Mutalyzer transcript mapping imports

import.sh

# NCBI36
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/BUILD.36.3/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg18.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg18 /tmp/hg18.seq_gene.sorted.md 'reference'
mutalyzer-admin assemblies import-reference -a hg18 'NC_001807.4'

# GRCh37
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/ANNOTATION_RELEASE.105/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg19.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg19 /tmp/hg19.seq_gene.sorted.md 'GRCh37.p13-Primary Assembly'
mutalyzer-admin assemblies import-reference -a hg19 'NC_012920.1'
wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/list_LRGs_transcripts_GRCh37.txt -O /tmp/hg19.lrgmap.txt
mutalyzer-admin assemblies import-lrgmap -a hg19 /tmp/hg19.lrgmap.txt

# GRCh38
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/ANNOTATION_RELEASE.107/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg38.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg38 /tmp/hg38.seq_gene.sorted.md 'GRCh38.p2-Primary Assembly'
mutalyzer-admin assemblies import-reference -a hg38 'NC_012920.1'
wget ftp://ftp.ebi.ac.uk/pub/databases/lrgex/list_LRGs_transcripts_GRCh38.txt -O /tmp/hg38.lrgmap.txt
mutalyzer-admin assemblies import-lrgmap -a hg38 /tmp/hg38.lrgmap.txt

# GRCm38
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Mus_musculus/sequence/ANNOTATION_RELEASE.105/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/mm10.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a mm10 /tmp/mm10.seq_gene.sorted.md 'GRCm38.p3-C57BL/6J'
mutalyzer-admin assemblies import-reference -a mm10 'NC_005089.1'

# Broad CanFam3.1
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Canis_lupus_familiaris/sequence/ANNOTATION_RELEASE.103/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/canFam3.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a canFam3 /tmp/canFam3.seq_gene.sorted.md 'CanFam3.1-Primary Assembly'
mutalyzer-admin assemblies import-reference -a canFam3 'NC_002008.4'

# SacCer_Apr2011
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Saccharomyces_cerevisiae/sequence/BUILD.3.1/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/sacCer3.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a sacCer3 /tmp/sacCer3.seq_gene.sorted.md 'SacCer_Apr2011-Primary Assembly'
mutalyzer-admin assemblies import-reference -a sacCer3 'AJ011856.1'