geney 1.2.20__py2.py3-none-any.whl → 1.2.22__py2.py3-none-any.whl

geney/tcga_annotations.py

@@ -1,352 +0,0 @@
-
-import pandas as pd
-import random
-from pathlib import Path
-class TCGACase:
-    def __init__(self, df):
-        # Here we get a dataframe of mutations within a gene
-        self.df = df
-        self.calculate_vaf()
-        self.space_variants(spacer_size=50)
-        self.case_id = df.case_id.tolist()[0]
-
-    def space_variants(self, spacer_size=100, group_likelihood_threshold=0):
-        df = self.df
-        if df.empty:
-            df['group'] = 0
-            return self
-        values = sorted(df.Start_Position.unique().tolist())
-        # groups = [list(group) for key, group in groupby(values, key=lambda x: (x - values[values.index(x) - 1] >
-        # spacer_size) if values.index(x) > 0 else False)] Initialize variables
-        groups = []
-        current_group = []
-
-        # Iterate through the values
-        for i in range(len(values)):
-            if i == 0:
-                current_group.append(values[i])
-            else:
-                if values[i] - values[i - 1] <= spacer_size:
-                    current_group.append(values[i])
-                else:
-                    groups.append(current_group)
-                    current_group = [values[i]]
-
-        # Append the last group if it's not empty
-        if current_group:
-            groups.append(current_group)
-
-        df.loc[:, 'group'] = 0
-        for i, g in enumerate(groups):
-            df.loc[df.Start_Position.isin(g), 'group'] = i
-        self.df = df
-        return self
-
-    def calculate_vaf(self):
-        df = self.df
-        df = df[df.t_depth > 0]
-        df.loc[:, 'vaf'] = df.apply(lambda row: row.t_alt_count / row.t_depth, axis=1)
-        self.df = df
-        return self
-
-    def find_overlayed_variants(self):
-        df = self.df
-        mut_counts = df.mut_id.value_counts()
-        mut_counts = mut_counts[mut_counts > 1].index
-
-        small_df = df.groupby('mut_id', as_index=False).agg({
-            't_depth': 'sum',
-            't_alt_count': 'sum',
-            't_ref_count': 'sum',
-        })
-
-        df = df.drop_duplicates(subset='mut_id', keep='first')
-
-        small_df = small_df[small_df.t_depth > 0]
-        small_df['vaf'] = small_df.t_alt_count / small_df.t_depth
-
-        small_df = small_df.set_index('mut_id')
-        df.set_index('mut_id', inplace=True)
-        df.update(small_df)
-        df.reset_index(inplace=True)
-        self.df = df
-        return self
-
-    def find_epistasis(self, pth=3, rth=0):
-        df = self.df
-        if df.empty:
-            return None
-        # df = df[df.t_alt_count > rth].sort_values('Start_Position', ascending=True)
-        df = df[(df.t_alt_count > df.t_ref_count / pth) & (df.t_alt_count >= rth)].sort_values('Start_Position',
-                                                                                               ascending=True)
-
-        # display(df[['mut_id', 't_alt_count', 't_ref_count']])
-
-        # Group by the group_key
-        grouped = df.groupby('group').agg({
-            'mut_id': lambda x: '|'.join(x),
-            't_alt_count': 'mean',
-            't_ref_count': 'mean',
-            'case_id': 'first'
-        }).reset_index(drop=True)
-
-        # Drop the group_key column
-        return grouped[grouped.mut_id.str.contains('\|')][['mut_id', 't_alt_count', 't_ref_count', 'case_id']]
-
-
-class TCGAGene:
-    def __init__(self, gene, cancer_path=Path('/tamir2/cancer_proj/gdc_db/data/filtered_feb_2021/AllGenes/'),
-                 valid_cases=None, extra_cols=[], exclude_filters=None, include_filter=None):
-        df = pd.read_csv(cancer_path / gene / 'GeneMutTble.txt',
-                         usecols=['Variant_Type', 'FILTER', 'vcf_tumor_gt', 'vcf_normal_gt',
-                                  'COSMIC', 't_depth', 't_ref_count', 't_alt_count', 'Proj_name',
-                                  'HGVSc', 'Chromosome', 'Start_Position', 'Reference_Allele',
-                                  'Tumor_Seq_Allele2', 'case_id', 'Gene_name', 'Variant_Type'] + extra_cols,
