[dev] succesfully run annotator one

.coveragerc

+[run]
+omit = */__init__.py

.gitignore

 # Project specific
-/data/
-/results/
+/examples/
+/htmlcov/
 
 # Logs 
 log/

README.md

@@ -12,7 +12,7 @@ see [VEP's options page](https://www.ensembl.org/info/docs/tools/vep/script/vep_
 
 ### 1.1. Manual parsing
 
-Relies on tags specified by the user to extract relevant info like genotype (GT), somatic status (SS), quality and filter info (QUAL, INFO) and most importantly reads information (AD, DP, FA, DP4, TAR, TIR). The parser has been tested on TCGA VCF files as produced by
+Relies on tags specified by the user to extract relevant info like genotype (GT), somatic status (SS), quality and filter info (QUAL, INFO) and most importantly reads information (AD, DP, FA, DP4, TAR, TIR). The parser has been tested on VCF files as produced by
 - Mutect v.1 (TCGA GA SNV) and Strelka (TCGA GA Indel)
 - sets of callers VarScanSomatic-Strelka-Sniper-Samtools (TCGA HS SNP), GatkSomaticIndel-Pindel-Strelka-VarScanSomatic (TCGA HS Indel).
 - Mutect v.1.1.7 with no header

src/manual.py

@@ -291,8 +291,7 @@ def process_assemble(df_vcf: DataFrame, df_vcf_info: DataFrame, df_vcf_reads: Da
 #### # MAIN FUNCTION
 #### #####################################################################################################
 
-def run_manual_annotator(vcf_path: str, out_path:str,  col_normal: str, col_tumor: str, infos_n_reads: list,
-                         infos_other: list):
+def run_manual_annotator(vcf_path: str, out_path:str,  col_normal: str, col_tumor: str, infos_n_reads: list, infos_other: list):
     """
     Manually parse VCF file and save at the path specified.
 

src/tests/test_main.py

+# -*- coding: utf-8 -*-
+"""
+Created on Thu Aug 13 2020
+
+@author: Yoann Pradat
+
+    CentraleSupelec
+    MICS laboratory
+    9 rue Juliot Curie, Gif-Sur-Yvette, 91190 France
+
+Test functions from vep module.
+"""
+
+import os
+from ..main import run_annotator_one
+
+def test_main():
+    vcf2maf    = "~/Documents/biotools/informatics/VCF/mskcc-vcf2maf-5453f80/vcf2maf.pl"
+    vep_folder = "~/Documents/biotools/informatics/VCF/ensembl-vep"
+    vep_data   = "~/.vep"
+    fasta      = "~/.vep/homo_sapiens/99_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa"
+
+    #### # 1. TCGA GA
+    #### # ########################################################################################################
+
+    vcf_folder = "./examples/data/TCGA_GA/"
+    out_folder = "./examples/results/TCGA_GA/"
+
+    #### paths to results folders
+    dt_folders = {
+        'manual_out_folder'  : os.path.join(out_folder, "tmp/out_manual"),
+        'vcf2maf_tmp_folder' : os.path.join(out_folder, "tmp/tmp_vcf2maf"),
+        'vcf2maf_out_folder' : os.path.join(out_folder, "tmp/out_vcf2maf"),
+        'vep_out_folder'     : os.path.join(out_folder, "tmp/out_vep"),
+        'maf_folder'         : os.path.join(out_folder, "maf"),
+    }
+
+    #### make folders if they do not exist already
+    for k, v in dt_folders.items():
+        os.makedirs(v, exist_ok=True)
+
+    #### Indel TCGA_GA
+    vcf_file      = "TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.indel.capture.tcga.vcf"
+    col_normal    = "NORMAL"
+    col_tumor     = "PRIMARY"
+    normal_id     = "TCGA-A1-A0SD-10A-01D-A110-09"
+    tumor_id      = "TCGA-A1-A0SD-01A-11D-A10Y-09"
+    infos_n_reads = ["AD", "DP4", "DP", "TAR", "TIR"]
+    infos_other   = ["SS", "GT"]
+
+    run_annotator_one(
+        vcf_folder    = vcf_folder,
+        vcf_file      = vcf_file,
+        col_normal    = col_normal,
+        col_tumor     = col_tumor,
+        normal_id     = normal_id,
+        tumor_id      = tumor_id,
+        infos_n_reads = infos_n_reads,
+        infos_other   = infos_other,
+        vcf2maf       = vcf2maf,
+        vep_folder    = vep_folder,
+        vep_data      = vep_data,
+        fasta         = fasta,
+        dt_folders    = dt_folders
+    )
+
+    #### SNP TCGA_GA
+    vcf_file = "TCGA-A1-A0SB_db9d40fb-bfce-4c3b-a6c2-41c5c88982f1_a3254f8e-3bbd-42fc-abea-a5f25b7648b3.oxoG.snp.capture.tcga.vcf"
+
+    #### # 2. TCGA HS
+    #### # ########################################################################################################
+
+    vcf_folder = "./examples/data/TCGA_HS/"
+
+    #### Indel TCGA_HS
+    vcf_file =  "genome.wustl.edu.TCGA-A1-A0SD.indel.0e81f9c986154ce89e59240c3f09534f.vcf"
+
+    #### SNP TCGA_HS
+    vcf_file =  "genome.wustl.edu.TCGA-A1-A0SD.snv.0e81f9c986154ce89e59240c3f09534f.vcf"

src/tests/test_manual.py

@@ -20,7 +20,7 @@ def test_manual():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_GA/"
-    out_folder = "./examples/results/TCGA_GA/out_manual"
+    out_folder = "./examples/results/TCGA_GA/tmp/out_manual"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_GA
@@ -61,7 +61,7 @@ def test_manual():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_HS/"
-    out_folder = "./examples/results/TCGA_HS/out_manual"
+    out_folder = "./examples/results/TCGA_HS/tmp/out_manual"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_HS

src/tests/test_vcf2maf.py

@@ -24,8 +24,8 @@ def test_vcf2maf():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_GA/"
-    tmp_folder = "./examples/results/TCGA_GA/tmp_vcf2maf"
-    out_folder = "./examples/results/TCGA_GA/out_vcf2maf"
+    tmp_folder = "./examples/results/TCGA_GA/tmp/tmp_vcf2maf"
+    out_folder = "./examples/results/TCGA_GA/tmp/out_vcf2maf"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_GA
@@ -68,8 +68,8 @@ def test_vcf2maf():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_HS/"
-    tmp_folder = "./examples/results/TCGA_HS/tmp_vcf2maf"
-    out_folder = "./examples/results/TCGA_HS/out_vcf2maf"
+    tmp_folder = "./examples/results/TCGA_HS/tmp/tmp_vcf2maf"
+    out_folder = "./examples/results/TCGA_HS/tmp/out_vcf2maf"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_HS

src/tests/test_vep.py

@@ -23,7 +23,7 @@ def test_vep():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_GA/"
-    out_folder = "./examples/results/TCGA_GA/out_vep"
+    out_folder = "./examples/results/TCGA_GA/tmp/out_vep"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_GA
@@ -54,7 +54,7 @@ def test_vep():
     #### # ########################################################################################################
 
     vcf_folder = "./examples/data/TCGA_HS/"
-    out_folder = "./examples/results/TCGA_HS/out_vep"
+    out_folder = "./examples/results/TCGA_HS/tmp/out_vep"
     os.makedirs(out_folder, exist_ok=True)
 
     #### Indel TCGA_HS