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11713 del header.infos[field_to_rename] 11714 11715 # Rename INFO patterns -11716 field_pattern = rf'(^|;)({field_to_rename})=([^;]*)' +11716 field_pattern = rf'(^|;)({field_to_rename})($|;|=[^;]*)' 11717 if field_renamed is not None: -11718 field_renamed_pattern = rf'\1{field_renamed}=\3' +11718 field_renamed_pattern = rf'\1{field_renamed}\3' 11719 else: 11720 field_renamed_pattern = '' 11721 @@ -12131,76 +12131,81 @@

11736 else: 11737 log.info(f"Rename or remove fields - field '{field_to_rename}' removed") 11738 -11739 # Rename INFO -11740 for regex_replace_key, regex_replace in regex_replace_dict.items(): -11741 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") -11742 query = f""" -11743 UPDATE {table} -11744 SET -11745 INFO = {regex_replace} -11746 """ -11747 log.debug(f"query={query}") -11748 self.execute_query(query=query) -11749 -11750 return fields_renamed -11751 -11752 def calculation_rename_info_fields( -11753 self, -11754 fields_to_rename: dict = None, -11755 table: str = None, -11756 operation_name: str = "RENAME_INFO_FIELDS", -11757 ) -> None: -11758 """ -11759 The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates -11760 fields to rename and table if provided, and then calls another function to rename the fields. -11761 -11762 :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be -11763 renamed in a table. Each key-value pair in the dictionary represents the original field name as -11764 the key and the new field name as the value -11765 :type fields_to_rename: dict -11766 :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to -11767 specify the name of the table for which the fields are to be renamed. It is a string type -11768 parameter -11769 :type table: str -11770 :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields` -11771 method is a string that specifies the name of the operation being performed. In this context, it -11772 is used as a default value for the operation name if not explicitly provided when calling the -11773 function, defaults to RENAME_INFO_FIELDS -11774 :type operation_name: str (optional) -11775 """ -11776 -11777 # Param -11778 param = self.get_param() -11779 -11780 # Get param fields to rename -11781 param_fields_to_rename = ( -11782 param.get("calculation", {}) -11783 .get("calculations", {}) -11784 .get(operation_name, {}) -11785 .get("fields_to_rename", None) -11786 ) -11787 -11788 # Get param table -11789 param_table = ( -11790 param.get("calculation", {}) -11791 .get("calculations", {}) -11792 .get(operation_name, {}) -11793 .get("table", None) -11794 ) -11795 -11796 # Init fields_to_rename -11797 if fields_to_rename is None: -11798 fields_to_rename = param_fields_to_rename -11799 -11800 # Init table -11801 if table is None: -11802 table = param_table -11803 -11804 renamed_fields = self.rename_info_fields( -11805 fields_to_rename=fields_to_rename, table=table -11806 ) -11807 -11808 log.debug(f"renamed_fields:{renamed_fields}") +11739 else: +11740 +11741 log.warning(f"Rename or remove fields - field '{field_to_rename}' not in header") +11742 +11743 +11744 # Rename INFO +11745 for regex_replace_key, regex_replace in regex_replace_dict.items(): +11746 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") +11747 query = f""" +11748 UPDATE {table} +11749 SET +11750 INFO = {regex_replace} +11751 """ +11752 log.debug(f"query={query}") +11753 self.execute_query(query=query) +11754 +11755 return fields_renamed +11756 +11757 def calculation_rename_info_fields( +11758 self, +11759 fields_to_rename: dict = None, +11760 table: str = None, +11761 operation_name: str = "RENAME_INFO_FIELDS", +11762 ) -> None: +11763 """ +11764 The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates +11765 fields to rename and table if provided, and then calls another function to rename the fields. +11766 +11767 :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be +11768 renamed in a table. Each key-value pair in the dictionary represents the original field name as +11769 the key and the new field name as the value +11770 :type fields_to_rename: dict +11771 :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to +11772 specify the name of the table for which the fields are to be renamed. It is a string type +11773 parameter +11774 :type table: str +11775 :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields` +11776 method is a string that specifies the name of the operation being performed. In this context, it +11777 is used as a default value for the operation name if not explicitly provided when calling the +11778 function, defaults to RENAME_INFO_FIELDS +11779 :type operation_name: str (optional) +11780 """ +11781 +11782 # Param +11783 param = self.get_param() +11784 +11785 # Get param fields to rename +11786 param_fields_to_rename = ( +11787 param.get("calculation", {}) +11788 .get("calculations", {}) +11789 .get(operation_name, {}) +11790 .get("fields_to_rename", None) +11791 ) +11792 +11793 # Get param table +11794 param_table = ( +11795 param.get("calculation", {}) +11796 .get("calculations", {}) +11797 .get(operation_name, {}) +11798 .get("table", None) +11799 ) +11800 +11801 # Init fields_to_rename +11802 if fields_to_rename is None: +11803 fields_to_rename = param_fields_to_rename +11804 +11805 # Init table +11806 if table is None: +11807 table = param_table +11808 +11809 renamed_fields = self.rename_info_fields( +11810 fields_to_rename=fields_to_rename, table=table +11811 ) +11812 +11813 log.debug(f"renamed_fields:{renamed_fields}") @@ -23896,9 +23901,9 @@

