Galaxy |

Changeset 0:c8e4d0b9ae8c (2020-01-06)

Next changeset 1:81a28c2705b0 (2020-01-18)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"

diff -r 000000000000 -r c8e4d0b9ae8c loompy_to_tsv.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/loompy_to_tsv.py Mon Jan 06 13:43:38 2020 -0500

[

@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+"""Converts a loompy file to tsv file(s). Each layer becomes a new file."""
+
+import argparse
+
+import loompy
+
+parser = argparse.ArgumentParser(description="Loompy file converter flags")
+parser.add_argument('--version', action='version', version='%(prog)s 0.1.0',
+                    help="Displays tool version")
+parser.add_argument("-f", "--file", help="loom file to import")
+args = parser.parse_args()
+
+file = args.file
+
+matrices = []
+allcols = []
+colstrings = []
+allrows = []
+
+# Build background info for all attributes and layers
+loompyfile = loompy.connect(file)
+row_attributes = loompyfile.ra.keys()  # List of row attributes
+for row in row_attributes:  # Each list represents rownames for row_attributes
+    c_row = loompyfile.ra[row]
+    c_row = [str(r) for r in c_row]
+    allrows.append(c_row)
+col_attributes = loompyfile.ca.keys()  # List of column attributes
+for col in col_attributes:  # each list represents colnames for col_attributes
+    c_col = loompyfile.ca[col]
+    c_col = [str(c) for c in c_col]
+    allcols.append(c_col)
+layers = loompyfile.layers.keys()  # List of layers
+for layer in layers:  # List with each element being a loompy layer
+    c_layer = loompyfile[layer]
+    c_layer = c_layer[:, :]
+    c_layer = c_layer.astype(str)
+    matrices.append(c_layer)
+
+# Create column attribute output
+with open("attributes/col_attr.tsv", "w") as colout:
+    col_attributes = "\t".join(col_attributes) + "\n"
+    colout.write(col_attributes)
+    for length in range(0, len(c_col)):
+        attributestring = ""
+        for col in allcols:
+            attributestring = attributestring + col[length] + "\t"
+        while attributestring[-1] == "\t":
+            attributestring = attributestring[:-1]
+        colout.write(attributestring)
+        colout.write("\n")
+# Create row attribute output
+with open("attributes/row_attr.tsv", "w") as rowout:
+    row_attributes = "\t".join(row_attributes) + "\n"
+    rowout.write(row_attributes)
+    for length in range(0, len(c_row)):
+        attributestring = ""
+        for row in allrows:
+            attributestring = attributestring + row[length] + "\t"
+        while attributestring[-1] == "\t":
+            attributestring = attributestring[:-1]
+        rowout.write(attributestring)
+        rowout.write("\n")
+
+# Build output files for each layer
+for x in range(0, len(layers)):
+    # Output file name generation
+    if layers[x] in layers[0: x]:  # Different output names if layers have same names somehow
+        repeats = layers[0, x].count(layer[x])
+        outputname = "output/" + layers[x] + repeats + ".tsv"
+    elif layers[x] == "":  # Empty layer name
+        outputname = "output/mainmatrix.tsv"
+    else:
+        outputname = "output/" + str(layers[x]) + ".tsv"  # Usual case
+# Matrix output
+    with open(outputname, "w") as outputmatrix:
+        for line in matrices[x]:
+            line = "\t".join(line)
+            line += "\n"
+            line = line
+            outputmatrix.write(line)

diff -r 000000000000 -r c8e4d0b9ae8c macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Mon Jan 06 13:43:38 2020 -0500

[

@@ -0,0 +1,80 @@
+<macros>
+    <token name="@VERSION@">0.6.22.post1</token>
+    <token name="@GALAXY_VERSION@">galaxy1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">anndata</requirement>
+            <requirement type="package" version="2.0.17">loompy</requirement>
+            <requirement type="package" version="2.9.0">h5py</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-017-1382-0</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import anndata as ad;print('anndata version: %s' % ad.__version__); import loompy;print('\nloompy version: %s' % loompy.__version__)"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cat '$script_file' &&
+python '$script_file'
+    ]]>
+    </token>
+    <token name="@LOOMCMD@"><![CDATA[
+mkdir ./output &&
+mkdir ./attributes &&
+python '$__tool_directory__/loompy_to_tsv.py' -f '${hd5_format.input}'
+    ]]>
+    </token>
+    <token name="@CMD_imports@"><![CDATA[
+import anndata as ad
+    ]]>
+    </token>
+    <token name="@HELP@"><![CDATA[
+**AnnData**
+
+AnnData provides a scalable way of keeping track of data together with learned annotations. It is used within `Scanpy <https://github.com/theislab/scanpy>`__, for which it was initially developed.
+
+AnnData stores a data matrix `X` together with annotations of observations `obs`, variables `var` and unstructured annotations `uns`.
+
+.. image:: https://falexwolf.de/img/scanpy/anndata.svg
+
+
+AnnData stores observations (samples) of variables (features) in the rows of a matrix. This is the convention of the modern classics
+of statistics (`Hastie et al., 2009 <https://web.stanford.edu/~hastie/ElemStatLearn/>`__)  and machine learning (Murphy, 2012), the convention of dataframes both in R and Python and the established statistics
+and machine learning packages in Python (statsmodels, scikit-learn).
+
+More details on the `AnnData documentation
+<https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`__
+
+
+**Loom data**
+
+Loom files are an efficient file format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations, and sparse graph objects.
+
+.. image:: https://linnarssonlab.org/loompy/_images/Loom_components.png
+
+
+Loom files to store single-cell gene expression data: the main matrix contains the actual expression values (one column per cell, one row per gene); row and column annotations contain metadata for genes
+and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age (for cells).
+
+    ]]>
+    </token>
+    <xml name="params_chunk_X">
+        <conditional name="chunk">
+            <param name="info" type="select" label="How to select the chunk?">
+                <option value="random">Random chunk of defined size</option>
+                <option value="specified">Specified indices</option>
+            </param>
+            <when value="random">
+                <param name="size" type="integer" value="1000" label="Size of chunk to randomly select"/>
+                <param name="replace" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Random sampling of indices with replacement?"/>
+            </when>
+            <when value="specified">
+                <param name="list" type="text" value="" label="List of comma-separated indices to return"/>
+            </when>
+        </conditional>
+    </xml>
+</macros>

diff -r 000000000000 -r c8e4d0b9ae8c modify_loom.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_loom.py Mon Jan 06 13:43:38 2020 -0500

[

@@ -0,0 +1,108 @@
+#!/usr/bin/env python
+"""This program adds layers, row attributes or column attributes for loom files"""
+
+import argparse
+
+import loompy
+import numpy as np
+
+parser = argparse.ArgumentParser(description="Loompy file converter flags")
+parser.add_argument('--VERSION', action='version', version='%(prog)s 0.1.0',
+                    help="Displays tool version")
+parser.add_argument('--file', '-f',
+                    help="Loom file to which data will be added")
+parser.add_argument('--rowfile', '-r', help="File of row attributes & values")
+parser.add_argument('--colfile', '-c',
+                    help="File of column attributes and values")
+parser.add_argument('--layers', '-l', nargs='*',
+                    help="Input tsv files. First file becomes main layer.")
+parser.add_argument('--add', '-a', choices=["rows", "cols", "layers"],
+                    help="Selects rows, columns or layers to be added to file")
+args = parser.parse_args()
+
+lfile = args.file
+if args.rowfile:
+    rowfile = args.rowfile
+if args.colfile:
+    colfile = args.colfile
+if args.layers:
+    alllayers = args.layers
+addselect = args.add
+# Check proper flags for chosen attributes are being added
+if addselect == "cols" and not args.colfile:
+    raise Exception("To add column attributes, column flag and file must be provided")
+if addselect == "rows" and not args.rowfile:
+    raise Exception("To add row attributes, row flag and file must be provided")
+if addselect == "layers" and not args.layers:
+    raise Exception("To add layers, a layer flag and file(s) must be provided")
+
+layernames = []
+rowdict = {}
+coldict = {}
+
+with loompy.connect(lfile) as loomfile:
+    # Loom file dimensions
+    nrow = loomfile.shape[0]
+    ncol = loomfile.shape[1]
+    if addselect == "layers":
+        layernames = []
+        # Generate layer names based on file names
+        for x in range(0, len(alllayers)):
+            layer = alllayers[x]
+            layer = layer.split("/")[-1].split(".")[-2]  # Takes away path, takes off extension
+            layernames.append(layer)
+        # Add in the layers themselves
+        for layer in range(0, len(alllayers)):
+            matrix = ""
+            with open(alllayers[layer], "r") as infile:
+                rows = 0
+                count = 0
+                for line in infile:
+                    if count == 0:
+                        cols = len(line.split("\t"))
+                        if cols != ncol:
+                            raise Exception("Dimensions of new matrix incorrect for this loom file. New matrices must be %d by %d" % (nrow, ncol))
+                    matrix = matrix + line + "\t"
+                    rows += 1
+                if rows != nrow:
+                    raise Exception("Dimensions of new matrix incorrect for this loom file. New matrices must be %d by %d")
+            matrix = matrix.split("\t")
+            matrix = [float(n) for n in matrix[:-1]]
+            matrix = np.asarray(matrix).reshape(nrow, ncol)
+            loomfile[layernames[layer]] = matrix
+    elif addselect == "rows":
+        with open(rowfile, "r") as rows:
+            count = 0
+            for line in rows:
+                line = line.strip().split("\t")
+                if count == 0:  # First time through
+                    row_attributes = line
+                    for x in row_attributes:
+                        rowdict[x] = []
+                    count += 1
+                else:
+                    for x in range(0, len(line)):
+                        rowdict[row_attributes[x]].append(line[x])
+        for x in row_attributes:
+            if len(rowdict[x]) != nrow:
+                raise Exception("Incorrect length of row. Row length must be: %d" % nrow)
+            loomfile.ra[x] = rowdict[x]
+    elif addselect == "cols":
+        with open(colfile, "r") as cols:
+            count = 0
+            for line in cols:
+                line = line.replace('\"', "")
+                line = line.replace(' ', "")
+                line = line.strip().split("\t")
+                if count == 0:  # First time through
+                    col_attributes = line
+                    for x in col_attributes:
+                        coldict[x] = []
+                    count += 1
+                else:
+                    for x in range(0, len(line)):
+                        coldict[col_attributes[x]].append(line[x])
+        for y in col_attributes:
+            if len(coldict[y]) != ncol:
+                raise Exception("Incorrect length of column. Column length must be: %d" % ncol)
+            loomfile.ca[y] = coldict[y]

