Merge branch 'release/v1.1.3'

scanpy-scripts-tests.bats

@@ -7,6 +7,8 @@ setup() {
     data_dir="${test_dir}/data"
     output_dir="${test_dir}/outputs"
     raw_matrix="${data_dir}/matrix.mtx"
+    raw_matrix_from_raw="${data_dir}/raw/matrix.mtx"
+    raw_matrix_from_layer="${data_dir}/layer/matrix.mtx"
     singlet_obs="${data_dir}/singlet_obs.txt"
     batch_obs="${data_dir}/batch_obs.txt"
     read_opt="-x $data_dir --show-obj stdout"
@@ -117,6 +119,28 @@ setup() {
     [ -f "$raw_matrix" ]
 }
 
+@test "Test MTX write from .raw" {
+    if [ "$resume" = 'true' ] && [ -f "$raw_matrix_from_raw" ]; then
+        skip "$raw_matrix exists"
+    fi
+
+    run rm -rf ${data_dir}/raw/* && eval "echo -e \"import scanpy as sc\nfrom scanpy_scripts.cmd_utils import write_mtx\nimport os\nos.makedirs('$data_dir/raw', exist_ok=True)\nadata=sc.datasets.pbmc3k();adata.raw=adata\nwrite_mtx(adata, '$data_dir/raw/', use_raw=True)\" | python"
+
+    [ "$status" -eq 0 ]
+    [ -f "$raw_matrix_from_raw" ]
+}
+
+@test "Test MTX write from layers" {
+    if [ "$resume" = 'true' ] && [ -f "$raw_matrix_from_layer" ]; then
+        skip "$raw_matrix exists"
+    fi
+
+    run rm -rf ${data_dir}/layer/* && eval "echo -e \"import scanpy as sc\nfrom scanpy_scripts.cmd_utils import write_mtx\nimport os\nos.makedirs('$data_dir/layer', exist_ok=True)\nadata=sc.datasets.pbmc3k();adata.layers['test']=adata.X\nwrite_mtx(adata, '$data_dir/layer/', use_layer='test')\" | python"
+
+    [ "$status" -eq 0 ]
+    [ -f "$raw_matrix_from_layer" ]
+}
+
 @test "Make .obs with a singlet cell group" {
 
     if [ "$resume" = 'true' ] && [ -f "$singlet_obs" ]; then

scanpy_scripts/cmd_utils.py

@@ -120,7 +120,6 @@ def _write_obj(
         click.echo(adata, err=show_obj == 'stderr')
     return 0
 
-
 def write_mtx(adata, fname_prefix='', var=None, obs=None, use_raw=False, use_layer=None):
     """Export AnnData object to mtx formt
     * Parameters
@@ -141,17 +140,21 @@ def write_mtx(adata, fname_prefix='', var=None, obs=None, use_raw=False, use_lay
         var = []
     if obs is None:
         obs = []
-    if use_raw:
-        adata = adata.raw
-    obs = list(set(obs) & set(adata.obs.columns))
-    var = list(set(var) & set(adata.var.columns))
 
     import scipy.sparse as sp
-    if use_layer is not None:
-        mat=sp.coo_matrix(adata.layer[use_layer])
+    if use_raw:
+        var_source = adata.raw.var
+        mat = sp.coo_matrix(adata.raw.X)
     else:
-        mat = sp.coo_matrix(adata.X)
-
+        var_source = adata.var
+        if use_layer is not None:
+            mat=sp.coo_matrix(adata.layers[use_layer])
+        else:
+            mat = sp.coo_matrix(adata.X)
+
+    obs = list(set(obs) & set(adata.obs.columns))
+    var = list(set(var) & set(var_source.columns))
+
     n_obs, n_var = mat.shape
     n_entry = len(mat.data)
     header = '%%MatrixMarket matrix coordinate real general\n%\n{} {} {}\n'.format(
@@ -166,7 +169,7 @@ def write_mtx(adata, fname_prefix='', var=None, obs=None, use_raw=False, use_lay
 
     obs_df = adata.obs[obs].reset_index(level=0)
     obs_df.to_csv(barcode_fname, sep='\t', header=False, index=False)
-    var_df = adata.var[var].reset_index(level=0)
+    var_df = var_source[var].reset_index(level=0)
     if not var:
         var_df['gene'] = var_df['index']
     var_df.to_csv(gene_fname, sep='\t', header=False, index=False)

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='scanpy-scripts',
-    version='1.1.2',
+    version='1.1.3',
     author='nh3',
     author_email='[email protected]',
     description='Scripts for using scanpy from the command line',
@@ -52,6 +52,7 @@
         'bbknn>=1.5.0',
         'mnnpy>=0.1.9.5',
         'scrublet',
-        'scikit-misc'
+        'scikit-misc',
+        'fa2'
     ],
 )