From a7aa2edd02861124b4c6910f18098038d9c282e1 Mon Sep 17 00:00:00 2001 From: joshuailevy Date: Mon, 11 Sep 2023 07:16:21 -0700 Subject: [PATCH] straggler updates from tree source switch --- freyja/_cli.py | 31 +++++++++---------------------- 1 file changed, 9 insertions(+), 22 deletions(-) diff --git a/freyja/_cli.py b/freyja/_cli.py index 319e7ccb..0b6aab78 100644 --- a/freyja/_cli.py +++ b/freyja/_cli.py @@ -25,7 +25,7 @@ @click.group() -@click.version_option('1.4.6') +@click.version_option('1.4.7') def cli(): pass @@ -52,28 +52,21 @@ def print_barcode_version(ctx, param, value): @click.option('--covcut', default=10, help='depth cutoff for\ coverage estimate') @click.option('--confirmedonly', is_flag=True, default=False) -@click.option('--wgisaid', is_flag=True, default=False, - help='larger library with non-public lineages') @click.option('--version', is_flag=True, callback=print_barcode_version, expose_value=False, is_eager=True) @click.option('--depthcutoff', default=0, help='exclude sites with coverage depth below this value and' 'group identical barcodes') def demix(variants, depths, output, eps, barcodes, meta, - covcut, confirmedonly, wgisaid, depthcutoff): + covcut, confirmedonly, depthcutoff): locDir = os.path.abspath(os.path.join(os.path.realpath(__file__), os.pardir)) # option for custom barcodes if barcodes != '-1': df_barcodes = pd.read_csv(barcodes, index_col=0) else: - if not wgisaid: - df_barcodes = pd.read_csv(os.path.join(locDir, - 'data/usher_barcodes.csv'), index_col=0) - else: - df_barcodes = pd.read_csv(os.path.join(locDir, - 'data/usher_barcodes_with_gisaid.csv'), - index_col=0) + df_barcodes = pd.read_csv(os.path.join(locDir, + 'data/usher_barcodes.csv'), index_col=0) if confirmedonly: confirmed = [dfi for dfi in df_barcodes.index if 'proposed' not in dfi and 'misc' not in dfi] @@ -136,7 +129,7 @@ def demix(variants, depths, output, eps, barcodes, meta, help='only include lineages in cov-lineages') @click.option('--buildlocal', is_flag=True, default=False, help='Perform barcode building locally') -def update(outdir, noncl, wgisaid, buildlocal): +def update(outdir, noncl, buildlocal): locDir = os.path.abspath(os.path.join(os.path.realpath(__file__), os.pardir)) if outdir != '-1': @@ -280,28 +273,22 @@ def variants(bamfile, ref, variants, depths, refname, minq, annot): @click.option('--boxplot', default='', help='file format of boxplot output (e.g. pdf or png)') @click.option('--confirmedonly', is_flag=True, default=False) -@click.option('--wgisaid', is_flag=True, default=False, - help='larger library with non-public lineages') @click.option('--rawboots', is_flag=True, default=False, help='return raw bootstraps') @click.option('--depthcutoff', default=0, help='exclude sites with coverage depth below this value and' 'group identical barcodes') def boot(variants, depths, output_base, eps, barcodes, meta, - nb, nt, boxplot, confirmedonly, wgisaid, depthcutoff, rawboots): + nb, nt, boxplot, confirmedonly, depthcutoff, rawboots): locDir = os.path.abspath(os.path.join(os.path.realpath(__file__), os.pardir)) # option for custom barcodes if barcodes != '-1': df_barcodes = pd.read_csv(barcodes, index_col=0) else: - if not wgisaid: - df_barcodes = pd.read_csv(os.path.join(locDir, - 'data/usher_barcodes.csv'), index_col=0) - else: - df_barcodes = pd.read_csv(os.path.join(locDir, - 'data/usher_barcodes_with_gisaid.csv'), - index_col=0) + df_barcodes = pd.read_csv(os.path.join(locDir, + 'data/usher_barcodes.csv'), index_col=0) + if confirmedonly: confirmed = [dfi for dfi in df_barcodes.index if 'proposed' not in dfi and 'misc' not in dfi]