diff -r 000000000000 -r c8e4d0b9ae8c modify_loom.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/modify_loom.xml Mon Jan 06 13:43:38 2020 -0500

[

@@ -0,0 +1,72 @@
+<tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+@GALAXY_VERSION@">
+    <description>Add layers, or row/column attributes to a loom file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/modify_loom.py' -f '${input}'
+#if $which_add.add_type == "cols":
+    -a cols -c '${which_add.cols}'
+#else if $which_add.add_type == "cols":
+    -a rows -r '${which_add.rows}'
+#else if $which_add.add_type == "layers":
+    -a layers -l '${which_add.layers}'
+#end if
+&& cp '${input}' loom_add_out.loom
+      ]]></command>
+    <inputs>
+        <param name="input" type="data" format="loom" label="Loom file"/>
+        <conditional name="which_add">
+            <param name="add_type" type="select" label="Select data attribute to add to loom">
+                <option value="cols">Columns</option>
+                <option value="rows">Rows</option>
+                <option value="layers">Layers</option>
+            </param>
+            <when value="cols">
+                <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
+            </when>
+            <when value="rows">
+                <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
+            </when>
+            <when value="layers">
+                <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="cols"/>
+            <param name="cols" value="cols.tsv"/>
+            <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="rows"/>
+            <param name="rows" value="rows.tsv"/>
+            <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="addtest.loom"/>
+            <param name="add_type" value="layers"/>
+            <param name="layers" value="addlayer1.tsv"/>
+            <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
+            author = "Linnarsson lab"
+            title = "Loompy"
+            year = "2013"
+            note = "https://github.com/linnarsson-lab/loompy"}
+        </citation>
+    </citations>
+</tool>

diff -r 000000000000 -r c8e4d0b9ae8c test-data/adata.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adata.csv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,4 @@
+,c1,c2
+r1,1.0,0.0
+r2,3.0,0.0
+r3,5.0,6.0
\ No newline at end of file

diff -r 000000000000 -r c8e4d0b9ae8c test-data/adata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adata.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,6 @@
+# A regular comment
+# The next comment is actually colnames
+# c1 c2
+r1 1.0 0.0
+r2 3.0 0.0
+r3 5.0 6.0

diff -r 000000000000 -r c8e4d0b9ae8c test-data/addlayer1.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/addlayer1.tsv Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,9 @@\n+-4.38397705861083\t14.292813312163\t-3.50113245239144\t0.822254333007829\t1.00150289648448\t2.43591204698924\t-0.356677013622828\t-6.11947364969354\t2.56281003005924\t6.63909009032078\t-0.78946499862756\t4.69845868698249\t0.555316773542253\t1.14493347970535\t-2.13170480396421\t0.671242754395511\t-1.24598424970653\t2.35762885939\t0.808249063291586\t2.13338650412044\t-0.442400711567299\t0.185262494040311\t2.11898976841304\t1.33325569029047\t-1.59297725345935\t-0.966752781646448\t3.58792591654639\t1.66406580309397\t0.63327385793388\t-0.308925411126234\t1.62030751470511\t-0.551680746030133\t0.481109445913889\t-1.29522624182828\t-1.2921145302749\t1.35092954319461\t0.357971803776218\t0.602387478388324\t-0.86450428384588\t-0.253516849675122\t-0.191991523300002\t-1.23045693386899\t1.10601149579208\t0.474927307151347\t0.0295127518668576\t0.347320109574423\t-0.124263697792595\t-1.1355438083115\t-0.408955132576027\t0.652951279673313\t-0.560853895759609\t-1.50956633618222\t-0.372228084801999\t0.649248591501578\t1.24501120925882\t-0.333165552309464\t-0.632289365875825\t-0.489136074968853\t0.606241184362324\t-0.0697756202083343\t0.723366081694609\t0.269156075893411\t-1.1927509857456\t1.82685437466378\t0.112075843817834\t-0.393322613665142\t1.28166028199521\t-1.44150233543534\t0.439168555592787\t0.344017904319427\t1.81395743926678\t0.508805925557063\t0.848238740356503\t1.11258006953971\t-0.54997200023266\t0.809927913686388\t-0.738427841761447\t-0.453122730649697\t-0.486373667035062\t0.746360065063862\t0.700920021470684\t-0.313589192332652\t-0.906138725835488\t-0.661793483747946\t-0.271124869295733\t-0.00930238204411152\t0.3215219758547\t-1.25380192942129\t-1.55728763598058\t0.0952110940501214\t0.00839453406532392\t-0.0541448293428013\t0.18477775291979\t-0.62373646202135\t-0.0772377796590389\t-0.662366716574923\t-1.03592409403641\t-0.89249106169138\t-0.717710251591651\t0.776880357163071\n+9.30281248024864\t11.5335015413635\t2.30875450845203\t-1.38857898424223\t1.03817215518254\t3.6567570331059\t10.4188385719381\t-16.3128929934454\t-3.60726875451658\t13.7068591589974\t1.33467070509089\t5.38122487635218\t0.0543994941205517\t-2.70133427961325\t0.0833615201988052\t0.536168996886923\t-0.0760546449729948\t-0.78214225809622\t-1.95248285633292\t-0.326587425115489\t-1.35500688419885\t2.95434733271686\t0.505653381720533\t-0.295669096974786\t2.26651004107081\t3.53486650501347\t3.220565758935\t6.7321178798513\t1.94091616482302\t-1.69913768324206\t-4.05100974370053\t-1.27783882963281\t-1.01355047824763\t3.74963974715759\t-2.58850482422048\t6.8833099016512\t0.662009356554069\t3.44073177658161\t-0.418512226093587\t4.47846431563314\t-1.74206293554388\t1.84260608944111\t-4.30015045993517\t0.685087251537494\t3.24882497326721\t1.8095695466243\t0.867087349923969\t-3.63680218472816\t4.1068657392081\t-1.47022937993631\t-5.04481250049395\t1.16372912821134\t-0.673610496402694\t-0.480268341823079\t-1.75373530199601\t0.89984292745755\t-0.685746934741278\t1.35462132079302\t-2.52570708801692\t-2.74016842015935\t-0.393885487708287\t1.35180900874174\t0.566787604497255\t3.47016490744519\t1.19410589958458\t0.0954571935227406\t0.465830133214735\t0.969800327817249\t-2.30608823177911\t-1.36361346526534\t-1.07384772734754\t-1.28884764388441\t-1.1808330583485\t-2.23980854377317\t-1.85162318607013\t-0.069323155428631\t-0.398294053191192\t0.533970283418857\t0.996857378845262\t0.0816831777715224\t0.444550338509664\t-2.91836706827678\t-0.267414770797715\t-0.892474756707529\t2.17409610136124\t1.74372514825455\t1.50066087410441\t2.38996632942927\t0.0469000573619218\t-0.664299183380684\t2.60790199917983\t-2.40710478607531\t1.24547812809717\t2.41674046127559\t-1.46444549406779\t0.364174652919165\t1.30109643082257\t-0.577449382132677\t-1.86505783133924\t-1.99746975425092\n+-5.89727512326108\t-1.77246933119333\t1.52782219208749\t2.53511205650502\t-2.53100068245452\t-0.024300692685485\t1.54330662794615\t-2.74799503275627\t-3.35444290166925\t4.19511229947865\t0.465153187650876\t1.75331948382231\t-1.16526308150911\t-0.0943840089716619\t-0.24095624876061\t1.66521052849681\t-2.11688113706039\t-0.812191599443991\t1.84008723741373\t1.09605489701982\t0.353335700092688\t-0.523288451494122\t-0.2990'..b'5107\t-0.0154265589569301\t0.389711467291695\t-0.239877266341895\t0.352795111764336\t-0.190135198230446\t-0.208684600336429\t2.07918244700086\t-0.361025972011884\t1.63078492845337\t0.488804843489253\t-0.682220518809875\t-0.29463668542297\t0.311427730874536\t0.503090238195356\t-0.373064491000882\t0.23417554807577\t-1.48465915072341\t-1.46085021332334\t-0.495461794448377\t-0.17775442234612\n+-3.97575208570735\t11.0544858387352\t7.6173060428113\t6.63048929774542\t-5.30994749122935\t1.88722422257416\t4.09251614216244\t1.44648639362641\t-7.25006907798796\t6.86869361179653\t0.491494050662433\t-2.25651388279331\t9.5161454340774\t1.01476184398758\t2.5399705796852\t-2.21669881532076\t3.98394683759498\t3.59383510388346\t6.12746355517479\t-0.715726354893143\t3.55159403974729\t-1.11574398116924\t-0.525929195057429\t0.878154489745832\t-0.230493171744922\t0.714464510169232\t-0.157245107145587\t-3.4342599800683\t0.48505980459346\t0.702993897575898\t-0.135378631070949\t2.07954004197705\t-0.690953937097613\t1.27624456885549\t1.21947693928713\t1.65808520486344\t0.961593556571414\t-0.311912078906821\t-0.188898767072046\t-0.840060825549656\t-1.12921186104506\t1.56017494876464\t0.411131589159066\t-0.0521633935484305\t-1.69684514175225\t-0.0333681471142678\t-0.13906225301883\t1.24899138448782\t-0.313535620881124\t-0.310399053687893\t0.998855535319549\t-0.491386912744097\t-2.65588822465539\t-0.262301430974959\t-0.37741200187771\t-0.41429490709306\t-0.561255237373123\t-1.15276356159977\t2.78298825141619\t-0.502905861300848\t-0.675640036112791\t0.861407188085173\t0.670870463440124\t1.79627949867291\t-1.49071314746396\t1.10513353172237\t0.892902985092724\t-0.050023000293664\t-2.0951156395428\t-1.56875762272546\t0.361989901125448\t-0.225302477699307\t0.169862551615696\t-0.49530667266779\t0.458175186664475\t-1.32231097560469\t0.786081372282524\t-0.0484494603142322\t0.706878176692001\t1.15487020448148\t0.531640766037383\t-0.138810686002109\t0.591943064902141\t1.1023101065439\t1.76277780537503\t-0.905355575172113\t0.134769770511889\t-0.497015408904865\t-0.742656863985804\t-0.067343788917104\t-0.540927632084057\t-0.0580727941856462\t-1.0462842718808\t-0.00500540976328367\t-0.824608358220491\t-1.44352688132908\t1.75740458742792\t-0.44311879378313\t-0.662584623920899\t0.888462747166643\n+-5.277006254183\t2.42397087953038\t-0.943798001822603\t2.85780940799815\t2.36895039654097\t-2.69659967635116\t1.54629605482182\t-8.96928156931566\t-1.64262157483957\t1.43852747962271\t-0.967981915016056\t-0.390735428021631\t-2.15024133526923\t0.277271702300901\t1.8053039804015\t-0.535107559431625\t1.67768924818208\t-0.421010853147353\t-1.16464550016846\t-0.0251453460136133\t0.436658055348297\t-0.29540721194163\t0.333748713475055\t-0.723208532365344\t0.471110811941787\t0.726089991234918\t-0.157382569241171\t-0.379234094421878\t0.748812558274635\t-0.41301464848253\t0.566057622213117\t-1.64460356067673\t0.891204658261791\t-0.34932773880327\t-1.30922369726531\t-0.173573387498366\t0.8056807178332\t0.208881576008633\t-1.60357889692679\t0.908540313457729\t-0.292428392920166\t-0.0118489017469322\t-0.891712950604345\t1.16207204758746\t0.430624050805364\t-0.410051657015908\t0.730349459202633\t-0.331488261254584\t-1.11548393909722\t0.956994457204229\t-0.175931934021692\t-1.2036342551925\t-0.231987307226876\t0.750428558384009\t1.32527020615915\t-0.0420682884240139\t-0.092958898049259\t-0.0122267448532016\t0.726126639304472\t-0.694555932842187\t-0.262226740797341\t-1.0291540856062\t0.0793211050194524\t-0.670890710123743\t2.29978649016219\t-1.04786389277271\t0.0673332449001132\t-0.0371298860750165\t-0.190086855611152\t0.569211538833251\t0.919033137444811\t0.0635277673597158\t1.00004676925338\t0.463824012820739\t-0.661533287421813\t-0.532636001812366\t0.13594592076042\t0.353092106176299\t0.362734586198694\t0.648858597916376\t-0.947487352382305\t-0.890204579930725\t-0.481659475836321\t-0.382386249884642\t-0.565389965376474\t0.69470847650723\t0.565209012057139\t-0.594122862421382\t0.374110007433118\t0.906000246931211\t1.14643222017558\t-0.864426844788516\t-0.107902667694253\t-1.33878812133165\t-0.648727117620733\t-0.682898186419176\t0.152703116395545\t1.18647033835958\t-0.730347642632863\t0.355381103259185\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/addloomout1.loom

