From 516a4f85c75b34c483e7bcc3a508a1cdfebafc77 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 14 Mar 2023 17:52:44 +0100 Subject: [PATCH 1/5] feat: support for SV TSV (#75) --- docs/file_formats.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/file_formats.rst b/docs/file_formats.rst index 94befa7..9c01a4f 100644 --- a/docs/file_formats.rst +++ b/docs/file_formats.rst @@ -10,9 +10,9 @@ In the case of the non-native TSV format, this section documents how the file fo Overall, the aim of clinvar-this is to support you in submitting data easily with restrictions (see :ref:`limitations`). If you need the full functionality of the NCBI ClinVar API then please consider using the ``clinvar_api`` Python module. --------------------------- -Small Variant TSV (Native) --------------------------- +----------------------------- +Sequence Variant TSV (Native) +----------------------------- The following headers are required. Clinvar-this will recognize the TSV file format based on these headers. From d018875ff748feeb4a06b73a2809e57e0071bc18 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 14 Mar 2023 17:54:23 +0100 Subject: [PATCH 2/5] feat: adding support for importing phenopackets (#46) --- requirements/base.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/base.txt b/requirements/base.txt index b619258..d68ae71 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -7,3 +7,4 @@ click >=8.1.3, <9.0 toml >=0.10.2, <0.11 tabulate >= 0.9.0 jsonschema >= 4.17.0, <5.0 +phenopackets >=2 From 431aade1abfcb1cf33c6e8bc7330caacae0256a7 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 14 Mar 2023 17:55:03 +0100 Subject: [PATCH 3/5] feat: adding support for clinvar excel (#42) --- requirements/base.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/requirements/base.txt b/requirements/base.txt index d68ae71..8f8697c 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -7,4 +7,6 @@ click >=8.1.3, <9.0 toml >=0.10.2, <0.11 tabulate >= 0.9.0 jsonschema >= 4.17.0, <5.0 + +pandas >=1.5 phenopackets >=2 From 7d2c241b31bbde64a3c99b3cb65bf6d196809e01 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 14 Mar 2023 17:55:51 +0100 Subject: [PATCH 4/5] dependency --- requirements/base.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/base.txt b/requirements/base.txt index 8f8697c..ba56842 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -9,4 +9,5 @@ tabulate >= 0.9.0 jsonschema >= 4.17.0, <5.0 pandas >=1.5 +xlrd >=2 phenopackets >=2 From aa7c273a129c9b59f9d58bb3849418538c3cea34 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 14 Mar 2023 17:58:26 +0100 Subject: [PATCH 5/5] feat: adding support for VCF files (#76) --- requirements/base.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements/base.txt b/requirements/base.txt index ba56842..a7af8c2 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -11,3 +11,4 @@ jsonschema >= 4.17.0, <5.0 pandas >=1.5 xlrd >=2 phenopackets >=2 +vcfpy >=0.20