code correction

Extract_PharmGKB_Variants.sh

@@ -24,7 +24,7 @@ if [ ${PRINT_HELP} -eq 1 ]
 then
 	echo "Usage:"
 	echo ""
-	echo "bash -p <PharmGKB file> -b <bam file> -s <path to hlascan files> -v <vcf file>  -o <output dir> -h [show this help] Extract_PharmGKB_Variants.sh"
+	echo "bash -p <path/to/PharmGKB/file> -b <path/to/bam/file> -s <path/to/hlascan/files> -v <path/to/vcf/file>  -o <path/to/output/dir> -h [print/this/help] Extract_PharmGKB_Variants.sh"
 	echo ""
 	echo "<Mandatory>: "
 	echo "-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site."
@@ -41,7 +41,6 @@ if [ "${PHARMGKB}" == "" ]
 then
 	1>&2 echo "Missing input pharmgkb tsv file (-p). Abort."
 	exit 2
-
 elif [ ! -f "${PHARMGKB}" ]
 then
 	1>&2 echo "pharmgkb tsv file not found. Abort."
@@ -53,7 +52,6 @@ if [ "${BAM}" == "" ]
 then
 	1>&2 echo "Missing input BAMs (-b). Abort."
 	exit 4
-
 elif [ ! -f "${BAM}" ]
 then
 	1>&2 echo "BAM file not found. Abort."
@@ -66,7 +64,6 @@ if [ "${HLASCAN}" == "" ]
 then
 	1>&2 echo "Missing input HLAscan path (-s). Abort."
 	exit 6
-
 elif [ ! -d "${HLASCAN}" ]
 then
 	1>&2 echo "HLAscan path not found. Abort."
@@ -78,7 +75,6 @@ if [ "${VCF}" == "" ]
 then
 	1>&2 echo "Missing input vcf (-v). Abort."
 	exit 8
-
 elif [ ! -f "${VCF}" ]
 then
 	1>&2 echo "vcf file not found. Abort."
@@ -90,13 +86,31 @@ if [ "${OUTPUTDIR}" == "" ]
 then
 	1>&2 echo "Missing input output dir path (-s). Abort."
 	exit 10
-
 elif [ ! -d "${OUTPUTDIR}" ]
 then
 	1>&2 echo "Output dir path not found. Abort."
 	exit 11
 fi
 
+# Check python version and PATH 
+pythonversion=$(python2.7 -V 2>&1)
+PythonExitCode=$?
+
+if [ $PythonExitCode -eq 0 ]
+then
+	echo "python2.7 is in PATH, continue"
+else
+	echo "missing python2.7 in PATH, use alias if necessary"
+	exit 12
+fi
+
+version=$(echo $pythonversion | cut -f2 -d" " | cut -f1,2 -d.)
+if [ $version != '2.7' ]
+then
+	echo "not the python version supported, please use python2.7"
+	exit 13
+fi
+
 echo "Input pharmgkb file: $PHARMGKB"
 echo "Path to HLAscan: $HLASCAN"
 echo "HLAscan executable: $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py"
@@ -108,7 +122,7 @@ echo "Output HLAscan: ${OUTPUTDIR}/HLAscan_result/"
 echo "Output HTML file: $OUTPUTDIR/Report.html" 
 
 #HLASCAN
-python $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py $BAM $HLASCAN/hla-ref-5gene/gene_list $OUTPUTDIR/HLAscan_result/ 1>> $OUTPUTDIR/HLAscan_log.txt 2>> $OUTPUTDIR/HLAscan_log.txt
+python2.7 $HLASCAN/hla-paper/haplo_scan_v4.0-hla.py $BAM $HLASCAN/hla-ref-5gene/gene_list $OUTPUTDIR/HLAscan_result/ 1>> $OUTPUTDIR/HLAscan_log.txt 2>> $OUTPUTDIR/HLAscan_log.txt
 
 #create HTML
-python create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
\ No newline at end of file
+python2.7 create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
\ No newline at end of file

Readme.md

@@ -19,10 +19,10 @@ pysam library. On output, you have a HTML file readable with any web navigator (
 
 Reference : Ka, S., Lee, S., Hong, J., Cho, Y., ... & Jung, J. (2017). HLAscan: genotyping of the HLA region using next-generation sequencing data. BMC bioinformatics, 18(1), 258.
 
-* Python:
-    * Tested with python2.7 and python3.9
+* Python2.7:
+    * Tested with python 2.7.18
     * library: pysam , htmltag (required sphinx)
-    * [download python](https://www.python.org/download/releases/)
+    * [download python](https://www.python.org/download/releases/python-2718/)
 
 * PharmGKB csv file
     * [download csv file](https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip)
@@ -33,9 +33,9 @@ Reference : Ka, S., Lee, S., Hong, J., Cho, Y., ... & Jung, J. (2017). HLAscan:
 ## Installation
 
 * First install library with pip:
-    * pip install pysam
-    * pip install sphinx
-    * pip install htmltag
+    * pip2.7 install pysam
+    * pip2.7 install sphinx
+    * pip2.7 install htmltag
 
 * Clone this repository
 
@@ -54,11 +54,11 @@ https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_
     bash -p <PharmGKB file> -b <bam file> -s <path to HLAscan files> -v <vcf file>  -o <output dir> Extract_PharmGKB_Variants.sh
 
     Options:
-	-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site.
-	-b <bam file>: Bam file provided by alignement.
-	-s <path to hlascan files>: Path to HLAscan tools download and unzipped.
-	-v <vcf file>: vcf file provided by variant calling
-	-o <OUTPUT_PATH>: Output path.
+	-p <path to PharmGKB file> : Path to PharmGKB tsv file download at PharmGKB site.
+	-b <path to bam file> : Path to bam file provided by alignement.
+	-s <path to hlascan files> : Path to HLAscan tools download and unzipped.
+	-v <path to vcf file> : Path to vcf file provided by variant calling
+	-o <output_path>: Output path.
     -h print help
 
 #### Data test

create_html.py

@@ -96,9 +96,11 @@ def writeBodyRS(Pheno,Drug,gene,LevelEvi,Publi,LevelModi,variant,body):
 
 def extractRS(data,vcfSNP,DictRs,body):
     """ rs information extraction """
+    countSNV=0
     vcf_reader_SNP = VariantFile(vcfSNP)
     for record in vcf_reader_SNP.fetch():
         if record.id in DictRs:
+            countSNV+=1
             for Drug in DictRs[record.id]:
                 for Pheno in DictRs[record.id][Drug]:
                     gene = DictRs[record.id][Drug][Pheno]["Gene"]
@@ -107,6 +109,7 @@ def extractRS(data,vcfSNP,DictRs,body):
                     Publi = DictRs[record.id][Drug][Pheno]["Publi"]
                     body =writeBodyRS(Pheno,Drug,gene,LevelEvi,Publi,LevelModi,record.id,body)
 
+    body = body.append(htmltag.H3("Number of SNV found = "+str(countSNV)))
     return body
 
 
@@ -244,6 +247,12 @@ def main():
 
     #execute
     dictRs,dictHLA = parsePharmGKB(tsvfile)
+
+    if len(dictRs.keys()) == 0:
+        print("WARNING : no rs variant found in PharmGKB file")
+    if len(dictHLA.keys()) == 0:
+        print("WARNING : no HLA variant found in PharmGKB file")
+
     head,body = contructHeader()
     body = extractRS(tsvfile,vcfSNP,dictRs,body)
     body = extractHLA(report,dictHLA,body)