-                         low_memory=False).sort_values('Start_Position', ascending=True)
-
-        if df.empty:
-            self.df = df
-
-        else:
-            df = df[df.Variant_Type.isin(['SNP', 'INS', 'DEL'])]
-
-            if include_filter is not None:
-                df = df[df.FILTER == include_filter]
-
-            elif exclude_filters is not None:
-                for exclude_filter in exclude_filters:
-                    df = df[~df.FILTER.str.contains(exclude_filter)]
-
-            if valid_cases is not None:
-                df = df[df.case_id.isin(valid_cases)]
-
-            df['mut_id'] = df.apply(lambda
-                                        row: f"{row.Gene_name}:{row.Chromosome.replace('chr', '')}:{row.Start_Position}:{row.Reference_Allele}:{row.Tumor_Seq_Allele2}",
-                                    axis=1)
-
-            df['ratio'] = df.t_alt_count + df.t_ref_count
-            df = df[df.ratio > 0]
-            df['ratio'] = df.t_alt_count / df.ratio
-            self.df = df
-
-
-    @property
-    def affected_cases(self):
-        return self.df.case_id.unique().tolist()
-
-    def get_patient_muts(self, case_id=None):
-        if case_id is None:
-            case_id = random.choice(self.affected_cases)
-        return self.df[self.df.case_id == case_id]
-
-
-class TCGAMut:
-    def __init__(self, mut_id):
-        data = []
-        for mut in mut_id.split('|'):
-            data.append(mut.split(':'))
-        data = pd.DataFrame(data, columns=['Gene_name', 'Chromosome', 'Start_Position', 'Reference_Allele',
-                                           'Tumor_Seq_Allele2'])
-        data.Chromosome = data.apply(lambda row: f'chr{row.Chromosome}', axis=1)
-        data = data.astype({'Start_Position': int})
-        self.gene = data.Gene_name.unique().tolist()[0]
-        self.df = data
-
-    def find_affected_patients(self):
-        gene = TCGAGene(self.gene)
-        return pd.merge(self.df, gene.df,
-                        on=['Gene_name', 'Chromosome', 'Start_Position', 'Reference_Allele', 'Tumor_Seq_Allele2'])
-
-# CLINICAL_DATA_FILE = Path('/tamir2/nicolaslynn/data/TCGA/cancer_reports/new_df_p_proc.pkl')
-# CLINICAL_DATA_FILE = Path('/tamir2/yoramzar/Projects/Cancer_mut/Explore_data/reports/df_p_all.pkl')
-# CANCER_DATA_PATH = Path('/tamir2/cancer_proj/gdc_db/data/filtered_feb_2021/AllGenes')
-# MAF_FILE_NAME = 'GeneMutTble.txt'
-# CASE_TRACKER = pd.read_csv('/tamir2/nicolaslynn/projects/TCGAParsed/case2proj.csv', index_col=0)
-# PROJ_COUNTS = CASE_TRACKER.proj.value_counts()
-# OKGP_DATA_FILE = Path('/tamir2/nicolaslynn/projects/1000GenomesProjMutations/parsed_1kgp_mutations_in_target_genes.csv')
-# MUTATION_FREQ_DF = pd.read_csv(OKGP_DATA_FILE, index_col=0)
-# PROTEIN_ANNOTATIONS = pd.read_csv('/tamir2/nicolaslynn/data/BioMart/protein_annotations.csv').rename(columns={'Interpro start': 'start', 'Interpro end': 'end', 'Interpro Short Description': 'name'})[['Gene stable ID', 'Transcript stable ID', 'start', 'end', 'name']]
-# PROTEIN_ANNOTATIONS['length'] = PROTEIN_ANNOTATIONS.apply(lambda row: abs(row.start - row.end), axis=1)
-
-# def prepare_gene_sets():
-#     # gene_annotations_file = Path('/tamir2/nicolaslynn/data/COSMIC/cancer_gene_roles.csv')
-#     # GENE_DF = pd.read_csv(gene_annotations_file, index_col=0)
-#     # all_oncogenes = GENE_DF[GENE_DF.OG==True].index.tolist()
-#     # all_oncogenes = list(set(all_oncogenes))
-#     return [], [], []
-#
-# CLIN_DF = prepare_clinical_data()
-# TSGS, ONCOGENES, CANCER_GENES = prepare_gene_sets()
-#
-#
-# def generate_survival_quantitative(affected_df, nonaffected_df):
-#     if affected_df.empty or nonaffected_df.empty:
-#         return np.nan, np.nan, np.nan
-#     results = logrank_test(affected_df['duration'], nonaffected_df['duration'],
-#                            event_observed_A=affected_df['event'],
-#                            event_observed_B=nonaffected_df['event'])
-#     p_value = results.p_value
-#     kmf = KaplanMeierFitter()
-#     kmf.fit(affected_df['duration'], affected_df['event'], label=f'With Epistasis ({len(affected_df)})')
-#     times, surv_probs = kmf.survival_function_.index.values, kmf.survival_function_.values.flatten()
