minor python lib fixes

pcgr/cna.py

@@ -142,15 +142,15 @@ def annotate_cna_segments(output_fname: str,
 
     ## Mark copy number amplifications (threshold defined by user) in input
     cna_query_segment_df['aberration_key'] = 'nan'
-    cna_query_segment_df['loss_cond'] = True
+    cna_query_segment_df['amp_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] < n_copy_amplifications,"amp_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] >= n_copy_amplifications,"amp_cond"] = True
 
     cna_query_segment_df.loc[cna_query_segment_df.amp_cond, 'aberration_key'] =  \
         cna_query_segment_df.loc[cna_query_segment_df.amp_cond, 'entrezgene'].astype(str) + '_amplification'
 
     ## Mark homozygous deletions in input
-    cna_query_segment_df['amp_cond'] = True
+    cna_query_segment_df['loss_cond'] = True
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] > 0,"loss_cond"] = False
     cna_query_segment_df.loc[cna_query_segment_df['n_major'] + cna_query_segment_df['n_minor'] == 0,"loss_cond"] = True
 

pcgr/maf.py

@@ -5,8 +5,7 @@
 import gzip
 import pandas as pd
 
-from pcgr import utils
-from pcgr.utils import getlogger, error_message, warn_message, check_file_exists
+from pcgr.utils import check_file_exists, remove_file
 
 def update_maf_allelic_support(maf_tmp_fname: str, 
                                maf_fname: str, 
@@ -90,7 +89,7 @@ def update_maf_allelic_support(maf_tmp_fname: str,
             f.write(f'{header_line}\n')
         f.close()
         raw_maf_data.to_csv(maf_fname, sep="\t", index=False, mode='a')
-        utils.remove(maf_tmp_fname)                     
+        remove_file(maf_tmp_fname)                     
 
 
 

pcgr/main.py

@@ -1,19 +1,17 @@
 #!/usr/bin/env python
 
-from pcgr import pcgr_vars, arg_checker, config, utils, variant, cna, vep
-from pcgr.utils import getlogger, check_subprocess
-from pcgr.config import populate_config_data
+from pcgr import pcgr_vars, arg_checker, utils, cna
+from pcgr.utils import getlogger, check_subprocess, remove_file, random_id_generator
+from pcgr.config import populate_config_data, create_config
 from pcgr.maf import update_maf_allelic_support
-
+from pcgr.vep import get_command
+from pcgr.variant import clean_annotations, set_allelic_support, append_annotations, calculate_tmb
 
 import re
 import argparse
 import pandas
 import yaml
 import os
-import sys
-import getpass
-import platform
 from glob import glob
 from argparse import RawTextHelpFormatter
 
@@ -134,7 +132,7 @@ def cli():
     arg_checker.check_args(arg_dict)
 
     # create config options
-    conf_options = config.create_config(arg_dict, workflow = "PCGR")
+    conf_options = create_config(arg_dict, workflow = "PCGR")
 
     # Verify existence of input files
     pcgr_paths = arg_checker.verify_input_files(arg_dict)
@@ -199,13 +197,14 @@ def run_pcgr(pcgr_paths, conf_options):
 
         check_subprocess(logger, f'mkdir -p {output_dir}', debug)
 
+        random_id = random_id_generator(15) 
         # Define temporary output file names
-        input_vcf_validated =             f'{conf_options["sample_id"]}.pcgr_ready.vcf.gz'
-        input_vcf_validated_uncompr =     f'{conf_options["sample_id"]}.pcgr_ready.vcf'
-        vep_vcf =                         f'{conf_options["sample_id"]}.vep.vcf'
-        vep_vcfanno_vcf =                 f'{conf_options["sample_id"]}.vep.vcfanno.vcf'
-        vep_vcfanno_summarised_vcf =      f'{conf_options["sample_id"]}.vep.vcfanno.summarised.vcf'
-        vep_vcfanno_summarised_pass_vcf = f'{conf_options["sample_id"]}.vep.vcfanno.summarised.pass.vcf'
+        input_vcf_validated =             f'{conf_options["sample_id"]}.{random_id}.pcgr_ready.vcf.gz'
+        input_vcf_validated_uncompr =     f'{conf_options["sample_id"]}.{random_id}.pcgr_ready.vcf'
+        vep_vcf =                         f'{conf_options["sample_id"]}.{random_id}.vep.vcf'
+        vep_vcfanno_vcf =                 f'{conf_options["sample_id"]}.{random_id}.vep.vcfanno.vcf'
+        vep_vcfanno_summarised_vcf =      f'{conf_options["sample_id"]}.{random_id}.vep.vcfanno.summarised.vcf'
+        vep_vcfanno_summarised_pass_vcf = f'{conf_options["sample_id"]}.{random_id}.vep.vcfanno.summarised.pass.vcf'
         prefix = os.path.join(output_dir, f'{conf_options["sample_id"]}.pcgr_acmg.{conf_options["genome_assembly"]}')
         output_vcf =             f'{prefix}.vcf.gz'
         output_pass_vcf =        f'{prefix}.pass.vcf.gz'
@@ -304,10 +303,10 @@ def run_pcgr(pcgr_paths, conf_options):
             outfile.write(yaml.dump(yaml_data))
         outfile.close()
 