11714 del header.infos[field_to_rename] 11715 11716 # Rename INFO patterns -11717 field_pattern = rf'(^|;)({field_to_rename})=([^;]*)' +11717 field_pattern = rf'(^|;)({field_to_rename})($|;|=[^;]*)' 11718 if field_renamed is not None: -11719 field_renamed_pattern = rf'\1{field_renamed}=\3' +11719 field_renamed_pattern = rf'\1{field_renamed}\3' 11720 else: 11721 field_renamed_pattern = '' 11722 @@ -23919,76 +23924,81 @@

11737 else: 11738 log.info(f"Rename or remove fields - field '{field_to_rename}' removed") 11739 -11740 # Rename INFO -11741 for regex_replace_key, regex_replace in regex_replace_dict.items(): -11742 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") -11743 query = f""" -11744 UPDATE {table} -11745 SET -11746 INFO = {regex_replace} -11747 """ -11748 log.debug(f"query={query}") -11749 self.execute_query(query=query) -11750 -11751 return fields_renamed -11752 -11753 def calculation_rename_info_fields( -11754 self, -11755 fields_to_rename: dict = None, -11756 table: str = None, -11757 operation_name: str = "RENAME_INFO_FIELDS", -11758 ) -> None: -11759 """ -11760 The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates -11761 fields to rename and table if provided, and then calls another function to rename the fields. -11762 -11763 :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be -11764 renamed in a table. Each key-value pair in the dictionary represents the original field name as -11765 the key and the new field name as the value -11766 :type fields_to_rename: dict -11767 :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to -11768 specify the name of the table for which the fields are to be renamed. It is a string type -11769 parameter -11770 :type table: str -11771 :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields` -11772 method is a string that specifies the name of the operation being performed. In this context, it -11773 is used as a default value for the operation name if not explicitly provided when calling the -11774 function, defaults to RENAME_INFO_FIELDS -11775 :type operation_name: str (optional) -11776 """ -11777 -11778 # Param -11779 param = self.get_param() -11780 -11781 # Get param fields to rename -11782 param_fields_to_rename = ( -11783 param.get("calculation", {}) -11784 .get("calculations", {}) -11785 .get(operation_name, {}) -11786 .get("fields_to_rename", None) -11787 ) -11788 -11789 # Get param table -11790 param_table = ( -11791 param.get("calculation", {}) -11792 .get("calculations", {}) -11793 .get(operation_name, {}) -11794 .get("table", None) -11795 ) -11796 -11797 # Init fields_to_rename -11798 if fields_to_rename is None: -11799 fields_to_rename = param_fields_to_rename -11800 -11801 # Init table -11802 if table is None: -11803 table = param_table -11804 -11805 renamed_fields = self.rename_info_fields( -11806 fields_to_rename=fields_to_rename, table=table -11807 ) -11808 -11809 log.debug(f"renamed_fields:{renamed_fields}") +11740 else: +11741 +11742 log.warning(f"Rename or remove fields - field '{field_to_rename}' not in header") +11743 +11744 +11745 # Rename INFO +11746 for regex_replace_key, regex_replace in regex_replace_dict.items(): +11747 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") +11748 query = f""" +11749 UPDATE {table} +11750 SET +11751 INFO = {regex_replace} +11752 """ +11753 log.debug(f"query={query}") +11754 self.execute_query(query=query) +11755 +11756 return fields_renamed +11757 +11758 def calculation_rename_info_fields( +11759 self, +11760 fields_to_rename: dict = None, +11761 table: str = None, +11762 operation_name: str = "RENAME_INFO_FIELDS", +11763 ) -> None: +11764 """ +11765 The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates +11766 fields to rename and table if provided, and then calls another function to rename the fields. +11767 +11768 :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be +11769 renamed in a table. Each key-value pair in the dictionary represents the original field name as +11770 the key and the new field name as the value +11771 :type fields_to_rename: dict +11772 :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to +11773 specify the name of the table for which the fields are to be renamed. It is a string type +11774 parameter +11775 :type table: str +11776 :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields` +11777 method is a string that specifies the name of the operation being performed. In this context, it +11778 is used as a default value for the operation name if not explicitly provided when calling the +11779 function, defaults to RENAME_INFO_FIELDS +11780 :type operation_name: str (optional) +11781 """ +11782 +11783 # Param +11784 param = self.get_param() +11785 +11786 # Get param fields to rename +11787 param_fields_to_rename = ( +11788 param.get("calculation", {}) +11789 .get("calculations", {}) +11790 .get(operation_name, {}) +11791 .get("fields_to_rename", None) +11792 ) +11793 +11794 # Get param table +11795 param_table = ( +11796 param.get("calculation", {}) +11797 .get("calculations", {}) +11798 .get(operation_name, {}) +11799 .get("table", None) +11800 ) +11801 +11802 # Init fields_to_rename +11803 if fields_to_rename is None: +11804 fields_to_rename = param_fields_to_rename +11805 +11806 # Init table +11807 if table is None: +11808 table = param_table +11809 +11810 renamed_fields = self.rename_info_fields( +11811 fields_to_rename=fields_to_rename, table=table +11812 ) +11813 +11814 log.debug(f"renamed_fields:{renamed_fields}") @@ -39111,9 +39121,9 @@