-#     auc1 = np.trapz(surv_probs, times)
-#     kmf.fit(nonaffected_df['duration'], nonaffected_df['event'], label=f'Without Epistasis ({len(nonaffected_df)})')
-#     times, surv_probs = kmf.survival_function_.index.values, kmf.survival_function_.values.flatten()
-#     auc2 = np.trapz(surv_probs, times)
-#     return p_value, auc1, auc2
-#
-# def generate_survival_pvalue(affected_df, unaffected_df):
-#     results = logrank_test(affected_df['duration'], unaffected_df['duration'],
-#                            event_observed_A=affected_df['event'],
-#                            event_observed_B=unaffected_df['event'])
-#
-#     p_value = results.p_value
-#     kmf = KaplanMeierFitter()
-#     # Fit data
-#     kmf.fit(affected_df['duration'], affected_df['event'], label=f'Without Epistasis ({len(affected_df)})')
-#     ax = kmf.plot()
-#
-#     kmf.fit(unaffected_df['duration'], unaffected_df['event'], label=f'With Epistasis ({len(unaffected_df)})')
-#     kmf.plot(ax=ax)
-#     plt.text(5, 0.95, f'pval: {p_value:.3e}')
-#     plt.show()
-#     return p_value
-#
-# def get_project_prevalence(cases_affected):
-#     ca = [c for c in cases_affected if c in CASE_TRACKER.index]
-#     prevalences = CASE_TRACKER.loc[ca].proj.value_counts() / PROJ_COUNTS
-#     prevalences.fillna(0, inplace=True)
-#     prevalences = prevalences[[i for i in prevalences.index if 'TCGA' in i]]
-#     prevalences.index = [s.replace('TCGA', 'prev') for s in prevalences.index]
-#     return prevalences
-#
-# def get_project_counts(cases_affected):
-#     ca = [c for c in cases_affected if c in CASE_TRACKER.index]
-#     prevalences = CASE_TRACKER.loc[ca].proj.value_counts()
-#     prevalences = prevalences[[i for i in prevalences.index if 'TCGA' in i]]
-#     prevalences.index = [s.replace('TCGA_', '') for s in prevalences.index]
-#     return prevalences
-#
-# def get_event_consequence(df):
-#     assert df.Transcript_ID.nunique() == 1, 'Too many transcripts to return a single consequenc.'
-#     return df.iloc[0].Consequence
-#
-# def get_dbSNP_id(df):
-#     return df.iloc[0].dbSNP_RS
-#
-# def load_variant_file(gene):
-#     df = pd.read_csv(CANCER_DATA_PATH / gene / MAF_FILE_NAME, low_memory=False)
-#     df['mut_id'] = df.apply(lambda row: f"{row.Gene_name}:{row.Chromosome.replace('chr', '')}:{row.Start_Position}:{row.Reference_Allele}:{row.Tumor_Seq_Allele2}", axis=1)
-#     return df
-#
-# def find_event_data(event):
-#     df = load_variant_file(event.gene)
-#     if df.empty:
-#         return None
-#
-#     df = df.query \
-#         ('Chromosome == @event.chromosome & Start_Position == @event.start & Reference_Allele == @event.ref & Tumor_Seq_Allele2 == @event.alt')
-#
-#     if df.empty:
-#         return None
-#
-#     if event.transcript_id is not None:
-#         df = df[df.Transcript_ID == event.transcript_id]
-#     df['mut_id'] = event.event_id
-#     return df
-#
-#
-# class GEvent:
-#     def __init__(self, event_id, transcript_id=None):
-#         self.gene, self.chromosome, self.start, self.ref, self.alt = event_id.split(':')
-#         self.transcript_id = transcript_id
-#         self.chromosome = f'chr{self.chromosome}'
-#         self.start = int(self.start)
-#         self.event_id = event_id
-#
-#
-#
-# def get_okgp_mutation_frequency(mut_id):
-#     if mut_id in MUTATION_FREQ_DF.index:
-#         return MUTATION_FREQ_DF.loc[mut_id].cases_affected
-#     else:
-#         return 0
-#
-# def get_df_filter_info(df):
-#     filter_artifact_values: list = ["oxog", "bPcr", "bSeq"]
-#     MuTect2_filters: list = ['Germline risk', 't_lod_fstar', 'alt_allele_in_normal', 'panel_of_normals', 'clustered_events',
-#                              'str_contraction', 'multi_event_alt_allele_in_normal', 'homologous_mapping_event', 'triallelic_site']
-#     filter_col_name: str = "FILTER_info"  # column name to add to the dataframe
-#     filter_info_list: list = []
-#     f_cnr_info = {}
-#
-#     for j, (prj, df_prj) in enumerate(df.groupby('Proj_name')):
-#         filter_vals = list(df_prj['FILTER'])
-#         num_pass, num_artifacts, num_mutect2_filters = 0, 0, 0
