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Copy pathreference.py
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66 lines (62 loc) · 4.56 KB
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import config
if config.ref == "mm10":
bwa_ref = "/installed_tools/RefGenomes/mm10_all/BWA/mm10_ordered_all.fa"
library = "SureSelect_XT_Mouse_All_Exome"
refgen = "/installed_tools/RefGenomes/mm10_all/BOWTIE2/mm10_ordered_all"
bwa_ref = "/installed_tools/RefGenomes/mm10_all/BWA/mm10_ordered_all.fa"
org = "MOUSE"
target_bed = "/installed_tools/RefGenomes/exome/mouse/S0276129_Regions_mm10.bed6"
refflat_file = "/installed_tools/RefGenomes/mm10_GTF/gencode.vM9.refFlat.txt"
rRNA_interval = "/installed_tools/RefGenomes/mm10_GTF/gencode.vM9.rRNA.interval"
rseqc_file = "/installed_tools/RefGenomes/mm10_GTF/RSeQC_GeneModel/GRCm38_mm10_Ensembl.bed"
star_genome = "/installed_tools/RefGenomes/mm10_all/RSEM/mm10_genM9_star_rsem_overhang125"
gtf_file = "/installed_tools/RefGenomes/mm10_GTF/gencode.vM9.annotation.gtf"
rsem_transcrtiptome = "/installed_tools/RefGenomes/mm10_all/RSEM/mm10_genM9_star_rsem_overhang125/mm10_genM9_star_rsem"
salmon_transcrtiptome = "/installed_tools/RefGenomes/mm10_all/kallisto/GRCm38_gencodeM9/GRCm38_gencodeM9"
if config.ref == "mm9":
refgen = "/installed_tools/RefGenomes/mm9_bowtie2/mm9"
star_genome = "/installed_tools/RefGenomes/STAR/mm9_STAR_with_ensembl_NCBIM37_annotaion_overhang125"
refflat_file = "/installed_tools/RefGenomes/mm9_mRNASplice/RefFlat/refFlat.txt"
rRNA_interval = "/installed_tools/RefGenomes/mm9_GTF/RSeQC_GeneModel/mm9_NCBI37_Ensembl.bed"
rseqc_file = "/installed_tools/RefGenomes/mm9_GTF/RSeQC_GeneModel/mm9_NCBI37_Ensembl.bed"
gtf_file = "/installed_tools/RefGenomes/mm9_GTF/mm9_ensembl_ncbim37_igenome_chr.gtf"
rsem_transcrtiptome = ""
salmon_transcrtiptome = ""
if config.ref == "hg19":
bwa_ref = "/installed_tools/RefGenomes/hg19_BWA/hg19_chrM_1st.fa"
org = "HUMAN"
target_bed = "/installed_tools/RefGenomes/exome/S04380219_V5-UTR_covered.bed6"
library = "SureSelect_hg_all_exon_v5_utr_exome"
refgen = "/installed_tools/RefGenomes/hg19_bowtie2/hg19"
refflat_file = "/installed_tools/RefGenomes/hg19_GTF/hg19_Ensembl_v70_refFlat.txt"
rRNA_interval = "/installed_tools/RefGenomes/hg19_GTF/star_GRCh37_ribosome_interval_list.txt"
rseqc_file = "/installed_tools/RefGenomes/hg19_GTF/RSeQC_GeneModel/hg19_Ensembl.bed"
gtf_file = "/installed_tools/RefGenomes/hg19_GTF/hg19_Ensembl_Gene_v70.GTF"
star_genome = "/installed_tools/RefGenomes/RSEM/RSEM_star_hg19_ens70_overhang125/"
rsem_transcrtiptome = "/installed_tools/RefGenomes/RSEM/RSEM_star_hg19_ens70_overhang125/hg19_ens70_star_rsem"
salmon_transcrtiptome = "/installed_tools/RefGenomes/hg19_cDNA/Homo_sapiens.GRCh37.70.cdna.all.ed.name.fa"
fregs="/installed_tools/ancestry/hapmap3.8populations.hg19.freqs"
fai = "/installed_tools/RefGenomes/hg19/fasta/hg19_genome_with_contigs.fa.fai"
svviz_gtf="/installed_tools/RefGenomes/hg19/GTF/gencode.v24.annotation.sort.gtf.gz"
if config.ref == "hg38":
bwa_ref = "/installed_tools/RefGenomes/hg38/BWA/hg38_genome_with_contigs.fa"
bwa_seqc = "/installed_tools/RefGenomes/hg38_SEQC/BWA/hg38.fasta"
org = "HUMAN"
target_bed = "/installed_tools/RefGenomes/exome/S04380219_Covered_liftover_to_hg38.bed6"
library = "SureSelect_hg_all_exon_v5_utr_exome"
refgen = "/installed_tools/RefGenomes/hg38/BOWTIE2/hg38"
bwa_ref = "/installed_tools/RefGenomes/hg38/BWA/hg38_genome_with_contigs.fa"
refflat_file = "/installed_tools/RefGenomes/hg38/Picard_and_RSeqc/gencode.v24.rRNA.refFlat.txt"
rRNA_interval = "/installed_tools/RefGenomes/hg38/Picard_and_RSeqc/gencode.v24.rRNA.interval_list"
rseqc_file = "/installed_tools/RefGenomes/hg38/Picard_and_RSeqc/RSeqc.GRCh38.79.bed"
gtf_file = "/installed_tools/RefGenomes/hg38/GTF/gencode.v24.annotation.gtf"
star_genome = "/installed_tools/RefGenomes/hg38/RSEM/RSEM_star_grch38_gencode24_overhang125"
rsem_transcrtiptome = "/installed_tools/RefGenomes/hg38/RSEM/RSEM_star_grch38_gencode24_overhang125/hg38_gen24_star_rsem"
salmon_transcrtiptome = "/installed_tools/RefGenomes/hg38/cDNA_transcriptome/gencode.v24.transcripts.single.name.fa"
melt1 = "/installed_tools/Software/tools/MELT/MELTv2.1.5/me_refs/Hg38/list.txt"
melt2 = "/installed_tools/Software/tools/MELT/MELTv2.1.5/add_bed_files/Hg38/Hg38.genes.bed"
msisensor_filter = "/installed_tools/RefGenomes/hg38_SEQC/hg38.filter.msisensor.txt"
fregs="/installed_tools/ancestry/hapmap3.8populations.hg38.freqs"
fai = "/installed_tools/RefGenomes/hg38/fasta/hg38_genome_with_contigs.fa.fai"
svviz_gtf="/installed_tools/RefGenomes/hg38/GTF/gencode.v24.annotation.sort.gtf.gz"
dbsnp_indel = "/installed_tools/RefGenomes/dbsnp_indel.vcf"