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run_partial_gapFilling.snakefile
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276 lines (207 loc) · 11.8 KB
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configfile: "./config.yaml"
from os.path import join
IS, = glob_wildcards(join("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_templates/", '{gap,gap_[^/]+}.fasta_ancestral'))
rule all:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/partTemplateCorrection.log",
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partTemplateCorrection.log"
rule copyUncovTemplates:
input:
"AGapEs_analysis/results_AGapEs/assemblies/consistent/uncov_list"
output:
temp("AGapEs_analysis/results_AGapEs/assemblies/consistent/copy2.SUCCESS")
shell:
"""
while read p; do cp AGapEs_analysis/results_AGapEs/finishing/alignments/consistent/${{p}}.fasta_ancestral \
AGapEs_analysis/results_AGapEs/gapFilling_partial/part_templates/${{p}}.fasta_ancestral; done < {input}
echo "" > AGapEs_analysis/results_AGapEs/assemblies/consistent/copy2.SUCCESS
"""
rule copyUncovAssemblies:
input:
succ="AGapEs_analysis/results_AGapEs/assemblies/consistent/copy2.SUCCESS",
list="AGapEs_analysis/results_AGapEs/assemblies/consistent/uncov_list"
output:
temp("AGapEs_analysis/results_AGapEs/assemblies/consistent/copyA.SUCCESS")
shell:
"""
while read p; do cp AGapEs_analysis/results_AGapEs/assemblies/consistent/${{p}}.* AGapEs_analysis/results_AGapEs/gapFilling_partial/part_assemblies/; done < {input.list}
echo "" > AGapEs_analysis/results_AGapEs/assemblies/consistent/copyA.SUCCESS
"""
rule computeStartStopFile:
input:
succ="AGapEs_analysis/results_AGapEs/assemblies/consistent/copyA.SUCCESS",
list="AGapEs_analysis/results_AGapEs/assemblies/consistent/uncov_list"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled_start_stop"
shell:
"while read p; do grep '>' AGapEs_analysis/results_AGapEs/gapFilling_partial/part_assemblies/${{p}}.fasta_assembly | awk '{{print $1,$5}}' | sed s/'-'/' '/| tr -d '>' ; done < {input.list} > AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled_start_stop"
rule computeUncovCoordinates:
input:
list="AGapEs_analysis/results_AGapEs/assemblies/consistent/uncov_list",
succ="AGapEs_analysis/results_AGapEs/assemblies/consistent/copyA.SUCCESS"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/merged_uncovered_coordinates_offset"
shell:
"""
rm AGapEs_analysis/results_AGapEs/gapFilling_partial/uncovered_coordinates
./scripts/getNotCoveredCoordinates.sh AGapEs_analysis/results_AGapEs/gapFilling_partial/part_assemblies/ {input.list} AGapEs_analysis/results_AGapEs/gapFilling_partial/
python2 ./scripts/mergeUncoveredRegions.py AGapEs_analysis/results_AGapEs/gapFilling_partial/uncovered_coordinates > AGapEs_analysis/results_AGapEs/gapFilling_partial/merged_uncovered_coordinates_offset
"""
rule computePartiallyCovCoords:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled_start_stop",
"AGapEs_analysis/results_AGapEs/gapFilling_partial/merged_uncovered_coordinates_offset"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps_coordinates"
shell:
"python2 ./scripts/partialGaps_choords.py {input} {output}"
rule runGapFillingPartially:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps_coordinates"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps.log"
shell:
"./scripts/run_gapFilling_partially.sh AGapEs_analysis/results_AGapEs/gapFilling_partial/part_assemblies/ AGapEs_analysis/results_AGapEs/gapFilling_partial/part_templates/ {input} AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled/ ./scripts/ > AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps.log"
rule correctTemplatesPartially:
input:
list="AGapEs_analysis/results_AGapEs/assemblies/consistent/uncov_list",
log="AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps.log",
coords="AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps_coordinates"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial/partTemplateCorrection.log"
shell:
"""
rm AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps_coordinates.index
while read GAP; do python2 ./scripts/correctTemplatesPartially.py AGapEs_analysis/results_AGapEs/gapFilling_partial/part_assemblies/${{GAP}}.fasta_assembly {input.coords} AGapEs_analysis/results_AGapEs/gapFilling_partial/part_templates/${{GAP}}.fasta_ancestral AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled/${{GAP}}.fasta_ancestral AGapEs_analysis/results_AGapEs/gapFilling_partial/partGaps_coordinates.index AGapEs_analysis/results_AGapEs/gapFilling_partial/part_filled/${{GAP}}_*.out ; done < {input.list} > {output}
"""
rule computeMarkerGapSeq_IS_part:
input:
coords="AGapEs_analysis/results_AGapEs/scaffold/gaps_coordinates_and_length",
align="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_templates/{ISgap}.fasta_ancestral",
fams="AGapEs_analysis/results_AGapEs/contigs/families.fasta",
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{ISgap}.fasta_assembly"
log:
"logs/markerGapSequences_IS.log"
shell:
"python2 ./scripts/computeMarkerGapSeq_IS_Fitch.py {wildcards.ISgap} {input.coords} {input.align} {input.fams} AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/"
rule bwa_index:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly"
output:
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.amb"),