-        vep_command = vep.get_command(file_paths = pcgr_paths, 
-                                      conf_options = yaml_data, 
-                                      input_vcf = input_vcf_validated, 
-                                      output_vcf = vep_vcf)
+        vep_command = get_command(file_paths = pcgr_paths, 
+                                conf_options = yaml_data, 
+                                input_vcf = input_vcf_validated, 
+                                output_vcf = vep_vcf)
 
         # PCGR|VEP - run consequence annotation with Variant Effect Predictor
         print('----')
@@ -358,7 +357,7 @@ def run_pcgr(pcgr_paths, conf_options):
                     )
             check_subprocess(logger, vcf2maf_command, debug)
             if not debug:                
-                utils.remove(output_vcf2maf_log)
+                remove_file(output_vcf2maf_log)
 
             ## add information on allelic support in MAF file (n_depth, n_ref_count, n_alt_count, t_depth, t_ref_count, t_alt_count)   
             update_maf_allelic_support(
@@ -435,7 +434,7 @@ def run_pcgr(pcgr_paths, conf_options):
         # do not delete if debugging
         if not debug:
             for fn in delete_files:
-                utils.remove(fn)
+                remove_file(fn)
 
         logger.info('Finished pcgr-summarise main command')
 
@@ -447,13 +446,13 @@ def run_pcgr(pcgr_paths, conf_options):
         ## Append additional (space-containing) annotations not suitable for VCF INFO        
         logger.info("Appending ClinVar traits, official gene names, and protein domain annotations")        
         variant_set = \
-           variant.append_annotations(
+           append_annotations(
               output_pass_vcf2tsv_gz, pcgr_db_dir = pcgr_paths["db_dir"], logger = logger)
-        variant_set = variant.set_allelic_support(variant_set, allelic_support_tags = yaml_data["conf"]['somatic_snv']['allelic_support'])
-        variant_set = variant.clean_annotations(variant_set, yaml_data, germline = False, logger = logger)        
-        variant_set.to_csv(output_pass_tsv_gz, sep="\t", compression="gzip", index=False)
+        variant_set = set_allelic_support(variant_set, allelic_support_tags = yaml_data["conf"]['somatic_snv']['allelic_support'])
+        variant_set = clean_annotations(variant_set, yaml_data, germline = False, logger = logger)        
+        variant_set.fillna('.').to_csv(output_pass_tsv_gz, sep="\t", compression="gzip", index=False)
         if not debug:
-            utils.remove(output_pass_vcf2tsv_gz)
+            remove_file(output_pass_vcf2tsv_gz)
 
         if yaml_data["conf"]['assay_properties']['type'] == 'WGS' or yaml_data["conf"]['assay_properties']['type'] == 'WES':
             # check that output file exist
@@ -499,7 +498,7 @@ def run_pcgr(pcgr_paths, conf_options):
 
         if yaml_data['conf']['somatic_snv']['tmb']['run'] == 1:
             logger_tmb = getlogger('pcgr-calculate-tmb')
-            variant.calculate_tmb(
+            calculate_tmb(
                 variant_set = variant_set,
                 tumor_dp_min = int(yaml_data['conf']['somatic_snv']['tmb']['tmb_dp_min']),
                 tumor_af_min = float(yaml_data['conf']['somatic_snv']['tmb']['tmb_af_min']),

pcgr/oncogenicity.py

@@ -120,11 +120,11 @@ def assign_oncogenicity_evidence(rec = None, tumortype = "Any"):
       "LOSS_OF_FUNCTION",
       "INTRON_POSITION",
       "EXON_POSITION",
-      "gnomAD_EAS_AF",
-      "gnomAD_NFE_AF",
-      "gnomAD_AFR_AF",
-      "gnomAD_AMR_AF",
-      "gnomAD_SAS_AF",
+      "gnomADe_EAS_AF",
+      "gnomADe_NFE_AF",
+      "gnomADe_AFR_AF",
+      "gnomADe_AMR_AF",
+      "gnomADe_SAS_AF",
       "DBNSFP_SIFT",
       "DBNSFP_PROVEAN",
       "DBNSFP_META_RNN",
@@ -152,7 +152,7 @@ def assign_oncogenicity_evidence(rec = None, tumortype = "Any"):
       else:
          if rec.INFO.get(col) == '':
             variant_data[col] = True
-         else:            
+         else: 
             variant_data[col] = rec.INFO.get(col)
 
    for code in clingen_vicc_ev_codes:
@@ -246,27 +246,27 @@ def assign_oncogenicity_evidence(rec = None, tumortype = "Any"):
             variant_data['CLINGEN_VICC_OP3'] = True
 
