tRAX/quickdb.bash at master · UCSC-LoweLab/tRAX · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
#!/usr/bin/env bash

# Supported genomes
GENOMES=("hg19" "hg38" "rn6" "mm10" "sacCer3" "hg19mito" "hg38mito" "mm10mito")

# Help function
function print_usage() {
  echo "USAGE: $0 databasename location(optional)" >&2
  echo "  databasename: ${GENOMES[@]}" >&2
  echo "  location: Directory to store the database (default = /rnadb)" >&2
}

# Function to build the database
function db_builder() {
  downloaddb=false
  echo "${2}"
  if test "${1}" = "hg19"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/genomes/eukaryota/Hsapi19/hg19-tRNAs.tar.gz"
    gtRNAdb_OUT="hg19-tRNAs-detailed.out"
    gtRNAdb_NAME="hg19-tRNAs_name_map.txt"
    GENOME_URL="http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz"
    FASTA=true
  elif test "${1}" = "hg38"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Hsapi38/hg38-tRNAs.tar.gz"
    gtRNAdb_OUT="hg38-tRNAs-detailed.out"
    gtRNAdb_NAME="hg38-tRNAs_name_map.txt"
    GENOME_URL="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz"
    FASTA=true
  elif test "${1}" = "mm10"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/mm10-tRNAs.tar.gz"
    gtRNAdb_OUT="mm10-tRNAs-confidence-set.out"
    gtRNAdb_NAME="mm10-tRNAs_name_map.txt"
    GENOME_URL="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit"
    FASTA=false
  elif test "${1}" = "mm10mito"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/genomes/eukaryota/Mmusc10/mm10-tRNAs.tar.gz"
    gtRNAdb_OUT="mm10-tRNAs-confidence-set.out"
    gtRNAdb_NAME="mm10-tRNAs_name_map.txt"
    GENOME_URL="https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit"
    FASTA=false
  elif test "${1}" = "rn6"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.102.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/genomes/eukaryota/Rnorv6/rn6-tRNAs.tar.gz"
    gtRNAdb_OUT="rn6-tRNAs-detailed.out"
    gtRNAdb_NAME="rn6-tRNAs_name_map.txt"
    GENOME_URL="https://hgdownload.soe.ucsc.edu/goldenPath/rn6/bigZips/rn6.fa.gz"
    FASTA=true
  elif test "${1}" = "sacCer3"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-97/gtf/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.97.gtf.gz"
    gtRNAdb_URL="http://gtrnadb.ucsc.edu/genomes/eukaryota/Scere3/sacCer3-tRNAs.tar.gz"
    gtRNAdb_OUT="sacCer3-tRNAs.out-noChrM"
    gtRNAdb_NAME="sacCer3-tRNAs_name_map.txt"
    GENOME_URL="https://hgdownload.soe.ucsc.edu/goldenPath/sacCer3/bigZips/sacCer3.2bit"
    FASTA=false
  elif test "${1}" = "hg19mito"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz"
    dburl="http://trna.ucsc.edu/tRAX/data/refdb/hg19mito.tar.gz"
    downloaddb=true
  elif test "${1}" = "hg38mito"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens/Homo_sapiens.GRCh38.102.gtf.gz"
    dburl="http://trna.ucsc.edu/tRAX/data/refdb/hg38mito.tar.gz"
    downloaddb=true
  elif test "${1}" = "mm10mito"; then
    GTF_URL="ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz"
    dburl="http://trna.ucsc.edu/tRAX/data/refdb/mm10mito.tar.gz"
    downloaddb=true
  else
    echo "Could not generate RNA database, non-supported DB or parameter missing"
    return
  fi

  # GTF File from Ensembl
  echo "Generating GTF"
  wget -q -O - ${GTF_URL} |
    gzip -cd |
    grep -v '^#' |
    awk '{print "chr" $0;}' |
    sed 's/chrMT/chrM/g' |
    grep -e Mt_rRNA -e Mt_tRNA -e miRNA -e misc_RNA -e rRNA -e snRNA -e snoRNA -e ribozyme -e sRNA -e scaRNA \
      >${2}/genes.gtf
  echo "Generating GTF Done"

  if test ${downloaddb} = true; then
    echo "Downloading TRAX db"
    wget -O ${2}/mitodb.tar.gz ${dburl}
    tar zxf ${2}/mitodb.tar.gz -C ${2}
    exit 0
  fi

  # gtRNAdb Files
  echo "Generating gtRNAdb"
  wget -q -O ${2}/tse.tar.gz ${gtRNAdb_URL}
  tar zxf ${2}/tse.tar.gz -C ${2}
  rm ${2}/tse.tar.gz
  echo "Generating gtRNAdb Done"

  # Genome Fasta File from UCSC
  echo "Generating Fasta"
  if test ${FASTA} = true; then
    wget -q -O - ${GENOME_URL} | gzip -cd >${DB_LOCATION}/genome.fa
  else
    wget -q -O ${2}/genome.2bit ${GENOME_URL}
    twoBitToFa ${DB_LOCATION}/genome.2bit ${DB_LOCATION}/genome.fa
  fi
  echo "Generating Fasta Done"

  # TRAX maketrnadb
  echo "Starting TRAX makernadb"
  maketrnadb.py \
    --databasename=${2}/db \
    --genomefile=${2}/genome.fa \
    --trnascanfile=${2}/${gtRNAdb_OUT} \
    --namemapfile=${2}/${gtRNAdb_NAME}
}

# Init test
if [ -z "$2" ]; then
  DB_LOCATION="/rnadb"
else
  DB_LOCATION=${2}
  mkdir -p ${2}
fi

if [ -z "$1" ]; then
  print_usage
else
  db_builder ${1} ${DB_LOCATION}
fi