-#         for filter_val in filter_vals:
-#             num_pass += ('PASS' in filter_val)
-#             num_artifacts += any([x in filter_val for x in filter_artifact_values])
-#             num_mutect2_filters += any([x in filter_val for x in MuTect2_filters])
-#         num_rest = max(0, (len(filter_vals) - num_pass - num_artifacts - num_mutect2_filters))
-#         f_cnr_info[str(prj)[5:]] = (num_pass, num_mutect2_filters, num_artifacts, num_rest)
-#     return f_cnr_info
-#
-# def yoram_mutid(row):
-#     return f'{row.Gene_name}:{row.Chromosome}:{row.Consequence}:{row.Start_Position}:{row.Reference_Allele}:{row.Tumor_Seq_Allele2}'
-#
-#
-# def annotate_level_two(mut_id, tid):
-#     mut = GEvent(mut_id, tid)
-#     df = find_event_data(mut)
-#
-#     if df.empty or df is None:
-#         return None
-#
-#     patients_affected = df.cases_affected.unique().tolist()
-#     p_val, auc_a, auc_n = generate_survival_quantitative(CLIN_DF[CLIN_DF.case_id.isin(patients_affected)], CLIN_DF[~CLIN_DF.case_id.isin(patients_affected)])
-#     project_prevalences = get_project_prevalence(patients_affected)
-#     prev_dict = project_prevalences.to_dict().sort()
-#     project_counts = get_project_counts(patients_affected)
-#
-#     s = pd.Series({
-#         'mut_id': mut_id,
-#         'yoram_mut_id': yoram_mutid(df.iloc[0]),
-#         'transcript_id': tid,
-#         'affected_cases': len(patients_affected),
-#         'dbSNP_id': get_dbSNP_id(df),
-#         'consequence': get_event_consequence(df),
-#         'survival_p_value': p_val,
-#         'auc_affected': auc_a,
-#         'auc_nonaffected': auc_n,
-#         'TSG': contains(TSGS, mut.gene),
-#         'oncogene': contains(ONCOGENES, mut.gene),
-#         'cases_1kgp': get_okgp_mutation_frequency(mut.event_id),
-#         'filter_inf': get_df_filter_info(df),
-#         'strand': df.Strand.unique().tolist()[0],
-#         'prevalences': prev_dict
-#     })
-#
-#     s['max_prev'] = project_prevalences.max()
-#     s['rel_proj'] = ','.join([c.split('_')[-1] for c in project_prevalences[project_prevalences == project_prevalences.max()].index.tolist()])
-#     s = pd.concat([s, project_prevalences, project_counts])
-#     del df
-#     return s
-#
-# def get_mut_counts():
-#     cases = unload_json('/tamir2/nicolaslynn/projects/TCGAParsed/recurring_single_muts_tcga.json')
-#     cases = pd.Series(cases)
-#     cases.name = 'num_cases'
-#     cases.index.name = 'mut_id'
-#     cases = cases.to_frame()
-#     cases.reset_index(inplace=True)
-#     return cases
-#
-#
-# def create_mut_id(row):
-#     return f"{row.Gene_name}:{row['Chromosome']}:{row['Start_Position']}:{row['Reference_Allele']}:{row['Tumor_Seq_Allele2']}"
-#
-#
-# def is_in_exon(mut_id, tid):
-#     from geney.Gene import Gene
-#     transcript = Gene(mut_id.split(':')[0]).generate_transcript(tid)
-#     return int(mut_id.split(':')[2]) in transcript.exonic_indices

geney-1.2.20.dist-info/RECORD

@@ -1,52 +0,0 @@
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-geney/oncosplice.py,sha256=sp6kfKbFqwpZIuLZadvCq0aj-JUnM_GE99eaGRm19eY,78240
-geney/oncosplice_mouse.py,sha256=LYLOukI9qI1IBkyl1qVRFR5d1NAw7Orlj8Zth-4xCW8,12962
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-geney/survival_utils.py,sha256=2CAkC2LsspicHIdrqsiPnjgvpr5KHDUfLFFqnRbPJqs,5762
-geney/tcga_annotations.py,sha256=DjRl6Pk5VAOL1yhbt8SXD6FZhYbcYNu3FtXYMeveGB0,15016
-geney/tcga_utils.py,sha256=vXSMf1OxoF_AdE_rMguy_BoYaart_E1t4FFMx2DS1Ak,15585
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-geney/immunotherapy/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney/immunotherapy/netchop.py,sha256=vLy-ahEKxU6IzwmnnqefXDJjZOeGIprLWbKU3t-M7sc,2800
-geney/mutations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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-geney/oncosplice/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney/pipelines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-geney/pipelines/dask_utils.py,sha256=J68bpbikdUGGirPERczu1cf_ajZmEvDfWEj8GIMJvII,5641
-geney/splicing/__init__.py,sha256=0x9Rt0znGnf3Hs92BYRBjdHZHOMsd_27QNTRlfohzLY,60
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