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.ann"),
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.bwt"),
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.pac"),
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.sa")
log:
"logs/bwa_index/{gap.log}"
shell:
"bwa0_7_9 index {input} > {log}"
rule bwa_map:
input:
ref="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly",
reads=config["reads"],
index1="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.amb",
index2="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.ann",
index3="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.bwt",
index4="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.pac",
index5="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.fasta_assembly.sa",
output:
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam")
message:
"Mapping to {wildcards.gap}"
log:
"logs/bwa_map/{gap}.log"
threads: 1
shell:
"(bwa0_7_9 mem -a -t {threads} {input.ref} {input.reads} | "
"samtools view -Sb -F 4 - > {output}) 2> {log}"
rule samtools_sort:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam"
output:
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_sorted")
message:
"Sorting {wildcards.gap} bam"
shell:
"samtools sort {input} -o {output}"
rule samtools_rmdup:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_sorted"
output:
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_sorted_dupl")
message:
"Remove duplicates for {wildcards.gap}"
shell:
"samtools rmdup -s {input} {output}"
rule noClips:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_sorted_dupl"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_noclips"
message:
"Remove clipped mappings for {wildcards.gap}"
shell:
"samtools view -h {input} | awk '$6 !~ /H|S/{{print}}' | samtools view -bS - > {output}"
rule computeCov:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_noclips"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bedGraph"
shell:
"bedtools genomecov -ibam {input} -bga > {output}"
rule samtools_view:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.bam_noclips"
output:
temp("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{gap}.mapped.sam")
shell:
"samtools view {input} > {output}"
rule computeStartStopFile_IS:
input:
list="AGapEs_analysis/results_AGapEs/assemblies/IS_gaps/gaps_notfilled",
all=expand("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{ISgap}.mapped.sam", ISgap=IS),
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_filled_start_stop"
shell:
"while read p; do grep '>' AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/${{p}}.fasta_assembly | awk '{{print $1,$5}}' | sed s/'-'/' '/| tr -d '>' ; done < {input.list} > AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_filled_start_stop"
rule computeUncovCoordinates_IS:
input:
list="AGapEs_analysis/results_AGapEs/assemblies/IS_gaps/gaps_notfilled",
all=expand("AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/{ISgap}.mapped.sam", ISgap=IS)
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/merged_uncovered_coordinates_offset"
shell:
"""
rm AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/uncovered_coordinates
./scripts/getNotCoveredCoordinates.sh AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/ {input.list} AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/
python2 ./scripts/mergeUncoveredRegions.py AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/uncovered_coordinates > AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/merged_uncovered_coordinates_offset
"""
rule computePartiallyCovCoords_IS:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_filled_start_stop",
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/merged_uncovered_coordinates_offset"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps_coordinates"
shell:
"python2 ./scripts/partialGaps_choords.py {input} {output}"
rule runGapFillingPartially_IS:
input:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps_coordinates"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps.log"
shell:
"./scripts/run_gapFilling_partially.sh AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/ AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_templates/ {input} AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_filled/ ./scripts/ > AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps.log"
rule correctTemplatesPartially_IS:
input:
list="AGapEs_analysis/results_AGapEs/assemblies/IS_gaps/gaps_notfilled",
log="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps.log",
coords="AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps_coordinates"
output:
"AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partTemplateCorrection.log"
shell:
"""
rm AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps_coordinates.index
while read GAP; do python2 ./scripts/correctTemplatesPartially.py AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_assemblies/${{GAP}}.fasta_assembly {input.coords} AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_templates/${{GAP}}.fasta_ancestral AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_filled/${{GAP}}.fasta_ancestral AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/partGaps_coordinates.index AGapEs_analysis/results_AGapEs/gapFilling_partial_IS/part_IS_filled/${{GAP}}_*.out ; done < {input.list} > {output}
"""