Returns
11714 del header.infos[field_to_rename] 11715 11716 # Rename INFO patterns -11717 field_pattern = rf'(^|;)({field_to_rename})=([^;]*)' +11717 field_pattern = rf'(^|;)({field_to_rename})($|;|=[^;]*)' 11718 if field_renamed is not None: -11719 field_renamed_pattern = rf'\1{field_renamed}=\3' +11719 field_renamed_pattern = rf'\1{field_renamed}\3' 11720 else: 11721 field_renamed_pattern = '' 11722 @@ -39134,18 +39144,23 @@
Returns
11737 else: 11738 log.info(f"Rename or remove fields - field '{field_to_rename}' removed") 11739 -11740 # Rename INFO -11741 for regex_replace_key, regex_replace in regex_replace_dict.items(): -11742 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") -11743 query = f""" -11744 UPDATE {table} -11745 SET -11746 INFO = {regex_replace} -11747 """ -11748 log.debug(f"query={query}") -11749 self.execute_query(query=query) -11750 -11751 return fields_renamed +11740 else: +11741 +11742 log.warning(f"Rename or remove fields - field '{field_to_rename}' not in header") +11743 +11744 +11745 # Rename INFO +11746 for regex_replace_key, regex_replace in regex_replace_dict.items(): +11747 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...") +11748 query = f""" +11749 UPDATE {table} +11750 SET +11751 INFO = {regex_replace} +11752 """ +11753 log.debug(f"query={query}") +11754 self.execute_query(query=query) +11755 +11756 return fields_renamed @@ -39188,63 +39203,63 @@

