relecture code YD

Extract_PharmGKB_Variants.sh

-
 #!/bin/bash
 
 PHARMGKB=""
@@ -6,7 +5,6 @@ HLASCAN=""
 BAM=""
 VCF=""
 OUTPUTDIR=""
-
 PRINT_HELP=0
 
 while [[ "$#" -gt 0 ]]; do
@@ -17,17 +15,16 @@ while [[ "$#" -gt 0 ]]; do
         -v|--vcf) VCF="$2" ; shift ;;
 	-o|--out-directory) OUTPUTDIR="$2" ; shift ;;
 	-h|--help) PRINT_HELP=1 ;;
-        *) echo "Unknown parameter passed: $1"; exit 1 ;;
+        *) echo "Unknown parameter passed: $1"; exit 0 ;;
     esac
     shift
 done
 
 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]"
+	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 ""
 	echo "<Mandatory>: "
 	echo "-p <PharmGKB file>: Path to PharmGKB tsv file download at PharmGKB site."
@@ -36,8 +33,7 @@ then
 	echo "-v <vcf file>: vcf file provided by variant calling"
 	echo "-o <OUTPUT_PATH>: Output path."
 	echo ""
-
-	exit 0
+	exit 1
 fi
 
 # Check pharmgkb file is provided and exists
@@ -112,8 +108,7 @@ echo "Output HLAscan: ${OUTPUTDIR}/HLAscan_result/"
 echo "Output HTML file: $OUTPUTDIR/Report.html" 
 
 #HLASCAN
-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
+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
 
 #create HTML
-python2.7 create_html.py -v $VCF -h $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
-
+python create_html.py -v $VCF -s $OUTPUTDIR/HLAscan_result/Report -t $PHARMGKB -o $OUTPUTDIR/Report.html
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Readme.md

@@ -19,9 +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.
 
-* Python2.7:
+* Python:
+    * Tested with python2.7 and python3.9
     * library: pysam , htmltag (required sphinx)
-    * [download python2.7](https://www.python.org/download/releases/2.7/)
+    * [download python](https://www.python.org/download/releases/)
 
 * PharmGKB csv file
     * [download csv file](https://api.pharmgkb.org/v1/download/file/data/clinicalAnnotations.zip)
@@ -32,9 +33,9 @@ Reference : Ka, S., Lee, S., Hong, J., Cho, Y., ... & Jung, J. (2017). HLAscan:
 ## Installation
 
 * First install library with pip:
-    * pip2.7 install pysam
-    * pip2.7 install sphinx
-    * pip2.7 install htmltag
+    * pip install pysam
+    * pip install sphinx
+    * pip install htmltag
 
 * Clone this repository
 
@@ -50,8 +51,16 @@ https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/Nebraska_NA12878_HG001_
 
 ### Execution
 
-    bash -p <PharmGKB file> -b <bam file> -s <path to HLAscan files> -v <vcf file>  -o <output dir>
+    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.
+    -h print help
 
 #### Data test
 
-    bash -p data_test/PharmGKB_Epilepsy.tsv -b data_test/NA12878.5gene.bam -s <path to HLAscan files> -v data_test/NIST-hg001-7001-b-gatk.vcf  -o data_test/
+    bash -p data_test/PharmGKB_Epilepsy.tsv -b data_test/NA12878.5gene.bam -s <path to HLAscan files> -v data_test/NIST-hg001-7001-b-gatk.vcf  -o data_test/ Extract_PharmGKB_Variants.sh
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