def deploy_track_files(in_files, out_header):
"""Copy UCSC tracks to public url"""
remote = cfg.get('visualization', 'remote_ssh_dir')
remote_host = remote.split(':')[0]
remote_dir = remote.split(':')[1]
for in_track in in_files:
sys_call('ssh %s mkdir -p %s' % (remote_host, remote_dir))
sys_call('scp %s %s' % (in_track, remote))
touch(out_header)
def deploy_track_files(in_files, out_header):
"""Copy UCSC tracks to public url"""
remote = cfg.get("visualization", "remote_ssh_dir")
remote_host = remote.split(":")[0]
remote_dir = remote.split(":")[1]
for in_track in in_files:
sys_call("ssh %s mkdir -p %s" % (remote_host, remote_dir))
sys_call("scp %s %s" % (in_track, remote))
touch(out_header)
def gene_ontology(in_peaks, out_files):
"""Calculate the significance of the peaks near genes using BioConductor"""
out_genes, out_go, out_raw = out_files
cmd = """echo '
peaks = read.table("%s", header=FALSE, sep="\t");
peaks = data.frame(chr=as.factor(peaks[,1]), start=as.numeric(peaks[,2]),
end=as.numeric(peaks[,3]));
peaks = RangedData(IRanges(start=peaks[,2], end=peaks[,3]), space=peaks[,1])
source("http://bioconductor.org/biocLite.R");
biocLite("ChIPpeakAnno");
library(ChIPpeakAnno);
mart<-useMart(biomart="ensembl",dataset="%s");
tss = getAnnotation(mart, featureType="TSS");
annopeaks = annotatePeakInBatch(peaks[, ], AnnotationData=tss);
write.table(annopeaks, file="%s", sep="\t");
' | R --vanilla --slave > %s""" % (in_peaks, cfg.get(
'DEFAULT', 'R_mart'), out_genes, out_go, out_raw)
print cmd
touch(out_raw)
def gene_ontology(in_peaks, out_files):
"""Calculate the significance of the peaks near genes using BioConductor"""
out_genes, out_go, out_raw = out_files
cmd = """echo '
peaks = read.table("%s", header=FALSE, sep="\t");
peaks = data.frame(chr=as.factor(peaks[,1]), start=as.numeric(peaks[,2]),
end=as.numeric(peaks[,3]));
peaks = RangedData(IRanges(start=peaks[,2], end=peaks[,3]), space=peaks[,1])
source("http://bioconductor.org/biocLite.R");
biocLite("ChIPpeakAnno");
library(ChIPpeakAnno);
mart<-useMart(biomart="ensembl",dataset="%s");
tss = getAnnotation(mart, featureType="TSS");
annopeaks = annotatePeakInBatch(peaks[, ], AnnotationData=tss);
write.table(annopeaks, file="%s", sep="\t");
' | R --vanilla --slave > %s""" % (in_peaks, cfg.get('DEFAULT', 'R_mart'),
out_genes, out_go, out_raw)
print cmd
touch(out_raw)
def all_complete(_, out_sentinel):
"""HTS workflow complete"""
touch(out_sentinel)
def get_genome(_, out_genome_path, touch_file=True):
'download the worldbase genome'
genome = worldbase(cfg.get('DEFAULT', 'worldbase_genome'), download=True)
if touch_file:
touch(out_genome_path)
return genome