Binary file test-data/addloomout1.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/addloomout2.loom

Binary file test-data/addloomout2.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/addloomout3.loom

Binary file test-data/addloomout3.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/addtest.loom

Binary file test-data/addtest.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/barcodes_10x_v1.2.0.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcodes_10x_v1.2.0.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+AACACGTGTACGCTGC-1
+AAGGAGCTCCGATATG-1
+AGGCCGTAGTGAAGTT-1
+CCTATTACAACGCACC-1
+CCTTTCTAGGGCTTCC-1
+CGTGTAAAGGATGGAA-1
+GACGCGTCAATGTAAG-1
+GACTACAAGATCACGG-1
+GGTGCGTGTTAAGACA-1
+TAGCCGGGTTAGATGA-1
+TCCACACCATGAGCGA-1
+TTTATGCCATCCGTGG-1

diff -r 000000000000 -r c8e4d0b9ae8c test-data/barcodes_10x_v3.0.0.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/barcodes_10x_v3.0.0.tsv Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,1107 @@\n+AAACCCAAGGAGAGTA-1\n+AAACGCTTCAGCCCAG-1\n+AAAGAACAGACGACTG-1\n+AAAGAACCAATGGCAG-1\n+AAAGAACGTCTGCAAT-1\n+AAAGGATAGTAGACAT-1\n+AAAGGATCACCGGCTA-1\n+AAAGGATTCAGCTTGA-1\n+AAAGGATTCCGTTTCG-1\n+AAAGGGCTCATGCCCT-1\n+AAAGGGCTCCGTAGGC-1\n+AAAGGTACAACTGCTA-1\n+AAAGTCCAGCGGGTTA-1\n+AAAGTCCCACCAGCCA-1\n+AAAGTGATCGTACACA-1\n+AAATGGAAGCCGCTTG-1\n+AAATGGACAATGCTCA-1\n+AAATGGAGTACCGCGT-1\n+AAATGGATCCTATTTG-1\n+AACAAAGGTGATGAAT-1\n+AACAACCCACGCTATA-1\n+AACAAGAGTTATAGAG-1\n+AACAGGGGTGGGAGAG-1\n+AACCCAACAACTGATC-1\n+AACCCAAGTGGGCTTC-1\n+AACCCAATCTTACCGC-1\n+AACCTGACATCCTATT-1\n+AACCTTTGTTTCGGCG-1\n+AACGAAAAGGTTGGTG-1\n+AACGAAACAGCGTTTA-1\n+AACGAAATCCATTTAC-1\n+AACGGGAGTCGCTCGA-1\n+AACGTCAAGACGCCCT-1\n+AAGAACAAGACCATTC-1\n+AAGAACAAGCCTCAGC-1\n+AAGAACATCTTGCAAG-1\n+AAGACAACACTTCAGA-1\n+AAGACAACAGATCACT-1\n+AAGACAATCCGCGAGT-1\n+AAGCATCAGGTCCGAA-1\n+AAGCATCCAGTCTTCC-1\n+AAGCGTTCACTGATTG-1\n+AAGCGTTTCGCTATTT-1\n+AAGGTAAAGGAAGTAG-1\n+AAGGTAAAGGCCACCT-1\n+AAGGTAAGTCCTTAAG-1\n+AAGTACCAGCGCCTTG-1\n+AAGTACCAGCTCCATA-1\n+AAGTACCCAAAGAACT-1\n+AAGTGAACATCAGCAT-1\n+AAGTGAATCGGAAGGT-1\n+AAGTTCGAGGATACAT-1\n+AAGTTCGGTCAACACT-1\n+AATCGACGTGAGACGT-1\n+AATGAAGCAGTATGAA-1\n+AATGACCGTGTCATCA-1\n+AATGGAACACTCATAG-1\n+AATGGAATCTGATGGT-1\n+AATTCCTTCCATTGGA-1\n+ACAAAGAAGCCTCAAT-1\n+ACAAAGAGTTCCATTT-1\n+ACAACCATCTATCCAT-1\n+ACAACCATCTGCCCTA-1\n+ACAAGCTGTAGGTCAG-1\n+ACACCAAAGAGTCAGC-1\n+ACACGCGGTGTTGCCG-1\n+ACACGCGTCACCTCGT-1\n+ACACGCGTCGCCGTGA-1\n+ACACTGATCACTGATG-1\n+ACACTGATCTTTCCGG-1\n+ACAGAAAAGTATTAGG-1\n+ACAGAAACACCAGCGT-1\n+ACAGCCGTCGCTGTTC-1\n+ACATCCCCACAAATGA-1\n+ACATCCCGTAAGATTG-1\n+ACATCGATCTAAGAAG-1\n+ACATCGATCTGAGAGG-1\n+ACATCGATCTTGGGCG-1\n+ACATGCAGTTGCTTGA-1\n+ACATTTCGTGCCGAAA-1\n+ACATTTCGTTTCTTAC-1\n+ACCACAAAGGCCTTGC-1\n+ACCACAAGTCTGTGGC-1\n+ACCATTTCATTGGGAG-1\n+ACCCAAAGTTGGGAAC-1\n+ACCCTTGGTATCGTAC-1\n+ACCCTTGTCATTTCGT-1\n+ACCTACCCAACGGTAG-1\n+ACCTGAACATGAGAAT-1\n+ACCTGTCTCAAGTCTG-1\n+ACCTGTCTCTCAACGA-1\n+ACGATCAGTCGTTCAA-1\n+ACGATCATCCACGGAC-1\n+ACGATCATCCGTTGGG-1\n+ACGCACGAGAGAGTGA-1\n+ACGGTCGTCACTACGA-1\n+ACGGTTAAGTGCTCAT-1\n+ACGTAACTCATATGGC-1\n+ACGTAACTCTTCGATT-1\n+ACGTACAAGCTGTTCA-1\n+ACGTACACAAAGCTCT-1\n+ACGTACACAGACGATG-1\n+ACGTAGTCACGCCACA-1\n+ACGTAGTCATTAGGAA-1\n+ACGTTCCGTGGGTCAA-1\n+ACTATCTGTGTGTACT-1\n+ACTATGGAGAAATCCA-1\n+ACTCCCAAGGTTGGTG-1\n+ACTCCCATCGTCCTCA-1\n+ACTGATGAGCAGCGAT-1\n+ACTGATGCACCAGCCA-1\n+ACTGTGACAACTCGAT-1\n+ACTTATCTCTAAGGAA-1\n+ACTTCGCAGAACCGCA-1\n+ACTTCGCGTACTCCGG-1\n+ACTTTCAAGTATGACA-1\n+ACTTTCAGTACGCGTC-1\n+AGAAATGTCATTCGTT-1\n+AGAAGCGGTCTAGATC-1\n+AGAAGCGTCTGCGTCT-1\n+AGACAAAGTAGCTTGT-1\n+AGACCATCATTACTCT-1\n+AGACTCATCAACGCTA-1\n+AGACTCATCAGAGCGA-1\n+AGAGAATAGAGGGTCT-1\n+AGAGAATCACCCAACG-1\n+AGAGAGCAGTTGTCGT-1\n+AGAGCAGGTCATAAAG-1\n+AGAGCAGGTTGAGTCT-1\n+AGAGCAGTCGCGCTGA-1\n+AGAGCCCGTCACTCGG-1\n+AGATAGAGTGACACGA-1\n+AGATCGTCAGGACTTT-1\n+AGATGAACAGGCACAA-1\n+AGATGCTGTACGGTTT-1\n+AGATGCTGTGTGGTCC-1\n+AGCATCAGTCGGTGTC-1\n+AGCATCAGTGGTCCGT-1\n+AGCCAATAGTCCCTAA-1\n+AGCCACGCAGGTTCGC-1\n+AGCCACGGTTCCGCGA-1\n+AGCCACGTCCGAGAAG-1\n+AGCCAGCGTAATGCGG-1\n+AGCCAGCGTAGTTAGA-1\n+AGCGTATTCAGTGGGA-1\n+AGCGTCGCATTGACCA-1\n+AGCTACACAGTCGGAA-1\n+AGCTACAGTCGTTTCC-1\n+AGGAAATTCACCATGA-1\n+AGGAATACAAACTCGT-1\n+AGGAATATCATTACGG-1\n+AGGACGAAGACCTTTG-1\n+AGGACGAAGATTAGTG-1\n+AGGACGATCACTGATG-1\n+AGGACGATCCAGTACA-1\n+AGGACTTTCCTACCAC-1\n+AGGATAAAGAACAAGG-1\n+AGGCCACAGGGCCAAT-1\n+AGGCTGCAGGGCTTCC-1\n+AGGCTGCGTGTGTGTT-1\n+AGGGAGTGTGTCGCTG-1\n+AGGGCTCCAATACGCT-1\n+AGGGTCCCAGGACATG-1\n+AGGGTCCCAGTAGTTC-1\n+AGGGTTTCAGCGTGCT-1\n+AGGTAGGAGGAAGTAG-1\n+AGGTAGGCAAAGCGTG-1\n+AGGTCATTCAAGTCGT-1\n+AGGTGTTCATTAAGCC-1\n+AGGTGTTGTCGATTAC-1\n+AGGTGTTTCAATGCAC-1\n+AGGTGTTTCGTTACCC-1\n+AGGTTACAGGTGCGAT-1\n+AGGTTACGTCTGATAC-1\n+AGTAACCCAAGCTCTA-1\n+AGTAACCTCGTTGTAG-1\n+AGTACCAGTGGGTCAA-1\n+AGTACCATCAGCTTGA-1\n+AGTAGCTAGGAGTACC-1\n+AGTAGCTCACTGCTTC-1\n+AGTAGCTCAGGCACTC-1\n+AGTAGCTGTTAGAAAC-1\n+AGTAGTCGTATGACAA-1\n+AGTCAACAGTCATGCT-1\n+AGTCAACGTACACGCC-1\n+AGTCTCCCAACCGTGC-1\n+AGTCTCCGTGAGTCAG-1\n+AGTGCCGCATCTGGGC-1\n+AGTTAGCAGTCAGGGT-1\n+AGTTAGCGTACCATAC-1\n+AGTTAGCGTTCATCGA-1\n+AGTTCCCCAAACAGGC-1\n+AGTTCCCGTTACACTG-1\n+AGTTCGAGTATGCGTT-1\n+ATACCGACACACGGTC-1\n+ATACTTCGTACGACTT-1\n+ATACTTCGTTCGGTAT-1\n+ATACTTCTCAGCTGAT-1\n+ATACTTCTCGCCGTGA-1\n'..b'TCGCTCACAAGATTGA-1\n+TCGCTTGAGAGACAAG-1\n+TCGCTTGAGCATTTGC-1\n+TCGGGACGTAACGGTG-1\n+TCGGGACTCTAGATCG-1\n+TCGGGCATCCGATTAG-1\n+TCGGGCATCTGAACGT-1\n+TCGGGTGCAGTCTGGC-1\n+TCGGTCTTCATTGCTT-1\n+TCGGTCTTCGACATAC-1\n+TCGTAGACAATGAAAC-1\n+TCGTGCTGTGATCATC-1\n+TCTAACTAGGTCCAGA-1\n+TCTACCGCAGTCGTTA-1\n+TCTACCGTCCACGGAC-1\n+TCTATACGTTATCCAG-1\n+TCTATCAGTATGCTAC-1\n+TCTATCAGTTGCCGAC-1\n+TCTCACGAGGCTCCCA-1\n+TCTCCGAAGTCAATCC-1\n+TCTCCGATCTCTCTTC-1\n+TCTCTGGCAAAGCAAT-1\n+TCTGCCAAGTTACGGG-1\n+TCTGCCAGTAACGCGA-1\n+TCTGCCAGTAGATGTA-1\n+TCTGGCTCATCCTGTC-1\n+TCTGTCGAGACTAGAT-1\n+TCTGTCGCACCAGCGT-1\n+TCTTAGTAGGCCTGCT-1\n+TCTTAGTCAACACGAG-1\n+TCTTAGTGTTGCCAAT-1\n+TCTTAGTTCAGAATAG-1\n+TCTTGCGAGATGAAGG-1\n+TCTTGCGCACTACTTT-1\n+TCTTGCGCAGAGGAAA-1\n+TCTTGCGGTCCAGCCA-1\n+TCTTTGAGTGGAGAAA-1\n+TGAACGTCAAATGAAC-1\n+TGAACGTGTAACTAAG-1\n+TGAATGCGTGGACTAG-1\n+TGAATGCTCGACGAGA-1\n+TGAATGCTCGCCGTGA-1\n+TGACAGTTCGAGATGG-1\n+TGACCCTTCTCATTGT-1\n+TGACGCGGTGGCTTAT-1\n+TGACTCCAGTCTCCTC-1\n+TGACTCCCACCATAAC-1\n+TGAGACTAGGCTGAAC-1\n+TGAGCATTCCATTGCC-1\n+TGAGCATTCCTTCACG-1\n+TGAGCATTCGATACTG-1\n+TGAGCATTCTGTCTCG-1\n+TGAGCGCCACTATGTG-1\n+TGAGCGCCAGCATACT-1\n+TGAGCGCTCGTCTAAG-1\n+TGAGGAGTCCATCGTC-1\n+TGAGGGATCAAACGTC-1\n+TGAGGGATCATAAGGA-1\n+TGAGGTTCAAACTAGA-1\n+TGAGGTTCAGGACATG-1\n+TGAGGTTGTAGCTTTG-1\n+TGAGTCACAGAACGCA-1\n+TGAGTCAGTAACCCTA-1\n+TGAGTCAGTCACTCTC-1\n+TGATCAGAGGATTCAA-1\n+TGATGCACAGGGCTTC-1\n+TGATGGTAGACCCGCT-1\n+TGCAGGCAGCGTTCAT-1\n+TGCAGGCCAGGAATAT-1\n+TGCAGTAAGTAGTCCT-1\n+TGCAGTATCCACATAG-1\n+TGCATCCCACCCAACG-1\n+TGCATGAAGCACCCAC-1\n+TGCGACGAGCGACAGT-1\n+TGCGATAAGAATCGCG-1\n+TGCGGCAAGTGGTGAC-1\n+TGCGGCACAAAGACGC-1\n+TGCTCCACAATCTAGC-1\n+TGCTCGTAGACGAGCT-1\n+TGCTCGTTCCCATTTA-1\n+TGCTGAACAGCACAAG-1\n+TGCTTCGCATAGCTGT-1\n+TGCTTGCGTGAACTAA-1\n+TGGAACTAGCGTCTCG-1\n+TGGAGAGCAGTCAGTT-1\n+TGGAGGAAGTAGGAAG-1\n+TGGATCAGTTCTCCCA-1\n+TGGATGTTCACGGGAA-1\n+TGGCGTGGTGGATTTC-1\n+TGGGAAGTCGATTGGT-1\n+TGGGAGAAGCAAGTGC-1\n+TGGGAGAAGTGGTGGT-1\n+TGGGATTAGTCACGAG-1\n+TGGGATTGTACGATGG-1\n+TGGGCGTAGTGGAATT-1\n+TGGGCTGAGAGGGTCT-1\n+TGGGCTGAGCGTTAGG-1\n+TGGGCTGCATCCGATA-1\n+TGGGCTGGTCGCGGTT-1\n+TGGGTTAGTATTGAGA-1\n+TGGGTTATCAGTAGGG-1\n+TGGTACACAAAGGGTC-1\n+TGGTAGTCAGGCATGA-1\n+TGGTAGTCATCACAGT-1\n+TGGTAGTTCCCTCATG-1\n+TGTACAGAGACTCGAG-1\n+TGTACAGAGTGAGTTA-1\n+TGTACAGGTGGATTTC-1\n+TGTAGACTCCATTTAC-1\n+TGTCAGACACTCACTC-1\n+TGTCCACCAACTGGTT-1\n+TGTCCACTCGCTTACC-1\n+TGTCCCAAGCTCCATA-1\n+TGTCCCAAGGTCATAA-1\n+TGTCCCACATACTTTC-1\n+TGTCCCAGTCAGGCAA-1\n+TGTCCCAGTCGGTGTC-1\n+TGTCCTGGTACTTGTG-1\n+TGTCCTGGTTGGCTAT-1\n+TGTGATGAGCGACTGA-1\n+TGTGATGCATTCTCTA-1\n+TGTGCGGGTCGTCGGT-1\n+TGTGCGGTCACATACG-1\n+TGTGGCGTCGTACCTC-1\n+TGTGTGATCTGACAGT-1\n+TGTTCATAGCTGCCTG-1\n+TGTTCATGTCCTGGGT-1\n+TGTTGAGCACAACGAG-1\n+TGTTGAGTCTCGACCT-1\n+TGTTTGTGTGGAAATT-1\n+TTAATCCAGCTACTAC-1\n+TTACAGGGTGATTCTG-1\n+TTACCGCGTCCGAAAG-1\n+TTACGCCCACGTCGTG-1\n+TTACGCCTCAATGCAC-1\n+TTACGTTGTTTACGAC-1\n+TTACGTTTCTCGCTTG-1\n+TTACTGTCATACATCG-1\n+TTACTGTGTAAGAACT-1\n+TTACTGTGTTAAGGGC-1\n+TTAGGGTGTCACATTG-1\n+TTAGTCTCACGTATAC-1\n+TTATTGCCAAACGGCA-1\n+TTATTGCGTACGTAGG-1\n+TTATTGCGTCAACACT-1\n+TTATTGCGTGTCTTCC-1\n+TTCACCGCAGCCCAGT-1\n+TTCACGCGTTAAGTCC-1\n+TTCACGCTCTATCCAT-1\n+TTCAGGAAGATTGGGC-1\n+TTCAGGAGTCTACAAC-1\n+TTCATGTAGGTCATAA-1\n+TTCCACGGTCAACACT-1\n+TTCCGTGCACTCACTC-1\n+TTCCGTGGTTCCAGGC-1\n+TTCCTCTGTACCTGTA-1\n+TTCCTTCAGGTAGTCG-1\n+TTCCTTCAGTAGTCAA-1\n+TTCCTTCGTGACACGA-1\n+TTCGCTGAGGGTTAGC-1\n+TTCGCTGAGGTTCCGC-1\n+TTCGCTGCACTAGTAC-1\n+TTCGCTGTCGGACTGC-1\n+TTCTCTCGTATCGTAC-1\n+TTCTTGAGTCTTGCTC-1\n+TTGACCCGTCTCGGGT-1\n+TTGACCCTCGTAGTGT-1\n+TTGATGGCATAAGATG-1\n+TTGCATTGTGCCTTCT-1\n+TTGCCTGAGAGTGACC-1\n+TTGCCTGAGTGGAAAG-1\n+TTGCCTGGTAGCTGCC-1\n+TTGCTGCCATTGCCGG-1\n+TTGGGATCAACGGGTA-1\n+TTGGGATTCAGGAAGC-1\n+TTGGGATTCTCTCTAA-1\n+TTGGGCGCACGGTGAA-1\n+TTGGGCGGTCGGAAAC-1\n+TTGGGTAGTGCTAGCC-1\n+TTGGGTATCACCGACG-1\n+TTGGTTTCACTGGATT-1\n+TTGTGGATCTAAGAAG-1\n+TTGTGTTGTGTGTCCG-1\n+TTGTTCACACTTGTGA-1\n+TTGTTCACAGTCGCTG-1\n+TTGTTCATCTTTACAC-1\n+TTGTTTGAGGTCGACA-1\n+TTGTTTGTCCAACCGG-1\n+TTTACTGTCACGGGAA-1\n+TTTATGCGTAACATAG-1\n+TTTATGCGTTGATCGT-1\n+TTTCACATCTCAGGCG-1\n+TTTCATGGTGCCTAAT-1\n+TTTCATGTCACTCACC-1\n+TTTCCTCCACAGAGCA-1\n+TTTCCTCTCCTACACC-1\n+TTTCCTCTCTCTTGCG-1\n+TTTGATCTCTTTGGAG-1\n+TTTGGTTAGTAACCTC-1\n+TTTGGTTGTAGAATAC-1\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/cols.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cols.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,101 @@
+Testing testing testing2
+PC1 0 200
+PC2 1 201
+PC3 2 202
+PC4 3 203
+PC5 4 204
+PC6 5 205
+PC7 6 206
+PC8 7 207
+PC9 8 208
+PC10 9 209
+PC11 10 210
+PC12 11 211
+PC13 12 212
+PC14 13 213
+PC15 14 214
+PC16 15 215
+PC17 16 216
+PC18 17 217
+PC19 18 218
+PC20 19 219
+PC21 20 220
+PC22 21 221
+PC23 22 222
+PC24 23 223
+PC25 24 224
+PC26 25 225
+PC27 26 226
+PC28 27 227
+PC29 28 228
+PC30 29 229
+PC31 30 230
+PC32 31 231
+PC33 32 232
+PC34 33 233
+PC35 34 234
+PC36 35 235
+PC37 36 236
+PC38 37 237
+PC39 38 238
+PC40 39 239
+PC41 40 240
+PC42 41 241
+PC43 42 242
+PC44 43 243
+PC45 44 244
+PC46 45 245
+PC47 46 246
+PC48 47 247
+PC49 48 248
+PC50 49 249
+PC51 50 250
+PC52 51 251
+PC53 52 252
+PC54 53 253
+PC55 54 254
+PC56 55 255
+PC57 56 256
+PC58 57 257
+PC59 58 258
+PC60 59 259
+PC61 60 260
+PC62 61 261
+PC63 62 262
+PC64 63 263
+PC65 64 264
+PC66 65 265
+PC67 66 266
+PC68 67 267
+PC69 68 268
+PC70 69 269
+PC71 70 270
+PC72 71 271
+PC73 72 272
+PC74 73 273
+PC75 74 274
+PC76 75 275
+PC77 76 276
+PC78 77 277
+PC79 78 278
+PC80 79 279
+PC81 80 280
+PC82 81 281
+PC83 82 282
+PC84 83 283
+PC85 84 284
+PC86 85 285
+PC87 86 286
+PC88 87 287
+PC89 88 288
+PC90 89 289
+PC91 90 290
+PC92 91 291
+PC93 92 292
+PC94 93 293
+PC95 94 294
+PC96 95 295
+PC97 96 296
+PC98 97 297
+PC99 98 298
+PC100 99 299

