Remove FusionGDB (#16)

* fix modules

* remove all fusiongdb

* remove print

* remove log

* change pull request template

* update changelog

.github/PULL_REQUEST_TEMPLATE.md

@@ -9,3 +9,9 @@ Thank you for contribution to `fusion-report` project.
 - [ ] Documentation in `docs` is updated
 - [ ] `CHANGELOG.md` is updated
 - [ ] `README` is updated
+
+### This [version](https://semver.org/) is a
+
+- [ ] **MAJOR** - when you make incompatible API changes
+- [ ] **MINOR** - when you add functionality in a backwards compatible manner
+- [ ] **PATCH** - when you make backwards compatible bug fixes or documentation/instructions

CHANGELOG.md

@@ -5,6 +5,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.1.8]
+
+### Removed
+
+- Removed FusionGDB
+
 ## [2.1.5](https://github.com/matq007/fusion-report/releases/tag/2.1.5)
 
 ### Added

README.md

@@ -40,7 +40,7 @@ python3 setup.py install
 
 ```bash
 # Download required databases
-# Currently supported databases: FusionGDB, Mitelman and COSMIC
+# Currently supported databases: FusionGDB2, Mitelman and COSMIC
 # COSMIC requires login credentials to download Fusion gene Database
 fusion_report download --cosmic_usr '<username>' --cosmic_passwd '<password>' /path/to/db/
 

docs/add_database.md

@@ -31,7 +31,7 @@ class Test(Db, metaclass=Singleton):
 
 ```python
 local_fusions: Dict[str, List[str]] = {
-    FusionGDB(path).name: FusionGDB(path).get_all_fusions(),
+    FusionGDB2(path).name: FusionGDB2(path).get_all_fusions(),
     MitelmanDB(path).name: MitelmanDB(path).get_all_fusions(),
     CosmicDB(path).name: CosmicDB(path).get_all_fusions(),
     TestDB(path).name: TestDB(path).get_all_fusions() # add your database here

docs/download.md

@@ -2,7 +2,7 @@
 
 Currently the tool supports three different databases:
 
-* [FusionGDB](https://ccsm.uth.edu/FusionGDB/index.html)
+* [FusionGDB2](https://compbio.uth.edu/FusionGDB2/tables)
 * [Mitelman](https://cgap.nci.nih.gov/Chromosomes/Mitelman)
 * [COSMIC](https://cancer.sanger.ac.uk/cosmic/fusion)
 
@@ -28,22 +28,6 @@ fusion_report download
 
 ## Manual download
 
-### FusionGDB
-
-Website: [https://ccsm.uth.edu/FusionGDB/index.html](https://ccsm.uth.edu/FusionGDB/index.html)
-
-```bash
-# Download all files
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_information_on_hg19.txt -O TCGA_ChiTaRS_combined_fusion_information_on_hg19.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt -O TCGA_ChiTaRS_combined_fusion_ORF_analyzed_gencode_h19v19.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/uniprot_gsymbol.txt -O uniprot_gsymbol.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fusion_uniprot_related_drugs.txt -O fusion_uniprot_related_drugs.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fusion_ppi.txt -O fusion_ppi.txt
-wget --no-check-certificate https://ccsm.uth.edu/FusionGDB/tables/fgene_disease_associations.txt -O fgene_disease_associations.txt
-# Create database and import the data
-sqlite3 fusiongdb.db < fusion_report/db/FusionGDB.sql
-```
-
 ### Mitelman
 
 Website: [https://cgap.nci.nih.gov/Chromosomes/Mitelman](https://cgap.nci.nih.gov/Chromosomes/Mitelman)

docs/score.md

@@ -4,17 +4,16 @@ One disadvantage of the tools is that they tend to report false positive results
 estimated score for a fusion. The only way how to correctly verify a fusion is biologically (RT-qPCR …).
 
 **fusion-report** uses weighted approach of assigning weights to tools and databases. By default, each tool
-is assigned the same weight. This is because each tool uses different approach of discovering fusions and 
+is assigned the same weight. This is because each tool uses different approach of discovering fusions and
 report different results, for example FusionCatcher will work best on somatic samples.
 
 You can customize weight of individual tool by specific parameter `<tool-name>_weight 30`.
 The sum of the weights has to be 100!
 
 Currently weights for databases are not adjustable. The weights for databases are as follows:
 
-* FusionGDB (20)
-* COSMIC (40)
-* MITELMAN (40)
+* COSMIC (50)
+* MITELMAN (50)
 * FusionGDB2 (0)
 
 > It is strongly suggested to use all supported databases in order to get the best estimated score.

fusion_report/app.py

@@ -21,7 +21,6 @@
 from fusion_report.common.models.fusion import Fusion
 from fusion_report.common.report import Report
 from fusion_report.data.cosmic import CosmicDB
-from fusion_report.data.fusiongdb import FusionGDB
 from fusion_report.data.fusiongdb2 import FusionGDB2
 from fusion_report.data.mitelman import MitelmanDB
 from fusion_report.download import Download
@@ -100,36 +99,16 @@ def generate_report(self, params: Namespace) -> None:
         )
         report.render(index_page)
 
