[WIP]

src/variantplaner/cli/__init__.py

@@ -40,9 +40,16 @@ def parser_process(value: typing.Any, state: typing.Any) -> typing.Any:
                         done = True
                     if not done:
                         value.append(state.rargs.pop(0))
+            print(len(value))
+            if len(value) == 1:
+                print(value)
+                value = value[0]
+                print(value)
+            else:
+                value = tuple(value)
+                self.nargs = len(value)
 
-            value = tuple(value)
-            self.nargs = len(value)
+            print(value)
 
             # call the actual process
             self._previous_parser_process(value, state)
@@ -90,3 +97,7 @@ def main(ctx: click.Context, *, threads: int = 1, verbose: int = 0, debug_info:
 
 
 # module import required after main definition
+from variantplaner.cli.metadata import *
+from variantplaner.cli.struct import *
+from variantplaner.cli.transmission import *
+from variantplaner.cli.vcf2parquet import *

src/variantplaner/cli/csv2parquet.py

@@ -0,0 +1,85 @@
+"""Module contains csv2parquet subcommand entry point function."""
+
+# std import
+from __future__ import annotations
+
+import logging
+import pathlib
+import sys
+
+# 3rd party import
+import click
+
+# project import
+from variantplaner import cli, exception, extract, io
+
+
+@cli.main.group("csv2parquet", chain=True)
+@click.pass_context
+@click.option(
+    "-i",
+    "--input-path",
+    help="Path to vcf input file",
+    type=click.Path(exists=True, dir_okay=False, readable=True, allow_dash=True, path_type=pathlib.Path),
+    required=True,
+)
+@click.option(
+    "-c",
+    "--chrom2length-path",
+    help="CSV file that associates a chromosome name with its size",
+    type=click.Path(dir_okay=False, writable=True, path_type=pathlib.Path),
+)
+@click.option(
+    "-a",
+    "--append",
+    help="Switch in append mode",
+    type=bool,
+    is_flag=True,
+)
+@click.option(
+    "-C",
+    "--chrom-col",
+    type=str,
+    default="chr",
+    show_default=True,
+)
+@click.option(
+    "-p",f
+    "--position-col",
+    type=str,
+    default="pos",
+    show_default=True,
+)
+@click.option(
+    "-r",
+    "--ref-col",
+    type=str,
+    default="ref",
+    show_default=True,
+)
+@click.option(
+    "-a",
+    "--alt-col",
+    type=str,
+    default="alt",
+    show_default=True,
+)
+@click.option(
+    "-s",
+    "--separator",
+    type=str,
+    default=","
+    show_default=True,
+)
+def csv2parquet(
+        ctx: click.Context,
+        input_path: pathlib.Path,
+        chrom2length_path: pathlib.Path,
+        *,
+        append: bool,
+        chrom_col: str | None,
+        pos_col: str | None,
+        ref_col: str | None,
+        alt_col: str | None,
+        separator_col: str | None,
+)

src/variantplaner/cli/metadata.py

@@ -33,7 +33,7 @@
     "-t",
     "--input-type",
     help="Type of input file",
-    type=click.Choices(["csv", "tsv", "ljson", "json"]),
+    type=click.Choice(["csv", "tsv", "ljson", "json"]),
     required=True,
 )
 def metadata(

src/variantplaner/cli/vcf2parquet.py

@@ -51,7 +51,7 @@ def vcf2parquet(
 
     try:
         logger.debug("Start extract header")
-        header = io.vcf.extract_header(input_path)
+        headers = io.vcf.extract_header(input_path)
         logger.debug("End extract header")
     except exception.NotAVCFError:
         logger.exception("")
@@ -65,7 +65,7 @@ def vcf2parquet(
     ctx.obj["vcf_path"] = input_path
     ctx.obj["lazyframe"] = lf
     ctx.obj["append"] = append
-    ctx.obj["header"] = header
+    ctx.obj["headers"] = headers
 
 
 @vcf2parquet.command("variants")
@@ -84,8 +84,6 @@ def variants(
     """Write variants."""
     logger = logging.getLogger("vcf2parquet.variants")
 
-    ctx.ensure_object(dict)
-
     lf = ctx.obj["lazyframe"]
     append = ctx.obj["append"]  # noqa: F841 not used now
 
@@ -144,16 +142,15 @@ def genotypes(
 @click.option(
     "-o",
     "--output-path",
-    help="Path where variants will be written",
+    help="Path where genotypes will be written",
     type=click.Path(writable=True, path_type=pathlib.Path),
     required=True,
 )
-@click.pass_context
 @click.option(
     "-i",
     "--info",
-    multiple=True,
     help="List of info fields that are kept if this list is empty all fields are kept only the first vcf file header is read",
+    cls=cli.MultipleValueOption,
     type=str,
 )
 @click.option(
@@ -171,17 +168,15 @@ def annotations(
     """Write annotations."""
     logger = logging.getLogger("vcf2parquet.annotations")
 
-    ctx.ensure_object(dict)
-
     lf = ctx.obj["lazyframe"]
     append = ctx.obj["append"]  # noqa: F841 not used now
-    header = ctx.obj["header"]
+    headers = ctx.obj["headers"]
     input_path = ctx.obj["vcf_path"]
 
     logger.debug(f"parameter: {output_path=}")
 
     logger.info("Start extract annotations")
-    annotations_lf = lf.with_columns(io.vcf.info2expr(header, input_path, info))
+    annotations_lf = lf.with_columns(io.vcf.info2expr(headers, input_path, info))
     annotations_lf = annotations_lf.drop(["chr", "pos", "ref", "alt", "filter", "qual", "info"])
     if rename_id:
         logger.info(f"Rename vcf variant id in {rename_id}")
@@ -191,3 +186,30 @@ def annotations(
     logger.info(f"Start write annotations in {output_path}")
     annotations_lf.sink_parquet(output_path, maintain_order=False)
     logger.info(f"End write annotations in {output_path}")
+
+
+@vcf2parquet.command("headers")
+@click.pass_context
+@click.option(
+    "-o",
+    "--output-path",
+    help="Path where header will be written",
+    type=click.Path(writable=True, path_type=pathlib.Path),
+    required=True,
+)
+def headers(
+    ctx: click.Context,
+    output_path: pathlib.Path,
+) -> None:
+    """Write vcf headers."""
+    logger = logging.getLogger("vcf2parquet.headers")
+
+    headers = ctx.obj["headers"]
+
+    logger.debug(f"parameter: {output_path=}")
+
+    logger.info(f"Start write headers in {output_path}")
+    with open(output_path, "w") as fh_out:
+        for line in headers:
+            print(line, file=fh_out)
+    logger.info(f"End write headers in {output_path}")

src/variantplaner/io/vcf.py

@@ -317,7 +317,7 @@ def into_lazyframe(
 
     if extension == IntoLazyFrameExtension.MANAGE_SV:
         drop_column = {"SVTYPE", "SVLEN"}
-        lf = lf.collect().select([col for col in lf.columns if col not in drop_column]).lazy()
+        lf = lf.select([col for col in lf.columns if col not in drop_column]).collect().lazy()
 
     return lf