From 1d3ed804b36fd7adf58ac3e8a195ef7e96fd9859 Mon Sep 17 00:00:00 2001 From: Release Auto-Commit Date: Mon, 15 Feb 2021 09:37:50 +0000 Subject: [PATCH 1/4] Updates version info for --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6307572..00a3ee6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ # Changelog +## [v0.0.13](https://github.com/bigbio/py-pgatk/tree/v0.0.13) (2021-02-15) + ## [v0.0.12](https://github.com/bigbio/py-pgatk/tree/v0.0.12) (2021-02-11) ## [v0.0.11](https://github.com/bigbio/py-pgatk/tree/v0.0.11) (2021-02-07) From e8c21d81c7b99c427ec7fa78f4bdfd8e5cd8efa7 Mon Sep 17 00:00:00 2001 From: husensofteng Date: Mon, 15 Feb 2021 13:01:49 +0100 Subject: [PATCH 2/4] fixed bug in column filtering cbio --- pypgatk/cgenomes/cgenomes_proteindb.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/pypgatk/cgenomes/cgenomes_proteindb.py b/pypgatk/cgenomes/cgenomes_proteindb.py index 664b7b1..b545e4f 100644 --- a/pypgatk/cgenomes/cgenomes_proteindb.py +++ b/pypgatk/cgenomes/cgenomes_proteindb.py @@ -187,7 +187,7 @@ def cosmic_to_proteindb(self): line_counter += 1 row = line.strip().split("\t") # filter out mutations from unspecified groups - if filter_col: + if filter_col is not None: if row[filter_col] not in self._accepted_values and self._accepted_values != ['all']: continue @@ -221,7 +221,7 @@ def cosmic_to_proteindb(self): output.write(entry) mutation_dic[header] = 1 - if self._split_by_filter_column and filter_col: + if self._split_by_filter_column and filter_col is not None: try: groups_mutations_dict[row[filter_col]][header] = entry except KeyError: @@ -262,8 +262,10 @@ def get_value_per_sample(self, local_clinical_sample_file, filter_column): # check for header and re-assign columns if 'SAMPLE_ID' in sl and filter_column in sl: filter_column_col, sample_id_col = self.get_sample_headers(sl, filter_column) - if filter_column_col and sample_id_col: + if filter_column_col is not None and sample_id_col is not None: sample_value[sl[sample_id_col]] = sl[filter_column_col].strip().replace(' ', '_') + else: + print("No column was for {}, {} in {}".format(filter_column, 'SAMPLE_ID', local_clinical_sample_file)) return sample_value @staticmethod @@ -299,6 +301,7 @@ def cbioportal_to_proteindb(self): if self._accepted_values != ['all'] or self._split_by_filter_column: if self._local_clinical_sample_file: sample_groups_dict = self.get_value_per_sample(self._local_clinical_sample_file, self._filter_column) + print('sample_groups_dict', self._local_clinical_sample_file, self._filter_column) if sample_groups_dict == {}: return else: @@ -353,7 +356,7 @@ def cbioportal_to_proteindb(self): try: seq = seq_dic[enst] except KeyError: - print("%s not found:" % enst) + print("No matching recored for gene ({}) from row {} in FASTA file:".format(enst, row)) continue if ":" in pos: From 586e582bd7b3276fd67f0b84e2a75224181afc1d Mon Sep 17 00:00:00 2001 From: husensofteng Date: Mon, 15 Feb 2021 13:06:18 +0100 Subject: [PATCH 3/4] updated version --- CHANGELOG.md | 2 ++ setup.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 00a3ee6..046870b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ # Changelog +## [v0.0.14](https://github.com/bigbio/py-pgatk/tree/v0.0.14) (2021-02-15) + ## [v0.0.13](https://github.com/bigbio/py-pgatk/tree/v0.0.13) (2021-02-15) ## [v0.0.12](https://github.com/bigbio/py-pgatk/tree/v0.0.12) (2021-02-11) diff --git a/setup.py b/setup.py index 39f3897..9997c14 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ def readme(): setup(name='pypgatk', - version='0.0.13', + version='0.0.14', description='Python tools for proteogenomics', url='http://github.com/bigbio/py-pgatk', long_description=readme(), From d62f1ee6a624b13ed3f338f7e47d80496796e1fa Mon Sep 17 00:00:00 2001 From: Release Auto-Commit Date: Mon, 15 Feb 2021 12:08:36 +0000 Subject: [PATCH 4/4] Updates version info for --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 046870b..00a3ee6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,5 @@ # Changelog -## [v0.0.14](https://github.com/bigbio/py-pgatk/tree/v0.0.14) (2021-02-15) - ## [v0.0.13](https://github.com/bigbio/py-pgatk/tree/v0.0.13) (2021-02-15) ## [v0.0.12](https://github.com/bigbio/py-pgatk/tree/v0.0.12) (2021-02-11)