-        # with tqdm(total=len(fusions)) as pbar:
-        #     for fusion in fusions:
-        #         fusion_page = report.create_page(
-        #             fusion.name, page_variables={"sample": params.sample}
-        #         )
-        #         fusion_page.add_module("fusion_summary", params={"fusion": fusion})
-        #         fusion_page.add_module(
-        #             "fusiongdb.variations",
-        #             params={"fusion": fusion.name, "db_path": params.db_path},
-        #         )
-        #         fusion_page.add_module(
-        #             "fusiongdb.transcripts",
-        #             params={"fusion": fusion.name, "db_path": params.db_path},
-        #         )
-        #         fusion_page.add_module(
-        #             "fusiongdb.ppi",
-        #             params={"fusion": fusion.name, "db_path": params.db_path},
-        #         )
-        #         fusion_page.add_module(
-        #             "fusiongdb.drugs",
-        #             params={"fusion": fusion.name, "db_path": params.db_path},
-        #         )
-        #         fusion_page.add_module(
-        #             "fusiongdb.diseases",
-        #             params={"fusion": fusion.name, "db_path": params.db_path},
-        #         )
-        #         report.render(fusion_page)
-        #         pbar.set_description(f"Processing {fusion.name}")
-        #         time.sleep(0.1)
-        #         pbar.update(1)
+        with tqdm(total=len(fusions)) as pbar:
+            for fusion in fusions:
+                fusion_page = report.create_page(
+                    fusion.name, page_variables={"sample": params.sample}
+                )
+                fusion_page.add_module("fusion_summary", params={"fusion": fusion})
+                report.render(fusion_page)
+                pbar.set_description(f"Processing {fusion.name}")
+                time.sleep(0.1)
+                pbar.update(1)
 
     def parse_fusion_outputs(self, params: Dict[str, Any]) -> None:
         """Executes parsing for each provided fusion detection tool."""
@@ -144,7 +123,6 @@ def enrich(self, path: str) -> None:
         local_fusions: Dict[str, List[str]] = {
             CosmicDB(path).name: CosmicDB(path).get_all_fusions(),
             MitelmanDB(path).name: MitelmanDB(path).get_all_fusions(),
-            # FusionGDB(path).name: FusionGDB(path).get_all_fusions(),
             FusionGDB2(path).name: FusionGDB2(path).get_all_fusions(),
         }
         for fusion in self.manager.fusions:

fusion_report/common/net.py

@@ -17,7 +17,6 @@
 from fusion_report.common.logger import Logger
 from fusion_report.data.cosmic import CosmicDB
 from fusion_report.settings import Settings
-from fusion_report.data.fusiongdb import FusionGDB
 from fusion_report.data.fusiongdb2 import FusionGDB2
 from fusion_report.data.mitelman import MitelmanDB
 
@@ -133,7 +132,6 @@ def get_cosmic_from_sanger(token: str, return_err: List[str]) -> None:
         }
         try:
             res = requests.get(url, headers=headers)
-            print(res)
             auth_url: str = res.json()["url"]
             LOG.info(f"auth_url: {auth_url}")
             Net.get_large_file(auth_url)
@@ -171,20 +169,6 @@ def get_cosmic_from_qiagen(token: str, return_err: List[str], outputpath: str) -
         except Exception as ex:
             return_err.append(f'{Settings.COSMIC["NAME"]}: {ex}')
 
-    @staticmethod
-    def get_fusiongdb(self, return_err: List[str]) -> None:
-        """Method for download FusionGDB database."""
-
-        for file in Settings.FUSIONGDB["FILES"]:
-            try:
-                url: str = f'{Settings.FUSIONGDB["HOSTNAME"]}/{file}'
-                Net.get_large_file(url)
-            except DownloadException as ex:
-                return_err.append(f"FusionGDB: {ex}")
-
-        db = FusionGDB(".")
-        db.setup(Settings.FUSIONGDB["FILES"], delimiter="\t", skip_header=False)
-
     @staticmethod
     def get_fusiongdb2(self, return_err: List[str]) -> None:
         """Method for download FusionGDB2 database."""

fusion_report/data/fusiongdb2.py

@@ -7,7 +7,7 @@
 
 
 class FusionGDB2(Db, metaclass=Singleton):
-    """Implementation of FusionGDB Database. All core functionality is handled by parent class."""
+    """Implementation of FusionGDB2 Database. All core functionality is handled by parent class."""
 
     def __init__(self, path: str) -> None:
         super().__init__(path, Settings.FUSIONGDB2["NAME"], Settings.FUSIONGDB2["SCHEMA"])

fusion_report/download.py

@@ -11,7 +11,7 @@
 
 class Download:
     """Class designed for downloading any type of required database.
-    Currently the script is able to download: Mitelman, FusionGDB and COSMIC with provided
+    Currently the script is able to download: Mitelman, FusionGDB2 and COSMIC with provided
     credentials.
 
     Attributes:
@@ -41,9 +41,6 @@ def download_all(self, params: Namespace) -> None:
         # MITELMAN
         Net.get_mitelman(self, return_err)
 
-        # FusionGDB
-        # Net.get_fusiongdb(self, return_err)
-
         # FusionGDB2
         Net.get_fusiongdb2(self, return_err)