59 lines
3.0 KiB
Python
59 lines
3.0 KiB
Python
|
#!/usr/bin/env python
|
||
|
|
|
||
|
|
import sys, os
|
||
|
|
use_message = '''
|
||
|
|
'''
|
||
|
|
|
||
|
|
# GRCh38 release 84
|
||
|
|
def build_indexes():
|
||
|
|
# Build indexes
|
||
|
|
if not os.path.exists("indexes"):
|
||
|
|
os.mkdir("indexes")
|
||
|
|
os.chdir("indexes")
|
||
|
|
aligners = ["HISAT2", "HISAT", "Bowtie", "STAR", "GSNAP", "BWA", "minimap2"]
|
||
|
|
genomes = ["22_20-21M", "22", "genome"]
|
||
|
|
for genome in genomes:
|
||
|
|
for aligner in aligners:
|
||
|
|
if genome == "genome":
|
||
|
|
dir = aligner
|
||
|
|
else:
|
||
|
|
dir = aligner + "_" + genome
|
||
|
|
if os.path.exists(dir):
|
||
|
|
continue
|
||
|
|
os.mkdir(dir)
|
||
|
|
os.chdir(dir)
|
||
|
|
if aligner == "HISAT2":
|
||
|
|
cmd = "../../aligners/bin/hisat2-build ../../data/%s.fa %s" % (genome, genome)
|
||
|
|
cmd = cmd + "; ../../aligners/bin/hisat2-build -p 4 ../../data/%s.fa --snp ../../data/%s.snp --haplotype ../../data/%s.haplotype %s_snp" % (genome, genome, genome, genome)
|
||
|
|
cmd = cmd + "; ../../aligners/bin/hisat2-build -p 4 ../../data/%s.fa --ss ../../data/%s.ss --exon ../../data/%s.exon %s_tran" % (genome, genome, genome, genome)
|
||
|
|
cmd = cmd + "; ../../aligners/bin/hisat2-build -p 4 ../../data/%s.fa --snp ../../data/%s.snp --haplotype ../../data/%s.haplotype --ss ../../data/%s.ss --exon ../../data/%s.exon %s_snp_tran" % (genome, genome, genome, genome, genome, genome)
|
||
|
|
elif aligner == "HISAT":
|
||
|
|
cmd = "../../aligners/bin/hisat-build ../../data/%s.fa %s" % (genome, genome)
|
||
|
|
cmd = cmd + "; ../../aligners/bin/tophat -G ../../data/%s.gtf --transcriptome-index=gtf %s; rm -rf tophat_out" % (genome, genome)
|
||
|
|
elif aligner == "Bowtie":
|
||
|
|
cmd = "../../aligners/bin/bowtie-build ../../data/%s.fa %s" % (genome, genome)
|
||
|
|
elif aligner == "Bowtie2":
|
||
|
|
cmd = "../../aligners/bin/bowtie2-build --threads 6 ../../data/%s.fa %s" % (genome, genome)
|
||
|
|
elif aligner == "STAR":
|
||
|
|
cmd = "../../aligners/bin/STAR --runMode genomeGenerate --genomeDir . --genomeFastaFiles ../../data/%s.fa" % (genome)
|
||
|
|
cmd = cmd + "; mkdir gtf; ../../aligners/bin/STAR --runMode genomeGenerate --genomeDir gtf --genomeFastaFiles ../../data/%s.fa --sjdbGTFfile ../../data/%s.gtf --sjdbOverhang 99 --runThreadN 4" % (genome, genome)
|
||
|
|
elif aligner == "GSNAP":
|
||
|
|
cmd = "../../aligners/bin/gmap_build -B ../../aligners/bin -D . -d %s ../../data/%s.fa" % (genome, genome)
|
||
|
|
elif aligner == "BWA":
|
||
|
|
cmd = "../../aligners/bin/bwa index -p %s.fa ../../data/%s.fa" % (genome, genome)
|
||
|
|
elif aligner == "minimap2":
|
||
|
|
cmd = "../../aligners/bin/minimap2 -x sr -d %s.mmi ../../data/%s.fa" % (genome, genome)
|
||
|
|
elif aligner == "VG":
|
||
|
|
assert False
|
||
|
|
else:
|
||
|
|
assert False
|
||
|
|
print >> sys.stderr, cmd
|
||
|
|
os.system(cmd)
|
||
|
|
os.chdir("..")
|
||
|
|
|
||
|
|
os.chdir("..")
|
||
|
|
|
||
|
|
|
||
|
|
if __name__ == "__main__":
|
||
|
|
build_indexes()
|