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Some miRBase downloads no longer require uncompressing. Fixes bcbio/b…
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…cbio-nextgen#3723
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Rob Chekaluk committed Nov 1, 2023
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9 changes: 6 additions & 3 deletions ggd-recipes/BDGP6/mirbase.yaml
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Expand Up @@ -13,12 +13,15 @@ recipe:
wget --random-wait --retry-connrefused -nv -c -O tmp.gtf.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.gff.gz
zgrep -v exon tmp.gtf.gz | grep -v region | sed 's/Name/name/g' | sed -e 's/NC_004353.4/chr4/g; s/NC_004354.4/chrX/g; s/NC_024511.2/chrM/g; s/NC_024512.1/chrY/g; s/NT_033777.3/chr3R/g; s/NT_033778.4/chr2R/g; s/NT_033779.5/chr2L/g; s/NT_037436.4/chr3L/g; s/NW_007931121.1/CP007120.1/g' | sed 's/=/ /g' > srna-transcripts.gtf
# mirbase
wget --random-wait --retry-connrefused -nv -c -O hairpin.t.fa.gz ftp://mirbase.org/pub/mirbase/22/hairpin.fa.gz && gunzip -f hairpin.t.fa.gz
wget --random-wait --retry-connrefused -nv -c -O hairpin.t.fa https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.t.fa | awk '{if ($0~/>dme/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -nv -c -O mature.t.fa.gz ftp://mirbase.org/pub/mirbase/22/mature.fa.gz && gunzip -f mature.t.fa.gz
rm hairpin.t.fa
wget --random-wait --retry-connrefused -nv -c -O mature.t.fa https://mirbase.org/download/CURRENT/mature.fa
cat mature.t.fa | awk '{if ($0~/>dme/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -nv -c -O miRNA.t.str.gz ftp://mirbase.org/pub/mirbase/22/miRNA.str.gz && gunzip -f miRNA.t.str.gz
rm mature.t.fa
wget --random-wait --retry-connrefused -nv -c -O miRNA.t.str https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.t.str | awk '{if ($0~/dme/)print $0}' > miRNA.str
rm miRNA.t.str
wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/dme.gff3
wget --no-check-certificate -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip -f Rfam_for_miRDeep.fa.gz
# targetscan analysis
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15 changes: 9 additions & 6 deletions ggd-recipes/canFam3/mirbase.yaml
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Expand Up @@ -17,12 +17,15 @@ recipe:
wget --random-wait --retry-connrefused -q -c -O refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/canFam3/database/refGene.txt.gz
zcat refGene.txt.gz | awk '{print $3"\t.\tgene\t"$5"\t"$6"\t.\t"$4"\t.\tname "$13";"}' >> srna-transcripts.gtf
# mirbase
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz ftp://mirbase.org/pub/mirbase/21/hairpin.fa.gz
zcat hairpin.fa.gz | awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -q -c -O mature.fa.gz ftp://mirbase.org/pub/mirbase/21/mature.fa.gz
zcat mature.fa.gz | awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz ftp://mirbase.org/pub/mirbase/21/miRNA.str.gz
zcat miRNA.str.gz | awk '{if ($0~/cfa/)print $0}' > miRNA.str
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.raw https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.fa.raw | awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
rm hairpin.fa.raw
wget --random-wait --retry-connrefused -q -c -O mature.fa.raw https://mirbase.org/download/CURRENT/mature.fa
cat mature.fa.raw | awk '{if ($0~/>cfa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
rm mature.fa.raw
wget --random-wait --retry-connrefused -q -c -O miRNA.dat.raw https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.dat.raw | awk '{if ($0~/cfa/)print $0}' > miRNA.str
rm miRNA.dat.raw
wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/cfa.gff3
# mintmap
# mirdeep2
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15 changes: 9 additions & 6 deletions ggd-recipes/hg19/mirbase.yaml
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Expand Up @@ -23,12 +23,15 @@ recipe:
# wget --random-wait --retry-connrefused -nv -c -O piR_hg19_v1.0.bed.gz http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
# zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf
# mirbase
wget --random-wait --retry-connrefused -nv -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz
zcat hairpin.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -nv -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz
zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -nv -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
wget --random-wait --retry-connrefused -nv -c -O hairpin.fa.raw https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.fa.raw | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
rm hairpin.fa.raw
wget --random-wait --retry-connrefused -nv -c -O mature.fa.raw https://mirbase.org/download/CURRENT/mature.fa
cat mature.fa.raw | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
rm mature.fa.raw
wget --random-wait --retry-connrefused -nv -c -O miRNA.dat.raw https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.dat.raw | awk '{if ($0~/hsa/)print $0}' > miRNA.str
