add a demo for PretextMap

scripts/run_yahs.sh

@@ -5,8 +5,10 @@ outdir="./outs/"
 contigs="./data/test.fa.gz" # need to be indexed, i.e., test.fa.gz.fai is available
 hicaln="./data/test.bed" # could be .bed, .bam or .bin file
 
-## need juicer_tools and samtools if want to do hic plot
+## need juicer_tools/pretextmap and samtools if want to do hic plot
 ## juicer_tools: https://github.com/aidenlab/juicer/wiki/Download
+## PretextMap: https://github.com/wtsi-hpag/PretextMap
+## PretexSnapshot: https://github.com/wtsi-hpag/PretextSnapshot
 ## samtools: https://github.com/samtools/samtools
 ## please adjust the path to juicer_tools and samtools
 ## here we use 12 CPUs and 32Gb memory for juicer_tools pre - adjust it according to your device
@@ -17,24 +19,30 @@ noplot=0
 #juicer_tools="java -Xmx32G -jar ~/bin/juicer_tools_1.22.01.jar pre --threads 12"
 ## v1.9.9 seems much faster than v1.22.01
 juicer_tools="java -Xmx32G -jar ~/bin/juicer_tools.1.9.9_jcuda.0.8.jar pre"
+pretext_map="~/bin/PretextMap"
+pretext_snapshot="~/bin/PretextSnapshot"
 samtools="~/bin/samtools"
 
 #### run yahs scaffolding
 ../yahs -o ${outdir}/${out} ${contigs} ${hicaln} >${outdir}/${out}.log 2>&1
 
 if [ ${noplot} -ne 0 ]; then exit 0; fi
 
-#### this is to generate input file for juicer_tools - non-assembly mode
+#### this is to generate input file for juicer_tools - non-assembly mode or for PretextMap
 ## here we use 8 CPUs and 32Gb memory for sorting - adjust it according to your device
 (../juicer_pre ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre.log | LC_ALL=C sort -k2,2d -k6,6d -T ${outdir} --parallel=8 -S32G | awk 'NF' > ${outdir}/alignments_sorted.txt.part) && (mv ${outdir}/alignments_sorted.txt.part ${outdir}/alignments_sorted.txt)
-## do juicer hic map
 ## prepare chromosome size file from samtools index file
 # ${samtools} faidx ${outdir}/${out}_scaffolds_final.fa
 # cut -f1-2 ${outdir}/${out}_scaffolds_final.fa.fai >${outdir}/${out}_scaffolds_final.chrom.sizes
 ## another way to prepare chromosome size file
 ## this is an easier way especially when we have >2G scaffolds which need scaling 
 cat ${outdir}/tmp_juicer_pre.log | grep "PRE_C_SIZE" | cut -d' ' -f2- >${outdir}/${out}_scaffolds_final.chrom.sizes
+## do juicer hic map
 (${juicer_tools} ${outdir}/alignments_sorted.txt ${outdir}/${out}.hic.part ${outdir}/${out}_scaffolds_final.chrom.sizes) && (mv ${outdir}/${out}.hic.part ${outdir}/${out}.hic)
+## do Pretext hic map
+(awk 'BEGIN{print "## pairs format v1.0"} {print "#chromsize:\t"$1"\t"$2} END {print "#columns:\treadID\tchr1\tpos1\tchr2\tpos2\tstrand1\tstrand2"}' ${outdir}/${out}_scaffolds_final.chrom.sizes; awk '{print ".\t"$2"\t"$3"\t"$6"\t"$7"\t.\t."}' alignments_sorted.txt) | ${pretext_map} -o ${outdir}/${out}.pretext
+# and a pretext snapshot
+${pretext_snapshot} -m ${outdir}/${out}.pretext --sequences "=full" -o ${outdir}
 
 #### this is to generate input file for juicer_tools - assembly (JBAT) mode (-a)
 ../juicer_pre -a -o ${outdir}/${out}_JBAT ${outdir}/${out}.bin ${outdir}/${out}_scaffolds_final.agp ${contigs}.fai 2>${outdir}/tmp_juicer_pre_JBAT.log