Returns
- 
11753    def calculation_rename_info_fields(
-11754        self,
-11755        fields_to_rename: dict = None,
-11756        table: str = None,
-11757        operation_name: str = "RENAME_INFO_FIELDS",
-11758    ) -> None:
-11759        """
-11760        The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates
-11761        fields to rename and table if provided, and then calls another function to rename the fields.
-11762
-11763        :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be
-11764        renamed in a table. Each key-value pair in the dictionary represents the original field name as
-11765        the key and the new field name as the value
-11766        :type fields_to_rename: dict
-11767        :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to
-11768        specify the name of the table for which the fields are to be renamed. It is a string type
-11769        parameter
-11770        :type table: str
-11771        :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields`
-11772        method is a string that specifies the name of the operation being performed. In this context, it
-11773        is used as a default value for the operation name if not explicitly provided when calling the
-11774        function, defaults to RENAME_INFO_FIELDS
-11775        :type operation_name: str (optional)
-11776        """
-11777
-11778        # Param
-11779        param = self.get_param()
-11780
-11781        # Get param fields to rename
-11782        param_fields_to_rename = (
-11783            param.get("calculation", {})
-11784            .get("calculations", {})
-11785            .get(operation_name, {})
-11786            .get("fields_to_rename", None)
-11787        )
-11788
-11789        # Get param table
-11790        param_table = (
-11791            param.get("calculation", {})
-11792            .get("calculations", {})
-11793            .get(operation_name, {})
-11794            .get("table", None)
-11795        )
-11796
-11797        # Init fields_to_rename
-11798        if fields_to_rename is None:
-11799            fields_to_rename = param_fields_to_rename
-11800
-11801        # Init table
-11802        if table is None:
-11803            table = param_table
-11804
-11805        renamed_fields = self.rename_info_fields(
-11806            fields_to_rename=fields_to_rename, table=table
-11807        )
-11808
-11809        log.debug(f"renamed_fields:{renamed_fields}")
+            
11758    def calculation_rename_info_fields(
+11759        self,
+11760        fields_to_rename: dict = None,
+11761        table: str = None,
+11762        operation_name: str = "RENAME_INFO_FIELDS",
+11763    ) -> None:
+11764        """
+11765        The `calculation_rename_info_fields` function retrieves parameters from a dictionary, updates
+11766        fields to rename and table if provided, and then calls another function to rename the fields.
+11767
+11768        :param fields_to_rename: `fields_to_rename` is a dictionary that contains the fields to be
+11769        renamed in a table. Each key-value pair in the dictionary represents the original field name as
+11770        the key and the new field name as the value
+11771        :type fields_to_rename: dict
+11772        :param table: The `table` parameter in the `calculation_rename_info_fields` method is used to
+11773        specify the name of the table for which the fields are to be renamed. It is a string type
+11774        parameter
+11775        :type table: str
+11776        :param operation_name: The `operation_name` parameter in the `calculation_rename_info_fields`
+11777        method is a string that specifies the name of the operation being performed. In this context, it
+11778        is used as a default value for the operation name if not explicitly provided when calling the
+11779        function, defaults to RENAME_INFO_FIELDS
+11780        :type operation_name: str (optional)
+11781        """
+11782
+11783        # Param
+11784        param = self.get_param()
+11785
+11786        # Get param fields to rename
+11787        param_fields_to_rename = (
+11788            param.get("calculation", {})
+11789            .get("calculations", {})
+11790            .get(operation_name, {})
+11791            .get("fields_to_rename", None)
+11792        )
+11793
+11794        # Get param table
+11795        param_table = (
+11796            param.get("calculation", {})
+11797            .get("calculations", {})
+11798            .get(operation_name, {})
+11799            .get("table", None)
+11800        )
+11801
+11802        # Init fields_to_rename
+11803        if fields_to_rename is None:
+11804            fields_to_rename = param_fields_to_rename
+11805
+11806        # Init table
+11807        if table is None:
+11808            table = param_table
+11809
+11810        renamed_fields = self.rename_info_fields(
+11811            fields_to_rename=fields_to_rename, table=table
+11812        )
+11813
+11814        log.debug(f"renamed_fields:{renamed_fields}")
 

 
 
diff --git a/docs/tips.pdf b/docs/tips.pdf
index 28cdc03..e615578 100644
Binary files a/docs/tips.pdf and b/docs/tips.pdf differ
diff --git a/docs/user_guide.pdf b/docs/user_guide.pdf
index eaf64ee..c099f38 100644
Binary files a/docs/user_guide.pdf and b/docs/user_guide.pdf differ
diff --git a/howard/objects/variants.py b/howard/objects/variants.py
index 0718f0d..6bd8a1d 100644
--- a/howard/objects/variants.py
+++ b/howard/objects/variants.py
@@ -11713,9 +11713,9 @@ def rename_info_fields(
                     del header.infos[field_to_rename]
 
                     # Rename INFO patterns
-                    field_pattern = rf'(^|;)({field_to_rename})=([^;]*)'
+                    field_pattern = rf'(^|;)({field_to_rename})($|;|=[^;]*)'
                     if field_renamed is not None:
-                        field_renamed_pattern = rf'\1{field_renamed}=\3'
+                        field_renamed_pattern = rf'\1{field_renamed}\3'
                     else:
                         field_renamed_pattern = ''
 
@@ -11736,6 +11736,11 @@ def rename_info_fields(
                     else:
                         log.info(f"Rename or remove fields - field '{field_to_rename}' removed")
 
