gt
            &ltallele&gtnormal&lt/allele&gt
            &ltallele&gtaffected&lt/allele&gt
        &lt/trait-info&gt
        &ltphenotype&gt
            &ltname&gtstraight&lt/name&gt
            &ltgenotype-resolutions&gt
                &lttrait-name&gtfunny-nose&lt/trait-name&gt
                &lthaplotypes&gt
                    &ltalleles&gt normal normal &lt/alleles&gt
                    &ltpenetrance&gt 1.0 &lt/penetrance&gt
                &lt/haplotypes&gt
            &lt/genotype-resolutions&gt
        &lt/phenotype&gt
        &ltphenotype&gt
            &ltname&gtbent&lt/name&gt
            &ltgenotype-resolutions&gt
                &lttrait-name&gtfunny-nose&lt/trait-name&gt
                &lthaplotypes&gt
                    &ltalleles&gt normal affected &lt/alleles&gt
                    &ltpenetrance&gt 1.0 &lt/penetrance&gt
                &lt/haplotypes&gt
                &lthaplotypes&gt
                    &ltalleles&gt affected normal &lt/alleles&gt
                    &ltpenetrance&gt 1.0 &lt/penetrance&gt
                &lt/haplotypes&gt
            &lt/genotype-resolutions&gt
        &lt/phenotype&gt
        &ltphenotype&gt
            &ltname&gtbroken&lt/name&gt
            &ltgenotype-resolutions&gt
                &lttrait-name&gtfunny-nose&lt/trait-name&gt
                &lthaplotypes&gt
                    &ltalleles&gt affected affected &lt/alleles&gt
                    &ltpenetrance&gt 1.0 &lt/penetrance&gt
                &lt/haplotypes&gt
            &lt/genotype-resolutions&gt
        &lt/phenotype&gt
    &lt/traits&gt
    &ltregions&gt
        &ltregion&gt
            &ltname&gtregion1&lt/name&gt
            &lteffective-popsize&gt1&lt/effective-popsize&gt
            &lttrait-location&gt
                &lttrait-name&gtfunny-nose&lt/trait-name&gt
            &lt/trait-location&gt
            &ltsegments&gt
                &ltsegment datatype="dna"&gt
                    &ltname&gtlocus_1&lt/name&gt
                    &ltmarkers&gt1000&lt/markers&gt
                    &ltfirst-position-scanned&gt1&lt/first-position-scanned&gt
                    &ltmap-position&gt1&lt/map-position&gt
                &lt/segment&gt
            &lt/segments&gt
        &lt/region&gt
    &lt/regions&gt
    &ltpopulations&gt
        &ltpopulation&gtpop1&lt/population&gt
    &lt/populations&gt
    &ltindividuals&gt
        &ltindividual&gt
            &ltname&gts0_s1&lt/name&gt
            &ltsample&gt&ltname&gts0&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts1&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtbroken&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts2_s3&lt/name&gt
            &ltsample&gt&ltname&gts2&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts3&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtbroken&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts4_s5&lt/name&gt
            &ltsample&gt&ltname&gts4&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts5&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtbroken&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts6_s7&lt/name&gt
            &ltsample&gt&ltname&gts6&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts7&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtbent&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts10_s11&lt/name&gt
            &ltsample&gt&ltname&gts10&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts11&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtstraight&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts12_s13&lt/name&gt
            &ltsample&gt&ltname&gts12&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts13&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtstraight&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts14_s15&lt/name&gt
            &ltsample&gt&ltname&gts14&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts15&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtstraight&lt/has-phenotype&gt
        &lt/individual&gt
        &ltindividual&gt
            &ltname&gts8_s9&lt/name&gt
            &ltsample&gt&ltname&gts8&lt/name&gt&lt/sample&gt
            &ltsample&gt&ltname&gts9&lt/name&gt&lt/sample&gt
            &lthas-phenotype&gtstraight&lt/has-phenotype&gt
        &lt/individual&gt
    &lt/individuals&gt
    &ltinfiles&gt
        &ltinfile format="migrate" datatype="dna" sequence-alignment="sequential"&gt
            &ltname&gttraitData.mig&lt/name&gt
            &ltpopulation-matching type="single"&gtpop1&lt/population-matching&gt
            &ltsegments-matching type="single"&gtlocus_1&lt/segments-matching&gt
        &lt/infile&gt
    &lt/infiles&gt
&lt/lamarc-converter-cmd&gt
</pre>
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