Merge branch 'master' into fix/uniform_extra_require_naming

README.md

@@ -76,7 +76,7 @@ vep --input_file <path to your input file> --format vcf --output_file <path to y
 ```
 
 Then you have to convert the VEP output to TSV using our own BCFTools script: 
-`/scripts/convert_vep_vcf_to_tsv_capice.sh -i </path/to/vep_output.vcf.gz> -o </path/to/capice_input.tsv.gz>`
+`./scripts/convert_vep_vcf_to_tsv_capice.sh -i </path/to/vep_output.vcf.gz> -o </path/to/capice_input.tsv.gz>`
 
 ### CAPICE
 CAPICE can be run by using the following command:

scripts/convert_vep_vcf_to_tsv_capice.sh

@@ -3,9 +3,6 @@
 # Stops script if any error occurs.
 set -e
 
-# Possibly variable variables
-PRE_HEADER="%CHROM\t%POS\t%REF\t%ALT\t%Consequence\t%SYMBOL\t%SYMBOL_SOURCE\t%Gene\t%Feature\t%Feature_type\t%cDNA_position\t%CDS_position\t%Protein_position\t%Amino_acids\t%STRAND\t%SIFT\t%PolyPhen\t%EXON\t%INTRON\t%SpliceAI_pred_DP_AG\t%SpliceAI_pred_DP_AL\t%SpliceAI_pred_DP_DG\t%SpliceAI_pred_DP_DL\t%SpliceAI_pred_DS_AG\t%SpliceAI_pred_DS_AL\t%SpliceAI_pred_DS_DG\t%SpliceAI_pred_DS_DL\t%gnomAD_AF"
-
 # Defines error echo.
 errcho() { echo "$@" 1>&2; }
 
@@ -57,8 +54,11 @@ digestCommandLine() {
 
   if [[ ${TRAIN} == true ]]
   then
-    id="\t%ID"
-    PRE_HEADER="$PRE_HEADER$id"
+    HEADER="CHROM\tPOS\tID\tREF\tALT\t"
+    FORMAT="%CHROM\t%POS\t%ID\t%REF\t%ALT\t%CSQ\n"
+  else
+    HEADER="CHROM\tPOS\tREF\tALT\t"
+    FORMAT="%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n"
   fi
 
   validateCommandLine
@@ -125,12 +125,11 @@ processFile() {
   local output="${output%.gz}" # Strips '.gz' to better work with code below.
   local output_tmp="${output}.tmp"
 
-  local format="${PRE_HEADER}\n"
-
   local args=()
   args+=("+split-vep")
   args+=("-d")
-  args+=("-f" "${format}")
+  args+=("-f" "${FORMAT}")
+  args+=("-A" "tab")
   args+=("-o" "${output_tmp}")
   args+=("${input}")
 
@@ -140,7 +139,7 @@ processFile() {
 
   echo "BCFTools finished, building output file."
 
-  echo -e "${PRE_HEADER}" | cat - "${output_tmp}" > "${output}" && rm "${output_tmp}"
+  echo -e "${HEADER}$(bcftools +split-vep -l "${input}" | cut -f 2 | tr '\n' '\t' | sed 's/\t$//')" | cat - "${output_tmp}" > "${output}" && rm "${output_tmp}"
 
   echo "Output file ready, gzipping."
 

src/molgenis/capice/utilities/load_file_postprocessor.py

@@ -20,24 +20,11 @@ def process(self):
         dataset :   pandas.DataFrame
                     Processed dataset with corrected % sign and renamed columns.
         """
-        self.log.debug('Starting correcting % sign.')
-        self._correct_percentage_sign()
-        self.log.debug('% sign corrected, starting renaming of columns.')
+        self.log.info('LoadFilePostProcessor starting.')
         self._col_renamer()
         self.log.info('LoadFilePostProcessor successful.')
         return self.dataset
 
-    def _correct_percentage_sign(self):
-        new_columns = []
-        for column in self.dataset.columns:
-            if column.startswith('%'):
-                new_columns.append(column.split('%')[1])
-            elif column.startswith('#'):
-                new_columns.append(column.split('#')[1])
-            else:
-                new_columns.append(column)
-        self.dataset.columns = new_columns
-
     def _col_renamer(self):
         """
         Function to rename "Gene, Feature, SYMBOL, INTRON and EXON" to

tests/capice/utilities/test_file_postprocessor.py

@@ -28,15 +28,15 @@ def test_load_file_pre_processor(self):
         print('Load file preprocessor.')
         data = pd.DataFrame(
             {
-                "%CHROM": [1, 2, 3],
-                "%POS": [100, 200, 300],
-                "%REF": ['A', 'T', 'G'],
-                "%ALT": ['T', 'G', 'A'],
-                "%SYMBOL_SOURCE": ['foo', 'foo', 'bar'],
-                "%Feature": ['bar', 'bar', 'buz'],
-                "%SYMBOL": ['g1', 'g2', 'g3'],
-                "%INTRON": [1, 0, 0],
-                "%EXON": [0, 1, 1]
+                "CHROM": [1, 2, 3],
+                "POS": [100, 200, 300],
+                "REF": ['A', 'T', 'G'],
+                "ALT": ['T', 'G', 'A'],
+                "SYMBOL_SOURCE": ['foo', 'foo', 'bar'],
+                "Feature": ['bar', 'bar', 'buz'],
+                "SYMBOL": ['g1', 'g2', 'g3'],
+                "INTRON": [1, 0, 0],
+                "EXON": [0, 1, 1]
             }
         )
 

tests/capice/utilities/test_load_file_postprocessor.py

@@ -10,13 +10,13 @@ def setUpClass(cls):
         print('Setting up.')
         df = pd.DataFrame(
             {
-                '#CHROM': [1],
+                'CHROM': [1],
                 'POS': [123],
                 'REF': ['A'],
                 'ALT': ['G'],
                 'Gene': [123],
                 'SYMBOL_SOURCE': ['hgnc'],
-                '%Feature': ['NM1.123'],
+                'Feature': ['NM1.123'],
                 'SYMBOL': ['ACDC'],
                 'INTRON': [5],
                 'EXON': [11],