Merge branch 'master' into dev

.gitignore

@@ -1,4 +1,5 @@
 docs/build/
+.DS_Store
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

.gitpod.yml

@@ -0,0 +1,10 @@
+# This configuration file was automatically generated by Gitpod.
+# Please adjust to your needs (see https://www.gitpod.io/docs/introduction/learn-gitpod/gitpod-yaml)
+# and commit this file to your remote git repository to share the goodness with others.
+
+# Learn more from ready-to-use templates: https://www.gitpod.io/docs/introduction/getting-started/quickstart
+
+tasks:
+  - init: pip install .
+
+

AMDirT/__init__.py

@@ -1 +1 @@
-__version__ = "1.4"
+__version__ = "1.6.1"

AMDirT/autofill/__init__.py

@@ -108,6 +108,8 @@ def run_autofill(accession, table_name=None, schema=None, dataset=None, sample_o
             lib_out[col] = None
     lib_out = lib_out[libraries_df.columns]
     lib_out = lib_out.loc[:,~lib_out.columns.duplicated()].copy()
+    lib_out['read_count'] = lib_out['read_count'].str.replace(",", "",
+                                                              regex=False)
     lib_out = lib_out.astype(libraries_df.dtypes.to_dict())
 
     if library_output:

AMDirT/cli.py

@@ -4,12 +4,38 @@
 from AMDirT.validate import run_validation
 from AMDirT.viewer import run_app
 from AMDirT.convert import run_convert
-from AMDirT.core import get_json_path
+from AMDirT.core import get_json_path, get_amdir_tags, get_latest_tag
 from AMDirT.autofill import run_autofill
 from AMDirT.merge import merge_new_df
+from AMDirT.download import download as download_amdir
 from json import load
 
 
+class MutuallyExclusiveOption(click.Option):
+    # Credits goes to Stan Chang for this code snippet
+    # https://gist.github.com/stanchan/bce1c2d030c76fe9223b5ff6ad0f03db
+
+    def __init__(self, *args, **kwargs):
+        self.mutually_exclusive = set(kwargs.pop("mutually_exclusive", []))
+        help = kwargs.get("help", "")
+        if self.mutually_exclusive:
+            ex_str = ", ".join(self.mutually_exclusive)
+            kwargs["help"] = help + (
+                " NOTE: This argument is mutually exclusive with "
+                " arguments: [" + ex_str + "]."
+            )
+        super(MutuallyExclusiveOption, self).__init__(*args, **kwargs)
+
+    def handle_parse_result(self, ctx, opts, args):
+        if self.mutually_exclusive.intersection(opts) and self.name in opts:
+            raise click.UsageError(
+                "Illegal usage: `{}` is mutually exclusive with "
+                "arguments `{}`.".format(self.name, ", ".join(self.mutually_exclusive))
+            )
+
+        return super(MutuallyExclusiveOption, self).handle_parse_result(ctx, opts, args)
+
+
 def get_table_list():
     json_path = get_json_path()
     with open(json_path, "r") as f:
@@ -110,6 +136,20 @@ def viewer(ctx, no_args_is_help=True, **kwargs):
     type=click.Path(exists=True),
     help="(Optional) JSON file listing AncientMetagenomeDir tables",
 )
+@click.option(
+    "--libraries",
+    type=click.Path(readable=True, file_okay=True, dir_okay=False, exists=True),
+    help=("(Optional) Path to a pre-filtered libraries table"),
+    cls=MutuallyExclusiveOption,
+    mutually_exclusive=["librarymetadata"],
+)
+@click.option(
+    "--librarymetadata",
+    is_flag=True,
+    help="Generate AncientMetagenomeDir libraries table of all samples in input table",
+    cls=MutuallyExclusiveOption,
+    mutually_exclusive=["libraries"],
+)
 @click.option(
     "-o",
     "--output",
@@ -123,11 +163,6 @@ def viewer(ctx, no_args_is_help=True, **kwargs):
     is_flag=True,
     help="Generate BibTeX file of all publications in input table",
 )
-@click.option(
-    "--librarymetadata",
-    is_flag=True,
-    help="Generate AncientMetagenomeDir libraries table of all samples in input table",
-)
 @click.option(
     "--curl",
     is_flag=True,
@@ -139,14 +174,19 @@ def viewer(ctx, no_args_is_help=True, **kwargs):
     help="Generate bash script with Aspera-based download commands for all libraries of samples in input table",
 )
 @click.option(
-    "--eager",
+    "--fetchngs",
     is_flag=True,
-    help="Convert filtered samples and libraries tables to eager input tables",
+    help="Convert filtered samples and libraries tables to nf-core/fetchngs input tables",
 )
 @click.option(
-    "--fetchngs",
+    "--sratoolkit",
     is_flag=True,
-    help="Convert filtered samples and libraries tables to nf-core/fetchngs input tables",
+    help="Generate bash script with SRA Toolkit fasterq-dump based download commands for all libraries of samples in input table",
+)
+@click.option(
+    "--eager",
+    is_flag=True,
+    help="Convert filtered samples and libraries tables to eager input tables",
 )
 @click.option(
     "--ameta",
@@ -167,6 +207,9 @@ def viewer(ctx, no_args_is_help=True, **kwargs):
 def convert(ctx, no_args_is_help=True, **kwargs):
     """\b
     Converts filtered samples and libraries tables to eager, ameta, taxprofiler, and fetchNGS input tables
+
+    Note: When supplying a pre-filtered libraries table with `--libraries`, the corresponding sample table is still required!
+
     \b
     SAMPLES: path to filtered AncientMetagenomeDir samples tsv file
     TABLE_NAME: name of table to convert
@@ -178,26 +221,27 @@ def convert(ctx, no_args_is_help=True, **kwargs):
 # Autofill tool #
 #################
 
