103 lines
3.7 KiB
Python
103 lines
3.7 KiB
Python
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#!/usr/bin/env python
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import sys, os
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from argparse import ArgumentParser, FileType
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def get_data(small = False):
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data_root = "http://www.ccb.jhu.edu/software/hisat2/downloads/evaluation"
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# Download the reference human genome, SNPs, and gene annotations
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if not os.path.exists("data"):
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os.mkdir("data")
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os.chdir("data")
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genome_files = ["genome.fa", "genome.fa.fai", "genome.gtf", "snpCommon.txt", "genome.snp", "genome.ss", "genome.exon"]
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small_genome_files = ["22.fa", "22.fa.fai", "22.gtf", "22.snp", "22.ss", "22.exon", \
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"22_20-21M.fa", "22_20-21M.fa.fai", "22_20-21M.gtf", "22_20-21M.snp", "22_20-21M.ss", "22_20-21M.exon"]
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files = []
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if not small:
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files += genome_files
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files += small_genome_files
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for file in files:
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if os.path.exists(file):
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continue
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wget_cmd = "wget %s/data/%s" % (data_root, file)
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print >> sys.stderr, wget_cmd
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os.system(wget_cmd)
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os.chdir("..")
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# Download indexes
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if not os.path.exists("indexes"):
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os.mkdir("indexes")
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os.chdir("indexes")
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aligners = ["HISAT2", "HISAT", "Bowtie", "STAR", "GSNAP"]
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for genome in ["genome", "22", "22_20-21M"]:
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if small and genome == "genome":
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continue
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for aligner in aligners:
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if genome == "genome":
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aligner_dir = aligner
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else:
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aligner_dir = aligner + "_" + genome
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if os.path.exists(aligner_dir):
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continue
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cmd = "wget %s/indexes/%s.tar.gz; tar xvzf %s.tar.gz; rm %s.tar.gz" % \
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(data_root, aligner_dir, aligner_dir, aligner_dir)
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print >> sys.stderr, cmd
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os.system(cmd)
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os.chdir("..")
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# Download simulated and real reads
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if not os.path.exists("reads"):
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os.mkdir("reads")
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os.chdir("reads")
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for type in ["simulation", "real"]:
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if small and type == "real":
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continue
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if not os.path.exists(type):
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os.mkdir(type)
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os.chdir(type)
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if type == "simulation":
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files = ["1M_DNA_reads_22",
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"1M_DNA_mismatch_reads_22",
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"1M_DNA_snp_reads_22",
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"1M_DNA_mismatch_snp_reads_22",
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"1M_RNA_reads_22",
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"1M_RNA_constant_reads_22",
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"1M_RNA_mismatch_reads_22",
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"1M_RNA_snp_reads_22",
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"1M_RNA_mismatch_snp_reads_22",
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"1M_RNA_reads_22_20-21M",
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"20M_DNA_reads_genome",
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"20M_DNA_snp_reads_genome",
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"20M_RNA_reads_genome",
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"20M_RNA_snp_reads_genome"]
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else:
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files = ["108M_RNA_wgEncodeCshlLongRnaSeq",
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"62M_RNA_SRR353653",
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"80M_DNA_SRR345300",
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"5M_DNA_NA12878D"]
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for file in files:
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if small and file.find("20M") != -1:
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continue
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if os.path.exists(file):
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continue
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cmd = "wget %s/reads/%s/%s.tar.gz; tar xvzf %s.tar.gz; rm %s.tar.gz" % \
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(data_root, type, file, file, file)
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print >> sys.stderr, cmd
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os.system(cmd)
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os.chdir("..")
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os.chdir("..")
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if __name__ == "__main__":
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parser = ArgumentParser(
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description='Get reference genome, annotations, and indexes')
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parser.add_argument('-s', '--small',
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dest='small',
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action='store_true',
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default=False,
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help='small testset')
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args = parser.parse_args()
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get_data(args.small)
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