Commit 5552f7e5 authored by Penom Nom's avatar Penom Nom
Browse files

add missing parameter to application.properties. Remove all add splitbc.pl in...

add missing parameter to application.properties. Remove all add splitbc.pl in bin and remove it from application.properties. 
parent 9a7cb4ab
......@@ -21,6 +21,8 @@
batch_system_type = local
# add these options to all batch submit files
batch_options =
# add these options to limit the number of jobs sumitted in parallel
limit_submission = 100
# on which socket host should run the web server
server_socket_host = 127.0.0.1
# on which socket port should run the web server
......@@ -75,7 +77,6 @@ tmp_directory = <path>/tmp
#bismark_genome_preparation = /nosave/software/bismark_v0.8.3/bismark_genome_preparation
#bismark_methylation_extractor = /nosave/software/bismark_v0.8.3/bismark_methylation_extractor
#fastx_reverse_complement = /usr/bin/fastx_reverse_complement
#splitbc = /usr/bin/splitbc.pl
# Set cluster parameters to some components
[components]
......@@ -91,10 +92,6 @@ phix_bwa = /bank/bwadb/phi.fa
ecoli_bwa = /bank/bwadb/ecoli536
yeast_bwa = /bank/bwadb/yeast.nt
# rad and rad tag for radseq data
sbfI_rad = CCTGCAGG
sbfI_radtag = TGCAGG
[454_mids]
MID1 = ACGAGTGCGT
MID2 = ACGCTCGACA
......
This diff is collapsed.
......@@ -24,6 +24,19 @@ from weaver.function import ShellFunction
class SplitBC (Component):
ENZYMES = {
'sbfI' : {
'rad' : 'CCTGCAGG',
'radtag' : 'TGCAGG'
}
}
def get_enzyme (self, name):
if not self.ENZYMES.has_key(name) :
raise ValueError("The enzyme name " + str(name) + " does not exists. Accepted names are " + str (self.ENZYMES.keys()))
return (self.ENZYMES[name]['rad'], self.ENZYMES[name]['radtag'])
def define_parameters(self, fastq_file1, fastq_file2, indiv_names, barcode_file, enzyme,
mismatches, tag_mismatch, trim = True, forward = True ):
self.indiv_names = indiv_names
......@@ -34,9 +47,7 @@ class SplitBC (Component):
self.barcode_file = InputFile(barcode_file, Formats.FASTQ)
self.mismatches = mismatches
self.enzyme = enzyme
self.rad = self.get_resource(self.enzyme + '_rad')
self.rad_tag = self.get_resource(self.enzyme + '_radtag')
self.rad, self.rad_tag = self.get_enzyme(enzyme )
self.tag_mismatch = tag_mismatch
self.trim = trim
self.forward = forward
......@@ -50,7 +61,7 @@ class SplitBC (Component):
strand = "--bol" if self.forward else "--eol"
if self.fastq2 is not None :
command = " ".join([
self.get_exec_path("splitbc"), self.fastq1, self.fastq2, "--mismatches", self.mismatches,
self.get_exec_path("splitbc.pl"), self.fastq1, self.fastq2, "--mismatches", self.mismatches,
"--bcfile", self.barcode_file, "--rad", self.rad, "--radTAG", self.rad_tag, "--TAG_mismatch", self.tag_mismatch,
"--trim" if self.trim else "", "--prefix-r1", self.prefix_r1, "--prefix-r2", self.prefix_r2, strand, ' 2>&1 > ', self.stdout
])
......@@ -59,7 +70,7 @@ class SplitBC (Component):
splitbc(inputs =[self.fastq1, self.fastq2], outputs = [self.output_read1, self.output_read2, self.stdout])
else :
command = " ".join([
self.get_exec_path("splitbc"), self.fastq1,"--mismatches", self.mismatches,
self.get_exec_path("splitbc.pl"), self.fastq1,"--mismatches", self.mismatches,
"--bcfile", self.barcode_file, "--rad", self.rad, "--radTAG", self.rad_tag, "--TAG_mismatch", self.tag_mismatch,
"--trim" if self.trim else "", "--prefix-r1", self.prefix_r1, strand, ' 2>&1 > ', self.stdout
])
......
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