 
-   if "gnomAD_EAS_AF" in variant_data.keys() and \
-      "gnomAD_SAS_AF" in variant_data.keys() and \
-      "gnomAD_AMR_AF" in variant_data.keys() and \
-      "gnomAD_AFR_AF" in variant_data.keys() and \
-      "gnomAD_NFE_AF" in variant_data.keys():
+   if "gnomADe_EAS_AF" in variant_data.keys() and \
+      "gnomADe_SAS_AF" in variant_data.keys() and \
+      "gnomADe_AMR_AF" in variant_data.keys() and \
+      "gnomADe_AFR_AF" in variant_data.keys() and \
+      "gnomADe_NFE_AF" in variant_data.keys():
 
       ## check if variant has MAF > 0.01 (SBVS1) or > 0.05 in any of five major gnomAD subpopulations (exome set)
-      for pop in ['gnomAD_SAS_AF','gnomAD_EAS_AF','gnomAD_AMR_AF','gnomAD_AFR_AF','gnomAD_NFE_AF']:
+      for pop in ['gnomADe_SAS_AF','gnomADe_EAS_AF','gnomADe_AMR_AF','gnomADe_AFR_AF','gnomADe_NFE_AF']:
          if not variant_data[pop] is None:
             ## MAF for this population >= 0.05
             if float(variant_data[pop]) >= 0.05:
                variant_data["CLINGEN_VICC_SBVS1"] = True
-      for pop in ['gnomAD_SAS_AF','gnomAD_EAS_AF','gnomAD_AMR_AF','gnomAD_AFR_AF','gnomAD_NFE_AF']:
+      for pop in ['gnomADe_SAS_AF','gnomADe_EAS_AF','gnomADe_AMR_AF','gnomADe_AFR_AF','gnomADe_NFE_AF']:
          if not variant_data[pop] is None:
             ## MAF for this population >= 0.01 (< 0.05)
             if float(variant_data[pop]) >= 0.01 and variant_data["CLINGEN_VICC_SBVS1"] is False:
                variant_data["CLINGEN_VICC_SBS1"] = True
 
       #missing_pop_freq = 0
       approx_zero_pop_freq = 0
-      for pop in ['gnomAD_SAS_AF','gnomAD_EAS_AF','gnomAD_AMR_AF','gnomAD_AFR_AF','gnomAD_NFE_AF']:
+      for pop in ['gnomADe_SAS_AF','gnomADe_EAS_AF','gnomADe_AMR_AF','gnomADe_AFR_AF','gnomADe_NFE_AF']:
          ## no MAF recorded in gnomAD for this population
          if variant_data[pop] is None:
             approx_zero_pop_freq = approx_zero_pop_freq + 1
@@ -278,6 +278,7 @@ def assign_oncogenicity_evidence(rec = None, tumortype = "Any"):
       ## check if variant is missing or with MAF approximately zero in all five major gnomAD subpopulations (exome set)
       if approx_zero_pop_freq == 5:
          variant_data["CLINGEN_VICC_OP4"] = True
+
 
    ## check if variant is a loss-of-function variant (LOFTEE) in a tumor suppressor gene (Cancer Gene Census/CancerMine)
    if "TSG" in variant_data.keys() and \
@@ -397,9 +398,6 @@ def assign_oncogenicity_evidence(rec = None, tumortype = "Any"):
    likely_oncogenic_lower_limit = 5
    likely_oncogenic_upper_limit = 9
    oncogenic_lower_limit = 10
-
-   #if variant_data['SYMBOL'] == "PIK3CA":
-   #   print(str(variant_data))
 
    variant_data['ONCOGENICITY_SCORE'] = onc_score_benign + onc_score_pathogenic
    if variant_data['ONCOGENICITY_SCORE'] <= likely_benign_upper_limit and \

pcgr/utils.py

@@ -129,7 +129,7 @@ def get_cpsr_version():
     return subprocess.check_output(v_cmd, shell=True).decode("utf-8")
 
 # https://stackoverflow.com/a/10840586/2169986
-def remove(filename):
+def remove_file(filename):
     try:
         os.remove(filename)
     except OSError as e: