"Petit dej de la Bioinfo" November, 12 2015. NGS data format & worflows: XML model and XSLT stylesheet converting model.xml to a Makefile

00README.md

usage

xsltproc  model2make.xsl model | make -j 3 -f -

model.xml

<?xml version="1.0" encoding="UTF-8"?>
<model ref="ref.fa">
	<sample name="S1">
		<fastq>
			<for>S1_01_R1.fq.gz</for>
			<rev>S1_01_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S1_02_R1.fq.gz</for>
			<rev>S1_02_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S1_03_R1.fq.gz</for>
			<rev>S1_03_R2.fq.gz</rev>
		</fastq>
	</sample>
	<sample name="S2">
		<fastq>
			<for>S2_01_R1.fq.gz</for>
			<rev>S2_01_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S2_02_R1.fq.gz</for>
			<rev>S2_02_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S2_03_R1.fq.gz</for>
			<rev>S2_03_R2.fq.gz</rev>
		</fastq>
	</sample>
	<sample name="S3">
		<fastq>
			<for>S3_01_R1.fq.gz</for>
			<rev>S3_01_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S3_02_R1.fq.gz</for>
			<rev>S3_02_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S3_03_R1.fq.gz</for>
			<rev>S3_03_R2.fq.gz</rev>
		</fastq>
		<fastq>
			<for>S3_04_R1.fq.gz</for>
			<rev>S3_04_R2.fq.gz</rev>
		</fastq>
	</sample>
	<sample name="S4">
		<fastq>
			<for>S4_01_R1.fq.gz</for>
			<rev>S4_01_R2.fq.gz</rev>
		</fastq>
	</sample>

</model>

model2make.xsl

<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output method="text" encoding="US-ASCII"/>

<xsl:template match="/">

samtools.dir=../samtools/
samtools.exe=${samtools.dir}samtools
wgsim.exe=${samtools.dir}misc/wgsim
bwa.exe=../bwa/bwa
picard.jar=../picard-tools-1.138/picard.jar
bcftools.exe=../bcftools/bcftools

<xsl:apply-templates select="model"/>
</xsl:template>

<xsl:template match="model">
REF=<xsl:value-of select="@ref"/>

mutations.vcf.gz : ${REF} <xsl:for-each select="sample">\
	$(addsuffix .bam.bai ,<xsl:value-of select="@name"/>) </xsl:for-each>
	${samtools.exe} mpileup  -u -f $&lt; $(filter %.bam,$(basename $^)) |\
	${bcftools.exe} call -c -v -O z -o $@ -

<xsl:apply-templates select="sample"/>

$(addsuffix .bwt,${REF}) : ${REF}
	${bwa.exe} index $&lt;
${REF}:
<![CDATA[	echo ">rotavirus" > $@
	echo "GGCTTTTAATGCTTTTCAGTGGTTGCTGCTCAAGATGGAGTCTACTCAGCAGATGGTAAGCTCTATTATT" >> $@
	echo "AATACTTCTTTTGAAGCTGCAGTTGTTGCTGCTACTTCAACATTAGAATTAATGGGTATTCAATATGATT" >> $@
	echo "ACAATGAAGTATTTACCAGAGTTAAAAGTAAATTTGATTATGTGATGGATGACTCTGGTGTTAAAAACAA" >> $@
	echo "TCTTTTGGGTAAAGCTATAACTATTGATCAGGCGTTAAATGGAAAGTTTAGCTCAGCTATTAGAAATAGA" >> $@
	echo "AATTGGATGACTGATTCTAAAACGGTTGCTAAATTAGATGAAGACGTGAATAAACTTAGAATGACTTTAT" >> $@
	echo "CTTCTAAAGGGATCGACCAAAAGATGAGAGTACTTAATGCTTGTTTTAGTGTAAAAAGAATACCAGGAAA" >> $@
	echo "ATCATCATCAATAATTAAATGCACTAGACTTATGAAGGATAAAATAGAACGTGGAGAAGTTGAGGTTGAT" >> $@
	echo "GATTCATATGTTGATGAGAAAATGGAAATTGATACTATTGATTGGAAATCTCGTTATGATCAGTTAGAAA" >> $@
	echo "AAAGATTTGAATCACTAAAACAGAGGGTTAATGAGAAATACAATACTTGGGTACAAAAAGCGAAGAAAGT" >> $@
	echo "AAATGAAAATATGTACTCTCTTCAGAATGTTATCTCACAACAGCAAAACCAAATAGCAGATCTTCAACAA" >> $@
	echo "TATTGTAGTAAATTGGAAGCTGATTTGCAAGGTAAATTTAGTTCATTAGTGTCATCAGTTGAGTGGTATC" >> $@
	echo "TAAGGTCTATGGAATTACCAGATGATGTAAAGAATGACATTGAACAGCAGTTAAATTCAATTGATTTAAT" >> $@
	echo "TAATCCCATTAATGCTATAGATGATATCGAATCGCTGATTAGAAATTTAATTCAAGATTATGACAGAACA" >> $@
	echo "TTTTTAATGTTAAAAGGACTGTTGAAGCAATGCAACTATGAATATGCATATGAGTAGTCATATAATTAAA" >> $@
	echo "AATATTAACCATCTACACATGACCCTCTATGAGCACAATAGTTAAAAGCTAACACTGTCAAAAACCTAAA" >> $@
	echo "TGGCTATAGGGGCGGTTTGTGACC" >> $@
	echo "" >> $@
]]>


graph.png:
	make -ndrB -f Makefile | ../makefile2graph/make2graph | dot -Tpng -o$@
</xsl:template>

<xsl:template match="sample">

$(addsuffix .bam.bai ,<xsl:value-of select="@name"/>):  $(addsuffix .bam,<xsl:value-of select="@name"/>)
	${samtools.exe} index $&lt;

$(addsuffix .bam,<xsl:value-of select="@name"/>): <xsl:for-each select="fastq"> \
		$(addsuffix .bam,<xsl:value-of select="for"/>) </xsl:for-each>
	java -jar ${picard.jar} MergeSamFiles AS=true O=$@ $(foreach B,$^, I=${B} )

<xsl:apply-templates select="fastq"/>
</xsl:template>

<xsl:template match="fastq">

$(addsuffix .bam,<xsl:value-of select="for"/>): $(addsuffix .bwt,${REF}) <xsl:value-of select="for"/> <xsl:text> </xsl:text> <xsl:value-of select="rev"/>
	${bwa.exe} mem  -R '@RG\tID:<xsl:value-of select="../@name"/>\tSM:<xsl:value-of select="../@name"/>' ${REF} $(filter %.gz,$^) |\
	${samtools.exe} view -Sbu  - |\
	${samtools.exe} sort -O sam -o $@ -T $(basename $@) -

<xsl:value-of select="rev"/> : <xsl:value-of select="for"/> 
	gzip --best -f $(basename $@)

<xsl:value-of select="for"/>  : ${REF}
	@sleep 1
	${wgsim.exe} -r 0.01 -S <xsl:value-of select="1 + count(../preceding-sibling::sample)"/> -N 1000  $&lt; $(basename <xsl:value-of select="for"/> <xsl:text> </xsl:text> <xsl:value-of select="rev"/>)
	gzip --best -f $(basename $@)

</xsl:template>


</xsl:stylesheet>