+
 @cli.command()
 @click.argument("accession", type=str, nargs=-1)
 @click.option(
     "-n",
-    "--table_name", 
+    "--table_name",
     type=click.Choice(get_table_list()),
-    default='ancientmetagenome-hostassociated',
-    show_default=True
+    default="ancientmetagenome-hostassociated",
+    show_default=True,
 )
 @click.option(
     "-l",
     "--library_output",
     type=click.Path(writable=True),
-    help="path to library output table file"
+    help="path to library output table file",
 )
 @click.option(
     "-s",
     "--sample_output",
     type=click.Path(writable=True),
-    help="path to sample output table file"
+    help="path to sample output table file",
 )
 @click.pass_context
 def autofill(ctx, no_args_is_help=True, **kwargs):
@@ -219,31 +263,26 @@ def autofill(ctx, no_args_is_help=True, **kwargs):
 @click.argument("dataset", type=click.Path(exists=True))
 @click.option(
     "-n",
-    "--table_name", 
+    "--table_name",
     type=click.Choice(get_table_list()),
-    default='ancientmetagenome-hostassociated',
-    show_default=True
+    default="ancientmetagenome-hostassociated",
+    show_default=True,
 )
 @click.option(
     "-t",
-    "--table_type", 
-    type=click.Choice(['samples', 'libraries']),
-    default='libraries',
-    show_default=True
-)
-@click.option(
-    "-m", 
-    "--markdown", 
-    is_flag=True, 
-    help="Output is in markdown format"
+    "--table_type",
+    type=click.Choice(["samples", "libraries"]),
+    default="libraries",
+    show_default=True,
 )
+@click.option("-m", "--markdown", is_flag=True, help="Output is in markdown format")
 @click.option(
     "-o",
     "--outdir",
     type=click.Path(writable=True),
     default=".",
     show_default=True,
-    help="path to sample output table file"
+    help="path to sample output table file",
 )
 @click.pass_context
 def merge(ctx, no_args_is_help=True, **kwargs):
@@ -255,5 +294,46 @@ def merge(ctx, no_args_is_help=True, **kwargs):
     """
     merge_new_df(**kwargs, **ctx.obj)
 
+
+@cli.command()
+@click.option(
+    "-t",
+    "--table",
+    help="AncientMetagenomeDir table to download",
+    type=click.Choice(get_table_list()),
+    default="ancientmetagenome-hostassociated",
+    show_default=True,
+)
+@click.option(
+    "-y",
+    "--table_type",
+    help="Type of table to download",
+    type=click.Choice(["samples", "libraries"]),
+    default="samples",
+    show_default=True,
+)
+@click.option(
+    "-r",
+    "--release",
+    help="Release tag to download",
+    type=click.Choice(get_amdir_tags()),
+    default=get_latest_tag(get_amdir_tags()),
+    show_default=True,
+)
+@click.option(
+    "-o",
+    "--output",
+    help="Output directory",
+    type=click.Path(writable=True),
+    default=".",
+    show_default=True,
+)
+def download(no_args_is_help=True, **kwargs):
+    """\b
+    Download a table from the AMDirT repository
+    """
+    download_amdir(**kwargs)
+
+
 if __name__ == "__main__":
     cli()