rm miRNA.dat.raw
wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
# tdrmapper
wget --random-wait --retry-connrefused --no-check-certificate -nv -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
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15 changes: 9 additions & 6 deletions ggd-recipes/hg38-noalt/mirbase.yaml
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Expand Up @@ -24,12 +24,15 @@ recipe:
# wget http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
# zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf
# mirbase
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz
zcat hairpin.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz
zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.raw https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.fa.raw | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
rm hairpin.fa.raw
wget --random-wait --retry-connrefused -q -c -O mature.fa.raw https://mirbase.org/download/CURRENT/mature.fa
cat mature.fa.raw| awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
rm mature.fa.raw
wget --random-wait --retry-connrefused -q -c -O miRNA.dat.raw https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.dat.raw | awk '{if ($0~/hsa/)print $0}' > miRNA.str
rm miRNA.dat.raw
wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
#tdrmapper
wget --random-wait --retry-connrefused --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
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15 changes: 9 additions & 6 deletions ggd-recipes/hg38/mirbase.yaml
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Expand Up @@ -24,12 +24,15 @@ recipe:
# wget http://www.regulatoryrna.org/database/piRNA/download/archive/v1.0/bed/piR_hg19_v1.0.bed.gz
# zcat piR_hg19_v1.0.bed.gz | awk '{print $1"\t.\tpiRNA\t"$2"\t"$3"\t.\t"$6"\t.\tname "$4";"}' >> srna-transcripts.gtf
# mirbase
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz
zcat hairpin.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz
zcat mature.fa.gz | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
zcat miRNA.str.gz | awk '{if ($0~/hsa/)print $0}' > miRNA.str
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.raw https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.fa.raw | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
rm hairpin.fa.raw
wget --random-wait --retry-connrefused -q -c -O mature.fa.raw https://mirbase.org/download/CURRENT/mature.fa
cat mature.fa.raw | awk '{if ($0~/>hsa/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
rm mature.fa.raw
wget --random-wait --retry-connrefused -q -c -O miRNA.dat.raw https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.dat.raw | awk '{if ($0~/hsa/)print $0}' > miRNA.str
rm miRNA.dat.raw
wget --random-wait --retry-connrefused -q -c -O mirbase.gff3 https://mirbase.org/download/hsa.gff3
#tdrmapper
wget --random-wait --retry-connrefused --no-check-certificate -q -c -O trna_mature_pre.fa https://github.com/sararselitsky/tDRmapper/raw/master/hg19_mature_and_pre.fa
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15 changes: 9 additions & 6 deletions ggd-recipes/mm10/mirbase.yaml
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Expand Up @@ -18,12 +18,15 @@ recipe:
zcat rmsk.txt.gz | awk '{print $6"\t.\trepeat\t"$7+1"\t"$8+1"\t.\t"$10"\t.\tname "$12";"}' >> srna-transcripts.gtf
wget --random-wait --retry-connrefused -q -N -c https://www.mirbase.org/ftp/20/genomes/mmu.gff3
awk '$3=="miRNA"' mmu.gff3 | sed 's/=/ /g' >> srna-transcripts.gtf
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.gz https://www.mirbase.org/ftp/21/hairpin.fa.gz
zcat hairpin.fa.gz | awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
wget --random-wait --retry-connrefused -q -c -O mature.fa.gz https://www.mirbase.org/ftp/21/mature.fa.gz
zcat mature.fa.gz | awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
wget --random-wait --retry-connrefused -q -c -O miRNA.str.gz https://www.mirbase.org/ftp/21/miRNA.str.gz
zcat miRNA.str.gz | awk '{if ($0~/mmu/)print $0}' > miRNA.str
wget --random-wait --retry-connrefused -q -c -O hairpin.fa.raw https://mirbase.org/download/CURRENT/hairpin.fa
cat hairpin.fa.raw | awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa
rm hairpin.fa.raw
wget --random-wait --retry-connrefused -q -c -O mature.fa.raw https://mirbase.org/download/CURRENT/mature.fa
cat mature.fa.raw | awk '{if ($0~/>mmu/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > mature.fa
rm mature.fa.raw
wget --random-wait --retry-connrefused -q -c -O miRNA.dat.raw https://mirbase.org/download/CURRENT/miRNA.dat
cat miRNA.dat.raw | awk '{if ($0~/mmu/)print $0}' > miRNA.str
rm miRNA.dat.raw
wget --random-wait --retry-connrefused -nv -c -O mirbase.gff3 https://mirbase.org/download/mmu.gff3
wget --random-wait --retry-connrefused --no-check-certificate -q -c -O Rfam_for_miRDeep.fa.gz https://github.com/lpantano/mirdeep2_core/raw/data/Rfam_for_miRDeep.fa.gz && gunzip Rfam_for_miRDeep.fa.gz
# targetscan analysis
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