diff -r 000000000000 -r c8e4d0b9ae8c test-data/converted.loom.test

Binary file test-data/converted.loom.test has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.X.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.X.tabular Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,640 @@\n+0.8032\t-0.0005\t-1e-04\t0.0003\t0.0013\t0.0011\t0.7997\t0.8017\t0.0006\t0.0009\t0.0002\n+0.7239\t0.0016\t-0.0003\t-0.001\t0.0011\t0.0022\t0.8195\t0.7256\t0.0784\t0.0077\t0.0941\n+0.6578\t0.0013\t-0.001\t-0.0027\t0.0025\t0.0011\t0.8358\t0.6624\t0.1105\t0.0239\t0.1497\n+0.5972\t0.0038\t-0.0009\t-0.0064\t0.0007\t-0.0036\t0.8534\t0.5992\t0.1271\t0.0311\t0.1702\n+0.5396\t0.0071\t-0.0029\t-0.0063\t0.0011\t-0.007\t0.8656\t0.547\t0.1385\t0.0379\t0.1752\n+0.4897\t0.011\t-0.0023\t-0.0061\t0.0013\t-0.0034\t0.8759\t0.4998\t0.1496\t0.0459\t0.1747\n+0.4449\t0.0153\t-0.002\t-0.0089\t0.0003\t-0.0057\t0.8854\t0.4516\t0.1569\t0.0489\t0.1727\n+0.4078\t0.0131\t-0.0013\t-0.0121\t-0.0024\t-0.0076\t0.8986\t0.4096\t0.1666\t0.0556\t0.1661\n+0.3719\t0.0156\t0.0021\t-0.0105\t-0.0007\t-0.0066\t0.9062\t0.3742\t0.1731\t0.0631\t0.1623\n+0.3424\t0.0175\t0.0027\t-0.0083\t-0.0045\t-0.0017\t0.9135\t0.3433\t0.1781\t0.0698\t0.1565\n+0.3143\t0.0179\t-1e-04\t-0.01\t-0.0042\t-0.0039\t0.9191\t0.3175\t0.1891\t0.0785\t0.1473\n+0.29\t0.0215\t-0.0007\t-0.0069\t-0.0034\t-0.0018\t0.928\t0.2934\t0.1988\t0.0844\t0.1371\n+0.2674\t0.0255\t-0.002\t-0.0074\t-0.003\t-0.0013\t0.9373\t0.2749\t0.2103\t0.0942\t0.1301\n+0.2519\t0.0284\t-0.0011\t-0.0029\t-0.0037\t-0.0022\t0.9424\t0.26\t0.2211\t0.102\t0.1193\n+0.2353\t0.0371\t0.0009\t-0.0017\t-0.0018\t0.0\t0.9492\t0.2439\t0.2336\t0.1114\t0.1089\n+0.221\t0.0413\t0.0009\t-0.0028\t0.0019\t0.0025\t0.9503\t0.2353\t0.2473\t0.1219\t0.1018\n+0.2077\t0.0423\t0.0003\t-0.0016\t0.0047\t0.0057\t0.9527\t0.2248\t0.2645\t0.1389\t0.0915\n+0.1986\t0.0464\t-0.0005\t0.0012\t0.0025\t0.0081\t0.9551\t0.2187\t0.2866\t0.1572\t0.0846\n+0.1914\t0.0531\t0.002\t0.0035\t0.0022\t0.0143\t0.9573\t0.2117\t0.3103\t0.1756\t0.0761\n+0.1818\t0.0613\t0.0037\t0.0063\t0.0018\t0.0179\t0.9579\t0.2034\t0.3332\t0.2\t0.0722\n+0.1734\t0.0666\t0.0069\t0.0066\t0.0053\t0.0218\t0.9585\t0.2051\t0.3505\t0.2227\t0.0672\n+0.172\t0.0715\t0.0052\t0.0112\t0.0066\t0.026\t0.9586\t0.2025\t0.3742\t0.2433\t0.0567\n+0.1638\t0.0762\t0.0084\t0.0177\t0.0096\t0.0289\t0.9655\t0.1981\t0.3971\t0.2726\t0.0492\n+0.1556\t0.0826\t0.009\t0.0151\t0.0125\t0.0374\t0.9661\t0.1974\t0.4208\t0.2965\t0.0461\n+0.1515\t0.0831\t0.0117\t0.0169\t0.0101\t0.0385\t0.9724\t0.1936\t0.445\t0.3236\t0.0395\n+0.1475\t0.0821\t0.0123\t0.0174\t0.015\t0.0429\t0.9757\t0.1898\t0.4697\t0.3503\t0.0346\n+0.148\t0.0842\t0.0137\t0.0186\t0.0133\t0.0468\t0.9751\t0.19\t0.4953\t0.3773\t0.0297\n+0.144\t0.087\t0.0101\t0.0184\t0.0152\t0.0544\t0.9734\t0.1893\t0.5165\t0.4037\t0.0264\n+0.1463\t0.0892\t0.009\t0.0231\t0.0156\t0.0551\t0.976\t0.1906\t0.532\t0.4323\t0.0203\n+0.1413\t0.0919\t0.0085\t0.0255\t0.0193\t0.0594\t0.9795\t0.1887\t0.5534\t0.4581\t0.0198\n+0.1415\t0.0919\t0.0067\t0.0273\t0.0218\t0.0629\t0.9853\t0.1891\t0.568\t0.4826\t0.0224\n+0.1385\t0.0952\t0.0072\t0.0306\t0.0209\t0.0687\t0.9866\t0.1904\t0.5856\t0.5025\t0.0213\n+0.1386\t0.0993\t0.0075\t0.0265\t0.0268\t0.073\t0.9878\t0.1916\t0.6031\t0.5224\t0.0198\n+0.1337\t0.1011\t0.0061\t0.0237\t0.0242\t0.0751\t0.9897\t0.1885\t0.619\t0.5403\t0.0177\n+0.1318\t0.1009\t0.0046\t0.0278\t0.0267\t0.0793\t0.9925\t0.1892\t0.6339\t0.5546\t0.0173\n+0.1295\t0.1035\t0.0074\t0.03\t0.0266\t0.0817\t0.9967\t0.1855\t0.6451\t0.5754\t0.0171\n+0.1284\t0.1001\t0.0063\t0.0299\t0.0293\t0.0868\t0.9949\t0.1841\t0.6546\t0.5917\t0.0112\n+0.1246\t0.1018\t0.0112\t0.0354\t0.0264\t0.0901\t0.9949\t0.1886\t0.6651\t0.6068\t0.0119\n+0.123\t0.1057\t0.0079\t0.0353\t0.03\t0.0972\t0.989\t0.1858\t0.6758\t0.621\t0.0118\n+0.1184\t0.104\t0.0087\t0.0357\t0.0303\t0.0996\t0.9889\t0.1861\t0.6811\t0.63\t0.0092\n+0.1191\t0.1036\t0.0092\t0.0322\t0.0303\t0.1016\t0.9881\t0.1853\t0.6913\t0.6417\t0.0084\n+0.1198\t0.1035\t0.0052\t0.0332\t0.0306\t0.1001\t0.9874\t0.187\t0.7005\t0.6513\t0.0069\n+0.1171\t0.1055\t0.0055\t0.0339\t0.0303\t0.1041\t0.9877\t0.1889\t0.7091\t0.659\t0.0077\n+0.1157\t0.1066\t0.0084\t0.0349\t0.0303\t0.1031\t0.9882\t0.1905\t0.7142\t0.6705\t0.0064\n+0.116\t0.1097\t0.0087\t0.0341\t0.0321\t0.1078\t0.9902\t0.1886\t0.7201\t0.6802\t0.0046\n+0.1141\t0.1096\t0.0116\t0.0362\t0.0363\t0.1088\t0.9904\t0.1884\t0.7225\t0.6883\t0.0035\n+0.1185\t0.1081\t0.0096\t0.0351\t0.0363\t0.1055\t0.9888\t0.1909\t0.7314\t0.6989\t0.0051\n+0.1174\t0.1046\t0.0098\t0.037\t0.0369\t0.1061\t0.989\t0.1883\t0.7348\t0.7054\t0.0022\n+0.1135\t0.1022\t0.011\t0.0408\t0.033\t0.1091\t0.9909\t0.1905\t0.7427\t0.7131\t-0.0011\n+0.1121\t0.1003\t0.0074\t0.0365\t0.0365\t0.1053\t0.9905\t0.1945\t0.7472\t0.7213