fixing commands to work correctly

churchill-lab · Jun 15, 2023 · 931082b · 931082b
1 parent 4a6a91d
commit 931082b
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Showing 5 changed files with 22 additions and 23 deletions.
diff --git a/src/g2gtools/commands.py b/src/g2gtools/commands.py
@@ -141,12 +141,12 @@ def vcf2vci(
     fasta_file: Annotated[Path, typer.Option('-f', '--fasta', exists=True, dir_okay=False, resolve_path=True, help='Fasta file matching VCF information')],
     strain: Annotated[str, typer.Option('-s', '--strain', help='Name of strain/sample (column in VCF file)')],
     output_file: Annotated[Path, typer.Option('-o', '--output', exists=False, dir_okay=False, writable=True, resolve_path=True, help='Name of output file')] = None,
-    num_processes: Annotated[int, typer.Option('-n', '--num-processes', hidden=True)] = None,
+    num_processes: Annotated[int, typer.Option('-p', '--num-processes', hidden=True)] = None,
     diploid: Annotated[bool, typer.Option('-d', '--diploid', help='Create diploid VCI file')] = False,
-    keep: Annotated[bool, typer.Option('-k', '--keep', help='Keep track of VCF lines that could not be converted to VCI file')] = False,
-    passed: Annotated[bool, typer.Option('-p', '--pass', help='Use only VCF lines that have a PASS for the filter value')] = False,
-    quality: Annotated[bool, typer.Option('-q', '--quality', help='Filter on quality, FI=PASS')] = False,
-    no_bgzip: Annotated[bool, typer.Option('-z', '--no-bgzip', help='DO NOT compress and index output')] = False,
+    keep: Annotated[bool, typer.Option('--keep', help='Keep track of VCF lines that could not be converted to VCI file')] = False,
+    passed: Annotated[bool, typer.Option('--pass', help='Use only VCF lines that have a PASS for the filter value')] = False,
+    quality: Annotated[bool, typer.Option('--quality', help='Filter on quality, FI=PASS')] = False,
+    no_bgzip: Annotated[bool, typer.Option('--no-bgzip', help='DO NOT compress and index output')] = False,
     verbose: Annotated[int, typer.Option('-v', '--verbose', count=True, help='specify multiple times for more verbose output')] = 0
 ) -> None:
     """

diff --git a/src/g2gtools/fasta.py b/src/g2gtools/fasta.py
@@ -241,7 +241,7 @@ def extract(
         output_file_name = g2g_utils.check_file(output_file_name, 'w')
         fasta_out = open(output_file_name, 'w')
     else:
-        fasta_out = sys.stdout
+        fasta_out = sys.stderr
 
     try:
         if not isinstance(locations, list):

diff --git a/src/g2gtools/g2g_utils.py b/src/g2gtools/g2g_utils.py
@@ -83,7 +83,7 @@ def configure_logging(
     Returns:
         logging.Logger: The logging object.
     """
-    ensimpl_app_debug = nvli(os.environ.get('G2GTOOLS_APP_DEBUG', '0'), -1)
+    g2g_app_debug = nvli(os.environ.get('G2GTOOLS_APP_DEBUG', '0'), -1)
 
     rich_handler = RichHandler(
         level=logging.NOTSET,
@@ -93,7 +93,7 @@ def configure_logging(
         omit_repeated_times=False,
     )
 
-    if ensimpl_app_debug == 1:
+    if g2g_app_debug == 1:
         rich_handler = RichHandler(
             level=logging.NOTSET,
             show_level=True,
@@ -117,7 +117,7 @@ def configure_logging(
     if level == 0:
         log.setLevel(logging.WARNING)
     elif level == 1:
-        log.setLevel(19)
+        log.setLevel(logging.INFO)
     elif level > 1:
         log.setLevel(logging.DEBUG)
 

diff --git a/src/g2gtools/vcf.py b/src/g2gtools/vcf.py
@@ -360,7 +360,7 @@ def parse_gt_tuple(
             gt_left = gt[0]
             gt_right = gt[1]
 
-            fi = sample_data['FI']
+            fi = vcf_record.format.get('FI')
         except ValueError:
             # LOG.debug(ve)
             pass

diff --git a/src/g2gtools/vcf2vci.py b/src/g2gtools/vcf2vci.py
@@ -181,6 +181,8 @@ def process_piece(vcf2vci_params: VCF2VCIInfo) -> dict[str, Any]:
         if vcf2vci_params.diploid:
             mi = ['L', 'R']
 
+        #logger = g2g_utils.configure_logging('g2tools', 10)
+
         logger.warning(f'Processing Chromosome {vcf2vci_params.chromosome}...')
 
         iterators = []
@@ -253,19 +255,19 @@ def discard_record(rec):
         n = 0
 
         line_numbers = 0
-        # print('iterators=' + str(type(iterators)))
-        # print('iterators[0]=' + str(type(iterators[0])))
+        #print('iterators=' + str(type(iterators)))
+        #print('iterators[0]=' + str(type(iterators[0])))
         for vcf_records in walk_vcfs_together(iterators):
             # print('vcf_records=' + str(type(vcf_records)))
             for i, vcf_record in enumerate(vcf_records):
-                # print('vcf_record=' + str(type(vcf_record)))
-                # logger.debug(vcf_record)
+                #print('vcf_record=' + str(type(vcf_record)))
+                #logger.debug(vcf_record)
                 if vcf_record is None:
                     continue
                 # logger.debug(vcf_record.alt)
                 # logger.debug(type(vcf_record.alt))
                 logger.debug('------------')
-                logger.debug(f'{vcf_record.pos=}')
+                #print(f'{vcf_record.pos=}')
 
                 if tabix:
                     gt = vcf.parse_gt_tuple_orig(
@@ -279,9 +281,6 @@ def discard_record(rec):
                 # logger.debug(gt)
                 logger.debug(f'{gt=}')
 
-                if not gt.is_snp:
-                    logger.critical('NO SNP DETECTED')
-
                 line_numbers = line_numbers + 1
                 if gt.is_snp:
                     # snp
@@ -421,10 +420,10 @@ def discard_record(rec):
 
                         orig_alt_seq = alt_seq
 
-                        s = vcf_record[
-                            vcf2vci_params.vcf_files[i].sample_index
-                        ]
-                        logger.debug(f'SAMPLE: {s}')
+                        #s = vcf_record[
+                        #    vcf2vci_params.vcf_files[i].sample_index
+                        #]
+                        #logger.debug(f'SAMPLE: {s}')
                         logger.debug(
                             f'REF="{gt.ref}", ALT_L="{gt.left}", '
                             f'ALT_R="{gt.right}", POS={vcf_record.pos}'
@@ -505,7 +504,7 @@ def discard_record(rec):
                             alt_str = alt_seq if alt_seq else '.'
                             out = (
                                 f'{vcf2vci_params.chromosome}{lr_out}\t'
-                                f'{vcf_record.pos + 1}\t'
+                                f'{vcf_record.pos + (1 if tabix else 0)}\t'
                                 f'{shared_bases}\t{ref_str}\t{alt_str}\t'
                                 f'{fragment_size}\n'
                             )