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message: " mapping homologous regions of both references using ISBPs markers as anchors for chromosome {wildcards.chrom}"
input:
#closestMarkers=config['results']+'/2.mergedClosestMarkers.txt',
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marker5prime=config['results']+'/2.closestbed_split/{chrom}.upstream.txt',
marker3prime=config['results']+'/2.closestbed_split/{chrom}.downstream.txt',
refQuery=config['queryFasta'],
faiQuery=config['queryFasta']+'.fai',
refTarget=config['targetFasta'],
faiTarget=config['targetFasta']+'.fai',
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markersOnTarget=config['results']+"/1.filteredISBPs.sorted.{chrom}.bed"
output:
allblat=config['results']+'/3.mapping/{chrom}/allBlat.csv',
summary=config['results']+'/3.mapping/{chrom}/mappingSummary.csv'
params: dir=directory(config['results']+'/3.mapping/{chrom}')
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log: config['results']+'/3.mapping/{chrom}/microMappingPipeline.log'
bin/microMappingPipeline.py {input.marker5prime} {input.marker3prime} {params.dir} {input.refQuery} {input.refTarget} {input.markersOnTarget} &> {log}
rule recalcBlatMapped:
message: " Recalc the coordinates of genes mapped with the Blat pipeline for chromosome {wildcards.chrom}"
input:
allBlat=config['results']+'/3.mapping/{chrom}/allBlat.csv',
summary=config['results']+'/3.mapping/{chrom}/mappingSummary.csv',
refQuery=config['queryFasta'],
faiQuery=config['queryFasta']+'.fai',
refTarget=config['targetFasta'],
faiTarget=config['targetFasta']+'.fai',
refGff=config['annotationQuery']
output: gff=temp(config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget.gff3')
log: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget.log'
shell:
"""
bin/recalcCoordsFromBlat.py -b {input.allBlat} -s {input.summary} -o {output.gff} -q {input.refQuery} -t {input.refTarget} -g {input.refGff} &> {log}
"""
rule gtCleanBlatGff:
message: " Clean the gff file recalculated based on Blat fine mapping for chromosome {wildcards.chrom}"
input: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget.gff3'
output: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.gff3'
log: config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.log'
shell:
gt gff3 -sort -tidy -retainids {input} 1> {output} 2> {log}
message: " Rescue anchoring of failed genes with gmap for chrom {wildcards.chrom}"
input: blat=config['results']+'/3.mapping/{chrom}/allBlat.csv', gmapindex=config['results']+"/target_gmapindex"
output: txt=config['results']+'/4.gmapRescue/{chrom}.txt',
targetgff=config['results']+'/4.gmapRescue/{chrom}.target.gff3',
wholegenomegff=config['results']+'/4.gmapRescue/{chrom}.wholeGenome.gff3'
params: blastdb=config['blastdb'], anchoringDir=config['results']+'/3.mapping/{chrom}/', gmapIndexDir=config['results']
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log: config['results']+'/4.gmapRescue/{chrom}.log'
bin/gmapRescue.sh {params.anchoringDir} {params.blastdb} {input.gmapindex} {params.gmapIndexDir} {output.targetgff} {output.wholegenomegff} 1> {output.txt} 2> {log}
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rule recalcGmapRescue:
message: "Recalc the coordinates of the GMAP on target GFF3 files for chromosome {wildcards.chrom}"
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input: config['results']+'/4.gmapRescue/{chrom}.target.gff3',
output: config['results']+'/4.recalcGmap/{chrom}/recalc.gff3'
params: anchoringDir=config['results']+'/3.mapping/{chrom}',
bindir=os.getcwd()
log: config['results']+'/4.recalcGmap/{chrom}/recalc.log'
shell:
"""
bin/recalcGmapRescue.sh {params.anchoringDir} {input} {output} {params.bindir} &> {log}
"""
rule saveGmapWG:
message: "Save the GMAP results of genes mapped on Whole Genome"
input: config['results']+'/4.gmapRescue/{chrom}.wholeGenome.gff3'
output: config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.gff3'
log: config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.log'
shell:
"""
cp {input} {output} &> {log}
"""
rule mergeFinalGff3:
message: " Merge Final GFF3 files: blat.gff3, rescue.gff3 and wholeGenome.gff3"
input: blat=config['results']+'/4.recalcBlat/{chrom}/RecalcAnnotOnTarget-clean.gff3',
rescue=config['results']+'/4.recalcGmap/{chrom}/recalc.gff3',
wg=config['results']+'/4.gmapWholeGenome/{chrom}.wholeGenome.gff3'
output: annot=config['results']+'/5.FINAL/{chrom}/annotation.gff3', gmapWGOnly=config['results']+'/5.FINAL/{chrom}/missing-gmap.gff3'
log: annot=config['results']+'/5.FINAL/{chrom}/annotation.log', gmap=config['results']+'/5.FINAL/{chrom}/missing-gmap.log'
shell:
"""
gt gff3 -sort -tidy -retainids {input.blat} {input.rescue} 1> {output.annot} 2> {log.annot}
gt gff3 -sort -tidy -retainids {input.wg} 1> {output.gmapWGOnly} 2> {log.gmap}
"""
rule checkMissing:
message: ""
input: gff=config['results']+'/5.FINAL/{chrom}/annotation.gff3',
gmap=config['results']+'/5.FINAL/{chrom}/missing-gmap.gff3',
ref=config['results']+"/1.features/{chrom}.bed"
output: config['results']+'/5.FINAL/{chrom}/missing.txt'
log: config['results']+'/5.FINAL/{chrom}/missing.log'
shell:
"""
bin/checkFinalAnnot.py -i {input.gff} -a {input.ref} -g {input.gmap} -m {output} &> {log}
"""
rule concatAllChromResults:
message: " concat all per chromosome results"
input: annot=expand(config['results']+'/5.FINAL/{chrom}/annotation.gff3',chrom=config['chromosomes']),
rescue=expand(config['results']+'/5.FINAL/{chrom}/missing-gmap.gff3',chrom=config['chromosomes']),
missing=expand(config['results']+'/5.FINAL/{chrom}/missing.txt', chrom=config['chromosomes'])
output: annot=temp(config['finalPrefix']+'tmp.gff3'),
rescue=config['finalPrefix']+'_rescue.gff3',
missing=config['finalPrefix']+'_missing.txt'
log: config['finalPrefix']+'.log'
shell:
"""
gt gff3 -sort -tidy -retainids {input.annot} 1> {output.annot} 2> {log}
gt gff3 -sort -tidy -retainids {input.rescue} 1> {output.rescue} 2> {log}
cat {input.missing} 1> {output.missing} 2>> {log}
"""
rule renameGeneIds:
message: " set final gene IDs for the new annotation"
input: gff=config['finalPrefix']+'tmp.gff3',
map=config['chromMapID']
output: gffhc=config['finalPrefix']+'_HC.gff3',
gfflc=config['finalPrefix']+'_LC.gff3',
correspondance=config['finalPrefix']+'_IDMapping.csv',
overlap=config['finalPrefix']+'_overlap.bed'
params: prefix='TraesCS', version='03G', source='IWGSC_v2.1'
log: config['finalPrefix']+'_IDMapping.log'
shell:
"""
bin/renameGffID.py -i {input.gff} -m {input.map} -o {output.gffhc} -l {output.gfflc} -c {output.correspondance} -p {params.prefix} -v {params.version} -s {params.source} -x {output.overlap} &> {log}
"""
rule generateFastaSequencesHC:
message: "generate fasta sequences using gffread for HC genes"
input: gff=config['finalPrefix']+'_HC.gff3',
fastaref=config['targetFasta']
output: mrna=config['finalPrefix']+'_HC.transcripts.fasta',
cds=config['finalPrefix']+'_HC.cds.fasta',
pep=config['finalPrefix']+'_HC.proteins.fasta'
log: config['finalPrefix']+'_HC.gffread.log'
shell:
"""
gffread {input.gff} -w {output.mrna} -x {output.cds} -y {output.pep} -g {input.fastaref} -W -O &> {log}
"""
rule generateFastaSequencesLC:
message: "generate fasta sequences using gffread for LC genes"
input:
gff=config['finalPrefix']+'_LC.gff3',
fastaref=config['targetFasta']
output: mrna=config['finalPrefix']+'_LC.transcripts.fasta',
cds=config['finalPrefix']+'_LC.cds.fasta',
pep=config['finalPrefix']+'_LC.proteins.fasta'
log: config['finalPrefix']+'_LC.gffread.log'
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shell:
"""
gffread {input.gff} -w {output.mrna} -x {output.cds} -y {output.pep} -g {input.fastaref} -W -O &> {log}
"""
rule generateFastaSequencesRescue:
message: "generate fasta sequences using gffread for rescue genes"
input:
gff=config['finalPrefix']+'_rescue.gff3',
fastaref=config['targetFasta']
output: mrna=config['finalPrefix']+'_rescue.transcripts.fasta',
cds=config['finalPrefix']+'_rescue.cds.fasta',
pep=config['finalPrefix']+'_rescue.proteins.fasta'
log: config['finalPrefix']+'_rescue.gffread.log'
shell:
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"""
gffread {input.gff} -w {output.mrna} -x {output.cds} -y {output.pep} -g {input.fastaref} -W -O &> {log}
"""