From deca4f001abb26dd55af3d9fa2241a19f3fd5c02 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 14:32:27 -0400 Subject: [PATCH 1/5] grabbing fragment columns --- genotype_variants/create_all_maf_dataframe.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index f44bf5a..26cf605 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -73,9 +73,9 @@ def create_all_maf_dataframe( try: df_s.rename( columns={ - "t_alt_count": "t_alt_count_standard", - "t_ref_count": "t_ref_count_standard", - "t_total_count": "t_total_count_standard", + "t_alt_count_fragment": "t_alt_count_standard", + "t_ref_count_fragment": "t_ref_count_standard", + "t_total_count_fragment": "t_total_count_standard", "t_variant_frequency": "t_variant_frequency_standard", "t_alt_count_forward": "t_alt_count_forward_standard", "t_ref_count_forward": "t_ref_count_forward_standard", From 0f9ba49330b1695660cf32c15476c87aee993db8 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 14:48:42 -0400 Subject: [PATCH 2/5] Update create_all_maf_dataframe.py --- genotype_variants/create_all_maf_dataframe.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index 26cf605..8ca906b 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -73,9 +73,12 @@ def create_all_maf_dataframe( try: df_s.rename( columns={ - "t_alt_count_fragment": "t_alt_count_standard", - "t_ref_count_fragment": "t_ref_count_standard", - "t_total_count_fragment": "t_total_count_standard", + "t_alt_count": "t_alt_count_standard", + "t_ref_count": "t_ref_count_standard", + "t_total_count": "t_total_count_standard", + "t_alt_count_fragment": "t_alt_count_fragment_standard", + "t_ref_count_fragment": "t_ref_count_fragment_standard", + "t_total_count_fragment": "t_total_count_fragment_standard", "t_variant_frequency": "t_variant_frequency_standard", "t_alt_count_forward": "t_alt_count_forward_standard", "t_ref_count_forward": "t_ref_count_forward_standard", From 9a2bfa7c0a3ec682ebefd94a62f4032dfefc7cb7 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 15:19:54 -0400 Subject: [PATCH 3/5] Update create_all_maf_dataframe.py --- genotype_variants/create_all_maf_dataframe.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index 8ca906b..ad78048 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -226,6 +226,9 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", + "t_total_count_standard", + "t_alt_count_fragment_standard", + "t_ref_count_fragment_standard", "t_variant_frequency_standard", "t_ref_count_forward_standard", "t_alt_count_forward_standard", @@ -285,6 +288,9 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", + "t_total_count_standard", + "t_alt_count_fragment_standard", + "t_ref_count_fragment_standard", "t_variant_frequency_standard", "t_ref_count_forward_standard", "t_alt_count_forward_standard", From 5dc47a9437fc1c6b18c6b9abc703261f5477c7f6 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 15:20:58 -0400 Subject: [PATCH 4/5] Update create_all_maf_dataframe.py --- genotype_variants/create_all_maf_dataframe.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index ad78048..b4ddff0 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -226,7 +226,7 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", - "t_total_count_standard", + "t_total_count_fragment", "t_alt_count_fragment_standard", "t_ref_count_fragment_standard", "t_variant_frequency_standard", @@ -288,7 +288,7 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", - "t_total_count_standard", + "t_total_count_fragment", "t_alt_count_fragment_standard", "t_ref_count_fragment_standard", "t_variant_frequency_standard", From 0e98609ebbc7663f40eeb65cf2db6efc3d1de5b2 Mon Sep 17 00:00:00 2001 From: buehlere Date: Fri, 26 Jul 2024 15:21:35 -0400 Subject: [PATCH 5/5] Update create_all_maf_dataframe.py --- genotype_variants/create_all_maf_dataframe.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/genotype_variants/create_all_maf_dataframe.py b/genotype_variants/create_all_maf_dataframe.py index b4ddff0..fca5c1e 100644 --- a/genotype_variants/create_all_maf_dataframe.py +++ b/genotype_variants/create_all_maf_dataframe.py @@ -226,7 +226,7 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", - "t_total_count_fragment", + "t_total_count_fragment_standard", "t_alt_count_fragment_standard", "t_ref_count_fragment_standard", "t_variant_frequency_standard", @@ -288,7 +288,7 @@ def create_all_maf_dataframe( "t_ref_count_standard", "t_alt_count_standard", "t_total_count_standard", - "t_total_count_fragment", + "t_total_count_fragment_standard", "t_alt_count_fragment_standard", "t_ref_count_fragment_standard", "t_variant_frequency_standard",