\t-0.0017\n+0.1081\t0.1033\t0.0071\t0.0346\t0.0347\t0.1052\t0.9898\t0.1982\t0.751\t0.7302\t-0.0023\n+0.1103\t0.1'..b'\t-0.0048\t-0.0074\t-0.0052\t-0.0027\t-0.0005\t0.9988\t1.0052\t0.016\t0.005\t0.9303\n+0.0031\t-0.0044\t-0.0053\t0.0004\t-0.002\t0.0006\t0.999\t1.0037\t0.017\t0.006\t0.9304\n+0.004\t-0.0049\t-0.0044\t0.002\t-0.0009\t-0.0012\t1.001\t1.0015\t0.0203\t0.0063\t0.9264\n+0.0024\t-0.0035\t-0.0028\t0.0016\t-0.0004\t-0.0013\t1.0027\t1.0006\t0.0214\t0.0027\t0.9278\n+0.0036\t-0.0006\t-0.0018\t0.0002\t-0.001\t0.0011\t1.0038\t1.0032\t0.0185\t0.0014\t0.9326\n+0.0036\t-0.0017\t-0.0026\t0.0049\t-0.0051\t0.0024\t1.0048\t1.0039\t0.0179\t-0.0011\t0.9367\n+0.0036\t-0.0032\t-0.0034\t0.0032\t-0.0023\t0.0036\t1.0062\t1.0058\t0.0195\t-0.0015\t0.9401\n+0.0018\t-0.0049\t1e-04\t0.001\t0.0\t0.0044\t1.0066\t1.0055\t0.0204\t-0.0021\t0.9432\n+-0.0\t-0.0055\t-0.0014\t-0.0013\t-0.0025\t0.002\t1.0021\t1.0051\t0.0189\t-0.0044\t0.9453\n+-0.0035\t-0.004\t-0.0032\t-0.0007\t-0.0018\t-0.0\t1.0024\t1.0047\t0.0187\t-0.0066\t0.9389\n+-0.0071\t-0.0056\t-0.0025\t0.0002\t-0.002\t-0.004\t1.0032\t1.0047\t0.0155\t-0.0102\t0.9278\n+-0.0053\t-0.0073\t-0.0031\t0.0033\t0.0006\t-0.0011\t1.0012\t1.0025\t0.0137\t-0.0045\t0.9215\n+-0.001\t-0.0068\t-0.0031\t0.0045\t-0.0015\t-0.0032\t0.9998\t1.0044\t0.0113\t-0.0052\t0.9236\n+-0.0017\t-0.0023\t-0.0046\t0.0052\t0.0033\t-0.0023\t0.9987\t1.0078\t0.0105\t-0.007\t0.9217\n+-0.0025\t0.0006\t-1e-04\t0.0069\t0.0048\t-0.0008\t0.9951\t1.005\t0.0144\t-0.0072\t0.9174\n+-0.0014\t0.0029\t-0.0026\t0.0083\t0.003\t0.0\t0.9967\t1.0052\t0.013\t-0.0051\t0.9144\n+1e-04\t0.0038\t-0.0015\t0.0065\t0.0026\t0.0015\t0.9945\t1.0036\t0.0144\t-0.003\t0.9207\n+0.0019\t0.002\t0.0014\t0.0059\t0.0048\t0.0008\t0.9966\t1.007\t0.0151\t-0.0008\t0.9236\n+0.0013\t0.0018\t-0.0016\t0.0077\t0.0045\t-0.0\t0.9966\t1.0074\t0.0135\t-0.0022\t0.9318\n+0.0014\t-0.0\t-0.0017\t0.006\t0.0053\t0.0002\t0.989\t1.0061\t0.014\t-0.0034\t0.9351\n+0.0012\t0.0023\t0.0008\t0.0046\t0.0053\t0.0032\t0.9867\t1.0054\t0.0131\t-0.0067\t0.938\n+0.0045\t0.0011\t0.0021\t0.0024\t0.007\t0.0006\t0.9872\t1.004\t0.0125\t-0.0076\t0.9325\n+0.0077\t0.0017\t0.0034\t0.0055\t0.0049\t-0.001\t0.9914\t1.0053\t0.0113\t-0.0099\t0.92\n+0.0061\t-0.0006\t0.0036\t0.0096\t0.0063\t-0.0023\t0.9914\t1.0067\t0.0126\t-0.0062\t0.9187\n+0.0046\t-0.0029\t0.0047\t0.0083\t0.0047\t-0.0058\t0.9915\t1.0034\t0.0144\t-0.0047\t0.9198\n+0.0025\t-0.002\t0.0026\t0.0064\t0.0047\t-0.0078\t0.9926\t1.003\t0.0153\t-0.0054\t0.9198\n+-0.0023\t-0.0027\t0.0013\t0.0059\t0.0014\t-0.0077\t0.9938\t1.0012\t0.0143\t-0.0046\t0.9246\n+0.0004\t-0.0045\t0.0011\t0.0046\t0.0035\t-0.0082\t0.9927\t1.0007\t0.0133\t-0.0049\t0.9222\n+-0.0006\t-0.0044\t0.001\t0.0071\t0.0049\t-0.0112\t0.9953\t1.0034\t0.0123\t-0.0061\t0.9246\n+-0.0025\t-0.0051\t-0.0003\t0.0076\t0.003\t-0.0067\t0.9932\t1.0029\t0.014\t-0.0055\t0.9267\n+-0.0038\t-0.0068\t0.0007\t0.0066\t-0.0003\t-0.0066\t0.9921\t1.0051\t0.013\t-0.0046\t0.9243\n+-0.0023\t-0.0119\t0.0046\t0.0063\t0.0037\t-0.0059\t0.9913\t1.004\t0.0146\t-0.0022\t0.9326\n+-0.0034\t-0.0117\t0.002\t0.0028\t0.003\t-0.0026\t0.9923\t1.0021\t0.0158\t-0.0021\t0.9364\n+-0.0047\t-0.0134\t0.0031\t0.0018\t0.0046\t-0.0006\t0.9908\t0.9996\t0.0136\t-0.0015\t0.9376\n+-0.0035\t-0.0163\t0.0017\t0.0016\t0.0035\t-0.0008\t0.9938\t0.9976\t0.013\t0.0009\t0.9446\n+-0.002\t-0.0149\t-0.0009\t0.0021\t0.0013\t-0.0018\t0.9938\t0.9941\t0.015\t-0.0055\t0.9497\n+-0.0036\t-0.0151\t0.0024\t-0.0013\t0.0012\t0.0004\t0.9976\t0.9917\t0.0123\t-0.0032\t0.9441\n+-0.0032\t-0.0116\t0.001\t0.0008\t-0.0024\t0.0006\t1.001\t0.9934\t0.0108\t-0.0065\t0.9492\n+-0.0023\t-0.0083\t0.0027\t0.0005\t0.0006\t-0.0014\t1.0014\t0.9927\t0.0136\t-0.0067\t0.94\n+-0.001\t-0.006\t0.0022\t0.0034\t-0.0011\t-0.0018\t0.9997\t0.9933\t0.0132\t-0.0049\t0.9404\n+-0.0024\t-0.0073\t-0.0011\t0.0036\t-0.0024\t-0.0008\t0.9975\t0.9958\t0.0165\t-0.0064\t0.9398\n+0.0007\t-0.0051\t0.0008\t0.0036\t-0.003\t-0.0012\t1.0006\t0.9932\t0.0161\t-0.0076\t0.9372\n+-0.0008\t-0.0076\t0.0025\t0.0028\t-0.0048\t-0.0003\t1.0016\t0.992\t0.015\t-0.0095\t0.9325\n+-0.0029\t-0.0045\t0.0027\t0.0051\t-0.0046\t-0.0039\t0.9989\t0.9913\t0.0177\t-0.0087\t0.9232\n+0.0002\t-0.002\t0.0061\t0.0048\t-0.0043\t-0.0016\t0.9989\t0.9911\t0.0152\t-0.0072\t0.916\n+-0.001\t-0.002\t0.0015\t0.0029\t-0.0055\t-0.0004\t0.999\t0.9915\t0.0107\t-0.0076\t0.9119\n+0.0028\t-0.003\t0.0009\t0.0049\t-0.0073\t0.002\t1.0\t0.9946\t0.0127\t-0.0082\t0.9095\n+0.003\t-0.0035\t0.0008\t0.0052\t-0.0066\t1e-04\t1.0014\t0.9977\t0.0125\t-0.0046\t0.9069\n+0.0063\t-0.0023\t-0.0005\t0.0081\t-0.0046\t-0.0006\t0.9983\t0.997\t0.0109\t-0.003\t0.9118\n+0.0049\t0.0002\t-0.0013\t0.0054\t-0.0036\t0.0009\t1.0011\t0.9967\t0.0066\t-0.0033\t0.9177\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.loom

