fix typo

patidarr · patidarr · commit a2b0e3d599e2 · 2017-03-01T09:32:53.000-05:00
diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile
@@ -246,7 +246,7 @@ for sample in config['sample_references'].keys():
 	if config['sample_captures'][sample] not in config['Panel_List']:
 		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/sequenza/"+sample+"/"+sample+"_alternative_fit.pdf"]
 		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/sequenza/"+sample+".txt"]
-		#COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/NeoAntigen/MHC_Class_I/"+sample+".final.tsv"]
+		COPY_NUMBER +=[subject+"/"+TIME+"/"+sample+"/NeoAntigen/MHC_Class_I/"+sample+".final.tsv"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".MuTect.annotated.txt"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".strelka.snvs.annotated.txt"]
 	SOMATIC     +=[subject+"/"+TIME+"/"+sample+"/calls/"+sample+".strelka.indels.annotated.txt"]
@@ -525,14 +525,14 @@ rule GENOTYPING:
 rule SampleGT:
 	input:
 		gtFiles=lambda wildcards: SUB_GT[wildcards.subject],
-		mail =NGS_PIPELINE + "/scripts/tsv2html.sh",
 		score=NGS_PIPELINE + "/scripts/scoreGenotyes.pl"
 	output:
 		"{subject}/{TIME}/qc/{subject}.genotyping.txt",
 	params:
 		rulename 	= "SampleGT",
 		batch    	= config[config['host']]["job_default"],
 		mail     	= config["mail"],
+		mail_tool 	= NGS_PIPELINE + "/scripts/tsv2html.sh",
 		host	 	= config["host"],
 		diagnosis	= lambda wildcards: config['Diagnosis'][SUBJECT_TO_SAMPLE[wildcards.subject][0]]
 	shell: """
@@ -557,7 +557,7 @@ rule SampleGT:
 	sed -i 's/Sample_//g' {wildcards.subject}/{TIME}/qc/{wildcards.subject}.genotyping.txt
 	sed -i 's/.bwa//g' {wildcards.subject}/{TIME}/qc/{wildcards.subject}.genotyping.txt
 	sed -i 's/.star//g' {wildcards.subject}/{TIME}/qc/{wildcards.subject}.genotyping.txt
-	ssh {params.host} "sh {input.mail} --name {wildcards.subject} --diagnosis '{params.diagnosis}' --head {WORK_DIR}/{wildcards.subject}/{TIME}/qc/{wildcards.subject}.genotyping.txt | mutt -e \\\"my_hdr Content-Type: text/html\\\" -s 'Genotyping Result on {wildcards.subject}' `whoami`@mail.nih.gov {params.mail} "
+	ssh {params.host} "sh {params.mail_tool} --name {wildcards.subject} --diagnosis '{params.diagnosis}' --head {WORK_DIR}/{wildcards.subject}/{TIME}/qc/{wildcards.subject}.genotyping.txt | mutt -e \\\"my_hdr Content-Type: text/html\\\" -s 'Genotyping Result on {wildcards.subject}' `whoami`@mail.nih.gov {params.mail} "
 	#######################
 	"""
 ############
diff --git a/scripts/process_pVACSeq.pl b/scripts/process_pVACSeq.pl
@@ -11,7 +11,7 @@
 	my @list =split("\t", $_);
 	print "$list[0]\t$list[2]\t$list[2]\t$list[3]\t$list[4]\t";
 	for (my $i=10; $i<=43; $i++){
-		if ($list[$i] =~ /^\d+/){
+		if ($list[$i] =~ /^\d+\.\d+/){
 			$list[$i] =  sprintf("%.2f", $list[$i]);
 		}
 	}
diff --git a/scripts/tsv2html.sh b/scripts/tsv2html.sh
@@ -121,7 +121,7 @@ echo "<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www
 <body>
 <p>
 Hello,<br><br>
-     Please check the genotyping result on <b>$diagnosis</b> patient \"$name\"; a cell with <font color=\"red\">red</font> color indicate that corrosponding library might not belong to the patient $name.<br><br>
+     Please check the genotyping result on <b>$diagnosis</b> patient \"$name\"; a cell with <font color=\"red\">red</font> color indicate that corresponding library might not belong to the patient $name.<br><br>
 </p>
 "
  

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,7 @@`
`11`	`11`	`my @list =split("\t", $_);`
`12`	`12`	`print "$list[0]\t$list[2]\t$list[2]\t$list[3]\t$list[4]\t";`
`13`	`13`	`for (my $i=10; $i<=43; $i++){`
`14`		`- if ($list[$i] =~ /^\d+/){`
	`14`	`+ if ($list[$i] =~ /^\d+\.\d+/){`
`15`	`15`	`$list[$i] = sprintf("%.2f", $list[$i]);`
`16`	`16`	`}`
`17`	`17`	`}`
Original file line number	Diff line number	Diff line change
`@@ -121,7 +121,7 @@ echo "<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www`
`121`	`121`	`<body>`
`122`	`122`	`<p>`
`123`	`123`	`Hello,<br><br>`
`124`		`- Please check the genotyping result on <b>$diagnosis</b> patient \"$name\"; a cell with <font color=\"red\">red</font> color indicate that corrosponding library might not belong to the patient $name.<br><br>`
	`124`	`+ Please check the genotyping result on <b>$diagnosis</b> patient \"$name\"; a cell with <font color=\"red\">red</font> color indicate that corresponding library might not belong to the patient $name.<br><br>`
`125`	`125`	`</p>`
`126`	`126`	`"`
`127`	`127`