def start_gv(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
genobox_modules.check_genome(args.genome)
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
if args.caller == 'samtools':
print "Starting genotyping (samtools)"
final_bcf = start_genotyping(args.bam, args.genome, args.fa,
args.prior, args.pp, args.queue,
final_bcf, args.sample, args.partition,
logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller,
args.Q, args.ex, args.rmsk, args.ab,
args.prune, args.ovar, args.queue,
args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp,
args.ovar, args.queue, args.partition,
logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp,
args.rmsk, 'genotyping/indels_for_filtering.vcf',
args.oref, args.queue, args.sample, args.partition,
logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(args.bam, args.genome, args.fa,
args.dbsnp, args.call_conf,
args.call_emit, args.output_mode,
args.queue, args.sample,
args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa,
args.Q, args.rmsk, args.ab,
args.prune, args.queue, args.sample,
args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
def start_gv(args, logger):
'''Perform alignment and bam processing'''
import os
import subprocess
genobox_modules.check_genome(args.genome)
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
if args.caller == 'samtools':
print "Starting genotyping (samtools)"
final_bcf = start_genotyping(args.bam, args.genome, args.fa, args.prior, args.pp, args.queue, final_bcf, args.sample, args.partition, logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller, args.Q, args.ex, args.rmsk, args.ab, args.prune, args.ovar, args.queue, args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp, args.ovar, args.queue, args.partition, logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp, args.rmsk, 'genotyping/indels_for_filtering.vcf', args.oref, args.queue, args.sample, args.partition, logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(args.bam, args.genome, args.fa, args.dbsnp, args.call_conf, args.call_emit, args.output_mode, args.queue, args.sample, args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa, args.Q, args.rmsk, args.ab, args.prune, args.queue, args.sample, args.partition, logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
def start_abgv(args, logger):
'''Start alignment, bam processing, genotyping, vcffiltering, dbsnp annotation, bcf2ref'''
import os
import subprocess
# check genome file
genobox_modules.check_genome(args.genome)
final_bam = 'alignment/%s.flt.sort.rmdup.bam' % args.sample
final_bcf = 'genotyping/%s.all.bcf' % args.sample
# initialize library file from given arguments
library = genobox_modules.initialize_library(args.libfile, args.se,
args.pe1, args.pe2,
args.sample, args.mapq,
args.libs, args.pl)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
# toggle start trimming
#if args.no_trim == False:
# print "Starting trimming"
# (se_files, pe1_files, pe2_files) = start_trim(args, logger)
# library.update(Trim=se_files+pe1_files+pe2_files)
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(library,
genobox_modules.unique(bamfiles.values()),
args.mapq, args.libs, args.tmpdir, args.queue,
final_bam, args.realignment, args.known,
args.fa, args.sample, args.partition, logger)
print "Starting bam stats"
start_bamstats(args, final_bam, args.partition, logger, wait=False)
print "Starting genotyping"
if args.caller == 'samtools':
final_bcf = start_genotyping(final_bam, args.genome, args.fa,
args.prior, args.pp, args.queue,
final_bcf, args.sample, args.partition,
logger)
print "Starting vcffiltering"
final_vcf = start_vcffilter(final_bcf, args.genome, args.caller,
args.Q, args.ex, args.rmsk, args.ab,
args.prune, args.ovar, args.queue,
args.sample, args.partition, logger)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp,
args.ovar, args.queue, args.partition,
logger)
print "Start bcf2ref"
start_bcf2ref(final_bcf, args.genome, args.Q, args.ex, args.dbsnp,
args.rmsk, 'genotyping/indels_for_filtering.vcf',
args.oref, args.queue, args.sample, args.partition,
logger)
elif args.caller == 'gatk':
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(final_bam, args.genome, args.fa,
args.dbsnp, args.call_conf,
args.args.call_emit, args.output_mode,
args.queue, args.sample,
args.partition, logger)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(vcffiles, args.genome, args.fa,
args.Q, args.rmsk, args.ab,
args.prune, args.queue, args.sample,
args.partition, args.logger)
# remove queuing system outfiles
genobox_modules.rm_files(['run_genobox_*', 'semaphores.*'])
print "Done"
print "--------------------------------------"
print "Raw genotyping is written in genotyping/all.bcf"
print "High confidence variants: %s" % args.ovar
print "High confidence reference: %s" % args.oref
print "--------------------------------------"
def start_abgv(args, logger):
"""Start alignment, bam processing, genotyping, vcffiltering, dbsnp annotation, bcf2ref"""
import os
import subprocess
# check genome file
genobox_modules.check_genome(args.genome)
final_bam = "alignment/%s.flt.sort.rmdup.bam" % args.sample
final_bcf = "genotyping/%s.all.bcf" % args.sample
# initialize library file from given arguments
library = genobox_modules.initialize_library(
args.libfile, args.se, args.pe1, args.pe2, args.sample, args.mapq, args.libs, args.pl
)
# start run
if args.sample:
print "--------------------------------------"
print "Processing sample: %s" % args.sample
print "--------------------------------------"
# toggle start trimming
# if args.no_trim == False:
# print "Starting trimming"
# (se_files, pe1_files, pe2_files) = start_trim(args, logger)
# library.update(Trim=se_files+pe1_files+pe2_files)
print "Starting alignment"
(bamfiles, library) = start_alignment(args, logger)
print "Starting bam processing"
final_bam = start_bamprocess(
library,
genobox_modules.unique(bamfiles.values()),
args.mapq,
args.libs,
args.tmpdir,
args.queue,
final_bam,
args.realignment,
args.known,
args.fa,
args.sample,
args.partition,
logger,
)
print "Starting bam stats"
start_bamstats(args, final_bam, args.partition, logger, wait=False)
print "Starting genotyping"
if args.caller == "samtools":
final_bcf = start_genotyping(
final_bam,
args.genome,
args.fa,
args.prior,
args.pp,
args.queue,
final_bcf,
args.sample,
args.partition,
logger,
)
print "Starting vcffiltering"
final_vcf = start_vcffilter(
final_bcf,
args.genome,
args.caller,
args.Q,
args.ex,
args.rmsk,
args.ab,
args.prune,
args.ovar,
args.queue,
args.sample,
args.partition,
logger,
)
print "Start dbsnp"
final_dbsnp_vcf = start_dbsnp(final_vcf, args.ex, args.dbsnp, args.ovar, args.queue, args.partition, logger)
print "Start bcf2ref"
start_bcf2ref(
final_bcf,
args.genome,
args.Q,
args.ex,
args.dbsnp,
args.rmsk,
"genotyping/indels_for_filtering.vcf",
args.oref,
args.queue,
args.sample,
args.partition,
logger,
)
elif args.caller == "gatk":
print "Start genotyping (gatk)"
vcffiles = start_genotyping_gatk(
final_bam,
args.genome,
args.fa,
args.dbsnp,
args.call_conf,
args.args.call_emit,
args.output_mode,
args.queue,
args.sample,
args.partition,
logger,
)
print "Start vcffiltering (gatk)"
final_vcfs = start_vcffilter_gatk(
vcffiles,
args.genome,
args.fa,
args.Q,
args.rmsk,
args.ab,
args.prune,
args.queue,
args.sample,
args.partition,
args.logger,
)
# remove queuing system outfiles
genobox_modules.rm_files(["run_genobox_*", "semaphores.*"])
print "Done"
print "--------------------------------------"
print "Raw genotyping is written in genotyping/all.bcf"
print "High confidence variants: %s" % args.ovar
print "High confidence reference: %s" % args.oref
print "--------------------------------------"