Binary file test-data/export.krumsiek11.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.obs.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.obs.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,641 @@
+index cell_type
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Mo
+81 Mo
+82 Mo
+83 Mo
+84 Mo
+85 Mo
+86 Mo
+87 Mo
+88 Mo
+89 Mo
+90 Mo
+91 Mo
+92 Mo
+93 Mo
+94 Mo
+95 Mo
+96 Mo
+97 Mo
+98 Mo
+99 Mo
+100 Mo
+101 Mo
+102 Mo
+103 Mo
+104 Mo
+105 Mo
+106 Mo
+107 Mo
+108 Mo
+109 Mo
+110 Mo
+111 Mo
+112 Mo
+113 Mo
+114 Mo
+115 Mo
+116 Mo
+117 Mo
+118 Mo
+119 Mo
+120 Mo
+121 Mo
+122 Mo
+123 Mo
+124 Mo
+125 Mo
+126 Mo
+127 Mo
+128 Mo
+129 Mo
+130 Mo
+131 Mo
+132 Mo
+133 Mo
+134 Mo
+135 Mo
+136 Mo
+137 Mo
+138 Mo
+139 Mo
+140 Mo
+141 Mo
+142 Mo
+143 Mo
+144 Mo
+145 Mo
+146 Mo
+147 Mo
+148 Mo
+149 Mo
+150 Mo
+151 Mo
+152 Mo
+153 Mo
+154 Mo
+155 Mo
+156 Mo
+157 Mo
+158 Mo
+159 Mo
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Ery
+81 Ery
+82 Ery
+83 Ery
+84 Ery
+85 Ery
+86 Ery
+87 Ery
+88 Ery
+89 Ery
+90 Ery
+91 Ery
+92 Ery
+93 Ery
+94 Ery
+95 Ery
+96 Ery
+97 Ery
+98 Ery
+99 Ery
+100 Ery
+101 Ery
+102 Ery
+103 Ery
+104 Ery
+105 Ery
+106 Ery
+107 Ery
+108 Ery
+109 Ery
+110 Ery
+111 Ery
+112 Ery
+113 Ery
+114 Ery
+115 Ery
+116 Ery
+117 Ery
+118 Ery
+119 Ery
+120 Ery
+121 Ery
+122 Ery
+123 Ery
+124 Ery
+125 Ery
+126 Ery
+127 Ery
+128 Ery
+129 Ery
+130 Ery
+131 Ery
+132 Ery
+133 Ery
+134 Ery
+135 Ery
+136 Ery
+137 Ery
+138 Ery
+139 Ery
+140 Ery
+141 Ery
+142 Ery
+143 Ery
+144 Ery
+145 Ery
+146 Ery
+147 Ery
+148 Ery
+149 Ery
+150 Ery
+151 Ery
+152 Ery
+153 Ery
+154 Ery
+155 Ery
+156 Ery
+157 Ery
+158 Ery
+159 Ery
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Mk
+81 Mk
+82 Mk
+83 Mk
+84 Mk
+85 Mk
+86 Mk
+87 Mk
+88 Mk
+89 Mk
+90 Mk
+91 Mk
+92 Mk
+93 Mk
+94 Mk
+95 Mk
+96 Mk
+97 Mk
+98 Mk
+99 Mk
+100 Mk
+101 Mk
+102 Mk
+103 Mk
+104 Mk
+105 Mk
+106 Mk
+107 Mk
+108 Mk
+109 Mk
+110 Mk
+111 Mk
+112 Mk
+113 Mk
+114 Mk
+115 Mk
+116 Mk
+117 Mk
+118 Mk
+119 Mk
+120 Mk
+121 Mk
+122 Mk
+123 Mk
+124 Mk
+125 Mk
+126 Mk
+127 Mk
+128 Mk
+129 Mk
+130 Mk
+131 Mk
+132 Mk
+133 Mk
+134 Mk
+135 Mk
+136 Mk
+137 Mk
+138 Mk
+139 Mk
+140 Mk
+141 Mk
+142 Mk
+143 Mk
+144 Mk
+145 Mk
+146 Mk
+147 Mk
+148 Mk
+149 Mk
+150 Mk
+151 Mk
+152 Mk
+153 Mk
+154 Mk
+155 Mk
+156 Mk
+157 Mk
+158 Mk
+159 Mk
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Neu
+81 Neu
+82 Neu
+83 Neu
+84 Neu
+85 Neu
+86 Neu
+87 Neu
+88 Neu
+89 Neu
+90 Neu
+91 Neu
+92 Neu
+93 Neu
+94 Neu
+95 Neu
+96 Neu
+97 Neu
+98 Neu
+99 Neu
+100 Neu
+101 Neu
+102 Neu
+103 Neu
+104 Neu
+105 Neu
+106 Neu
+107 Neu
+108 Neu
+109 Neu
+110 Neu
+111 Neu
+112 Neu
+113 Neu
+114 Neu
+115 Neu
+116 Neu
+117 Neu
+118 Neu
+119 Neu
+120 Neu
+121 Neu
+122 Neu
+123 Neu
+124 Neu
+125 Neu
+126 Neu
+127 Neu
+128 Neu
+129 Neu
+130 Neu
+131 Neu
+132 Neu
+133 Neu
+134 Neu
+135 Neu
+136 Neu
+137 Neu
+138 Neu
+139 Neu
+140 Neu
+141 Neu
+142 Neu
+143 Neu
+144 Neu
+145 Neu
+146 Neu
+147 Neu
+148 Neu
+149 Neu
+150 Neu
+151 Neu
+152 Neu
+153 Neu
+154 Neu
+155 Neu
+156 Neu
+157 Neu
+158 Neu
+159 Neu

