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Update of DNAscan.py #6

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Update of DNAscan.py #6

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32 changes: 17 additions & 15 deletions scripts/DNAscan.py
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Original file line number Diff line number Diff line change
Expand Up @@ -589,7 +589,7 @@

annovar_operations = "g,f,f"

annovar_protocols = "refGene,dbnsfp30a,clinvar_20170905,"
annovar_protocols = "refGene,dbnsfp30a,clinvar_20200316"

# Y. adapt DB to reference

Expand Down Expand Up @@ -852,7 +852,7 @@
rg_option_hisat2 = " --rg-id %s --rg LB:%s --rg PL:%s --rg PU:%s --rg SM:%s " % (
RG_ID, RG_LB, RG_PL, RG_PU, RG_SM)

rg_option_bwa = " -R '@RG\tID:%s\tLB:%s\tPL:%s\tRGPU:%s\tSM:%s' " % (
rg_option_bwa = " -R '@RG\\tID:%s\\tLB:%s\\tPL:%s\\tPU:%s\\tSM:%s' " % (
RG_ID, RG_LB, RG_PL, RG_PU, RG_SM)

else:
Expand Down Expand Up @@ -946,12 +946,14 @@
rg_option_hisat2 = " --rg-id %s --rg LB:%s --rg PL:%s --rg PU:%s --rg SM:%s " % (
RG_ID, RG_LB, RG_PL, RG_PU, RG_SM)

rg_option_bwa = " -R '@RG\tID:%s\tLB:%s\tPL:%s\tRGPU:%s\tSM:%s' " % (
rg_option_bwa = " -R '@RG\\tID:%s\\tLB:%s\\tPL:%s\\tPU:%s\\tSM:%s' " % (
RG_ID, RG_LB, RG_PL, RG_PU, RG_SM)

else:

rg_option = ""
rg_option_hisat2 = ""

rg_option_bwa = ""

os.system(
"%shisat2 %s --no-softclip --no-spliced-alignment -p %s -x %s -U %s | %s %ssamtools view -Sb - | %ssambamba sort -t %s --tmpdir=%s -o %ssorted.bam /dev/stdin; %ssamtools index -@ %s %ssorted.bam"
Expand Down Expand Up @@ -1047,7 +1049,7 @@
"WARNING: The presence of VC.log in logs is telling you that the variant calling was already peformed, please remove VC.log if you wish to perform this stage anyway\n"
)

variant_results_file = "%sresults/%s_sorted.vcf.gz" % (out,
variant_results_file = "%s%s_sorted.vcf.gz" % (out,
sample_name)

else:
Expand Down Expand Up @@ -1107,7 +1109,7 @@

while counter < int(num_cpu) + 1:

command = "%sjava -jar %sGenomeAnalysisTK.jar %s -R %s -T HaplotypeCaller -I %s -L %smpileup_positions%s.bed -o %sgatk_indels%s.vcf" % (
command = "%sjava -jar %sgatk-package-4.1.9.0-local.jar %s HaplotypeCaller -R %s -I %s -L %smpileup_positions%s.bed -O %sgatk_indels%s.vcf" % (
path_java, path_gatk, gatk_HC_custom_options, path_reference, bam_file, out,
str(counter), out, str(counter))

Expand Down Expand Up @@ -1182,7 +1184,7 @@
"%svcftools --vcf %sfreebayes.vcf --minGQ 30 --minDP 2 --exclude-bed %smpileup_positions.bed --recode --recode-INFO-all --out %sSNPs_only"
% (path_vcftools, out, out, out))

os.system("%sSNPs_only.log" % (out))
os.system("touch %sSNPs_only.log" % (out))

os.system(
"bgzip %sSNPs_only.recode.vcf ; bgzip %sindels_only.recode.vcf "
Expand All @@ -1193,7 +1195,7 @@
% (path_tabix, out, path_tabix, out))

os.system(
"%sjava -jar %sGenomeAnalysisTK.jar -T CombineVariants -minimalVCF -R %s --variant %sSNPs_only.recode.vcf.gz --variant %sindels_only.recode.vcf.gz -o %s%s.vcf --genotypemergeoption UNSORTED"
"%sjava -jar %sgatkpackage-4.1.9.0-local.jar MergeVcfs -R %s -I %sSNPs_only.recode.vcf.gz -I %sindels_only.recode.vcf.gz -O %s%s.vcf "
% (path_java, path_gatk, path_reference, out, out, out,
sample_name))

Expand Down Expand Up @@ -1350,11 +1352,11 @@
reference, annovar_protocols, annovar_operations, out))
if not debug and not alsgenescanner:
os.system(
"rm %sannovar.vcf.hg19_multianno.txt %sannovar.vcf.avinput" %
"rm %sannovar.vcf.hg38_multianno.txt %sannovar.vcf.avinput" %
(out, out))

os.system(
"mv %s/annovar.vcf.hg19_multianno.vcf %sresults/%s_annotated.vcf ; bgzip -f %sresults/%s_annotated.vcf ; %stabix -fp vcf %sresults/%s_annotated.vcf.gz"
"mv %s/annovar.vcf.hg38_multianno.vcf %sresults/%s_annotated.vcf ; bgzip -f %sresults/%s_annotated.vcf ; %stabix -fp vcf %sresults/%s_annotated.vcf.gz"
% (out, out, sample_name, out, sample_name, path_tabix, out,
sample_name))

Expand All @@ -1371,9 +1373,9 @@

if variant_results_file:

os.system("mv %s* %sresults/" % (variant_results_file, out))
os.system("mv %s* %s" % (variant_results_file, out))

variant_results_file = "%sresults/%s_sorted.vcf.gz" % (out,
variant_results_file = "%s%s_sorted.vcf.gz" % (out,
sample_name)

# 15. Microbes screening
Expand Down Expand Up @@ -1599,7 +1601,7 @@

if path_java != "":

java_option = "-j " + path_java + " "
java_option = "-j " + path_java + "java"

else:

Expand Down Expand Up @@ -1742,7 +1744,7 @@
os.system("touch %slogs/iobio.log" % (out))

print(
"\n\nIobio serces have been started at http://localhost:%s\n\nCopy and paste http://localhost:%s to select the service (vcf, bam, gene) and upload your data into the selected service\n\nIf you want to explore your variant calling results please copy and paste the following URL into your browser and upload the vcf file (../%sresults/%s_sorted.vcf.gz):\n\n"
"\n\nIobio services have been started at http://localhost:%s\n\nCopy and paste http://localhost:%s to select the service (vcf, bam, gene) and upload your data into the selected service\n\nIf you want to explore your variant calling results please copy and paste the following URL into your browser and upload the vcf file (../%s%s_sorted.vcf.gz):\n\n"
% (port_num, port_num, out, sample_name),
end='',
flush=True)
Expand Down Expand Up @@ -1783,7 +1785,7 @@
if alsgenescanner:

os.system(
"python3 %s/alsgenescanner.py %s/annovar.vcf.hg19_multianno.txt %s/results/%s_alsgenescanner_all.txt"
"python3 %s/alsgenescanner.py %s/annovar.vcf.hg38_multianno.txt %s/results/%s_alsgenescanner_all.txt"
% (path_scripts, out, out, sample_name))
os.system(
"cat %s/results/%s_alsgenescanner_all.txt | head -1 > %s/results/%s_alsgenescanner_alsod.txt; cat %s/results/%s_alsgenescanner_all.txt | grep -iwf %s/list_genes_alsod.txt >> %s/results/%s_alsgenescanner_alsod.txt"
Expand Down