+                else:
+
+                    log.warning(f"Rename or remove fields - field '{field_to_rename}' not in header")
+
+
             # Rename INFO
             for regex_replace_key, regex_replace  in regex_replace_dict.items():
                 log.info(f"Rename or remove fields - Process [{regex_replace_key+1}/{len(regex_replace_dict)}]...")
diff --git a/plugins/README.pdf b/plugins/README.pdf
index 1d66dc1..40f2849 100644
Binary files a/plugins/README.pdf and b/plugins/README.pdf differ
diff --git a/tests/data/example.annotation_names.vcf b/tests/data/example.annotation_names.vcf
index a53d70e..681ebb0 100644
--- a/tests/data/example.annotation_names.vcf
+++ b/tests/data/example.annotation_names.vcf
@@ -24,6 +24,7 @@
 ##INFO=
 ##INFO=
 ##INFO=
+##INFO=
 ##contig=
 ##contig=
 ##contig=
@@ -57,8 +58,8 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2	sample3	sample4
 chr1	28736	.	A	C	100	PASS	CLNSIG=pathogenic	GT:AD:DP:GQ	0/1:525,204:729:99	0/1:12659,4994:17664:99	1/1:12658,4995:17663:99	1/1:401,175:576:99
 chr1	35144	.	A	C	100	PASS	CLNSIG=non-pathogenic	GT:AD:DP:GQ	./.:.:.:.	0/1:12659,4994:17664:99	0/1:12658,4995:17663:99	0/1:401,175:576:99
-chr1	69101	.	A	G	100	PASS	DP=50;CLNSIG=non-pathogenic;SIFT=D	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
-chr1	768251	.	A	G	100	PASS	CLNSIG=NP;PREFIXCLNSIG=NP;CLNSIGSUFFIX=P	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
+chr1	69101	.	A	G	100	PASS	DP=50;CLNSIG=non-pathogenic;SIFT=D;SPiP_Alt	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
+chr1	768251	.	A	G	100	PASS	CLNSIG=NP;PREFIXCLNSIG=NP;SPiP_Alt;CLNSIGSUFFIX=P	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
 chr1	768252	.	A	G	100	PASS	PREFIXCLNSIG=NP	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
-chr1	768253	.	A	G	100	PASS	CLNSIGSUFFIX=P	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
+chr1	768253	.	A	G	100	PASS	SPiP_Alt;CLNSIGSUFFIX=P	GT:AD:DP:GQ	0/1:525,204:729:99	./.:.:.:.	0/1:12658,4995:17663:99	0/1:401,175:576:99
 chr7	55249063	rs1050171	G	A	5777	PASS	CLNSIG=NP;DP=125;CLNSIG=NP	GT:AD:DP:GQ	0/1:525,204:729:99	0/1:12659,4994:17664:99	./.:.:.:.	0/1:401,175:576:99
diff --git a/tests/test_objects_variants.py b/tests/test_objects_variants.py
index 2fd6f27..bf987c0 100644
--- a/tests/test_objects_variants.py
+++ b/tests/test_objects_variants.py
@@ -2196,13 +2196,16 @@ def test_rename_fields():
             "field_not_in_header": "field_not_in_header_renamed",
             "": "",
             "SIFT": None,
+            "SPiP_Alt": "SPiP_alternative",
+            "SPiP_alternative": None,
         }
 
         # Rename fields
         fields_renamed = variants.rename_info_fields(fields_to_rename=fields_to_rename)
-        assert fields_renamed == {'CLNSIG': 'CLNSIG_renamed', 'PREFIXCLNSIG': 'PREFIXCLNSIG_renamed', 'DP': 'depth', 'SIFT': None}
+        assert fields_renamed == {'CLNSIG': 'CLNSIG_renamed', 'PREFIXCLNSIG': 'PREFIXCLNSIG_renamed', 'DP': 'depth', 'SIFT': None, 'SPiP_Alt': 'SPiP_alternative', 'SPiP_alternative': None}
         assert len(variants.get_query_to_df("SELECT INFO FROM variants WHERE INFO LIKE '%SIFT%'")) == 0
         assert len(variants.get_query_to_df("SELECT INFO FROM variants WHERE INFO LIKE '%None=%'")) == 0
+        assert len(variants.get_query_to_df("SELECT INFO FROM variants WHERE INFO LIKE '%SPiP%'")) == 0
 
         # Check if VCF is in correct format with pyVCF
         remove_if_exists([output_vcf])
@@ -2235,6 +2238,8 @@ def test_rename_fields_to_param_and_export():
                     "field_not_in_header": "field_not_in_header_renamed",
                     "": "",
                     "SIFT": None,
+                    "SPiP_Alt": "SPiP_alternative",
+                    "SPiP_alternative": None,
                 }
             }
         }