Commit 91da3aa8 authored by Gerald Salin's avatar Gerald Salin
Browse files

remove samtools calmd and sorting due to errors in the generated bam (view in...

remove samtools calmd and sorting due to errors in the generated bam (view in further analysis with methylkit)
parent 93e8eb67
......@@ -75,9 +75,7 @@ class Bismark (Analysis):
# self.get_exec_path("samtools") + " sort $3 $3 " + ";mv $3.bam $4; " + \
# self.get_exec_path("samtools") + " index $4; " + self.get_exec_path("samtools") +" calmd -b $4 "+self.reference_genome+" > $4.calmd 2>>$5; rm -f $4; mv $4.calmd $4 " , cmd_format='{EXE} {IN} {OUT}')
bismark_fn = ShellFunction(self.get_exec_path("bismark") + " " + self.args + " -o " + self.output_directory + \
" " + self.reference_directory + " -1 $1 -2 $2 2> $5 ;" + \
self.get_exec_path("samtools") + " sort $3 $3 ;" + "mv $3.bam $4; " + \
self.get_exec_path("samtools") + " index $4; " + self.get_exec_path("samtools") +" calmd -b $4 "+self.reference_genome+" > $4.calmd 2>>$5; rm -f $4; mv $4.calmd $4 " , cmd_format='{EXE} {IN} {OUT}')
" " + self.reference_directory + " -1 $1 -2 $2 2> $5 ; mv $3 $4;" , cmd_format='{EXE} {IN} {OUT}')
bismark_map = MultiMap(bismark_fn, inputs=[self.read1, self.read2], outputs=[self.output_bam,self.output_sorted_bam,self.stderrs,self.output_report], includes=self.reference_genome)
else:
# bismark_fn = ShellFunction(self.get_exec_path("bismark") + " " + self.args + " -o " + self.output_directory + \
......
......@@ -54,7 +54,7 @@ class BismarkMethylationExtractor (Analysis):
logging.getLogger("BismarkMethylationExtractor.define_parameters").debug("Leaving")
def process(self):
bismark_extract = ShellFunction("mkdir $2; cd $2; " + self.get_exec_path("samtools") + " sort -n $1 $1; rm $1; mv $1.bam $1;" + self.get_exec_path("bismark_methylation_extractor") + " $1 " + self.args + \
bismark_extract = ShellFunction("mkdir $2; cd $2; " + self.get_exec_path("bismark_methylation_extractor") + " $1 " + self.args + \
" --genome_folder " + os.path.dirname(self.reference_genome) + " -o $2 2>> $3; " + self.get_exec_path("samtools") + " sort $1 $1 2>> $3; rm $1; mv $1.bam $1 2>> $3;", cmd_format='{EXE} {IN} {OUT}')
bismark_map = MultiMap(bismark_extract, inputs=self.bams, outputs=[self.output_directories,self.stderrs], includes=self.reference_genome)
......
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