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.obsm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.obsm.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,641 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.var.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.var.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+index
+Gata2
+Gata1
+Fog1
+EKLF
+Fli1
+SCL
+Cebpa
+Pu.1
+cJun
+EgrNab
+Gfi1

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export.krumsiek11.varm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.varm.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+
+
+
+
+
+
+
+
+
+
+
+

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export_csv_X.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_X.csv Mon Jan 06 13:43:38 2020 -0500

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export_csv_obs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_obs.csv Mon Jan 06 13:43:38 2020 -0500

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export_csv_obsm.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_obsm.csv Mon Jan 06 13:43:38 2020 -0500

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export_csv_var.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_var.csv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+index
+Gata2
+Gata1
+Fog1
+EKLF
+Fli1
+SCL
+Cebpa
+Pu.1
+cJun
+EgrNab
+Gfi1

diff -r 000000000000 -r c8e4d0b9ae8c test-data/export_csv_varm.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_varm.csv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+
+
+
+
+
+
+
+
+
+
+
+

diff -r 000000000000 -r c8e4d0b9ae8c test-data/features_10x_v3.0.0.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features_10x_v3.0.0.tsv Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,507 @@\n+ENSG00000279493\tCH507-9B2.2\tGene Expression\n+ENSG00000277117\tCH507-9B2.1\tGene Expression\n+ENSG00000279687\tCH507-9B2.8\tGene Expression\n+ENSG00000280071\tCH507-9B2.3\tGene Expression\n+ENSG00000276612\tCH507-9B2.4\tGene Expression\n+ENSG00000275464\tCH507-9B2.5\tGene Expression\n+ENSG00000280433\tCH507-9B2.9\tGene Expression\n+ENSG00000279669\tRP11-717F1.1\tGene Expression\n+ENSG00000279094\tCH507-24F1.1\tGene Expression\n+ENSG00000274333\tRP11-717F1.2\tGene Expression\n+ENSG00000279784\tCH507-39O4.1\tGene Expression\n+ENSG00000279064\tCH507-39O4.2\tGene Expression\n+ENSG00000280191\tCH507-42P11.5\tGene Expression\n+ENSG00000280095\tCH507-42P11.7\tGene Expression\n+ENSG00000280179\tCH507-42P11.6\tGene Expression\n+ENSG00000275993\tCH507-42P11.8\tGene Expression\n+ENSG00000275496\tCH507-24F1.2\tGene Expression\n+ENSG00000278903\tCH507-145C22.1\tGene Expression\n+ENSG00000274276\tCBSL\tGene Expression\n+ENSG00000275895\tU2AF1L5\tGene Expression\n+ENSG00000278927\tCH507-152C13.6\tGene Expression\n+ENSG00000276076\tCH507-152C13.3\tGene Expression\n+ENSG00000280145\tCH507-154B10.1\tGene Expression\n+ENSG00000278878\tCH507-145C22.3\tGene Expression\n+ENSG00000280164\tCH507-254M2.3\tGene Expression\n+ENSG00000279998\tCH507-210P18.1\tGene Expression\n+ENSG00000278955\tCH507-210P18.4\tGene Expression\n+ENSG00000279751\tCH507-210P18.5\tGene Expression\n+ENSG00000280018\tCH507-154B10.2\tGene Expression\n+ENSG00000279313\tCH507-145C22.4\tGene Expression\n+ENSG00000278884\tCH507-236L23.1\tGene Expression\n+ENSG00000277067\tCH507-254M2.1\tGene Expression\n+ENSG00000276077\tCH507-254M2.2\tGene Expression\n+ENSG00000277991\tCH507-338C24.1\tGene Expression\n+ENSG00000273590\tSMIM11B\tGene Expression\n+ENSG00000278961\tCH507-396I9.3\tGene Expression\n+ENSG00000276289\tKCNE1B\tGene Expression\n+ENSG00000278996\tCH507-513H4.1\tGene Expression\n+ENSG00000280800\tCH507-513H4.6\tGene Expression\n+ENSG00000281383\tCH507-513H4.5\tGene Expression\n+ENSG00000280441\tCH507-528H12.1\tGene Expression\n+ENSG00000280614\tCH507-513H4.4\tGene Expression\n+ENSG00000281181\tCH507-513H4.3\tGene Expression\n+ENSG00000279579\tbP-2189O9.3\tGene Expression\n+ENSG00000279501\tbP-2171C21.3\tGene Expression\n+ENSG00000278932\tbP-21264C1.2\tGene Expression\n+ENSG00000280081\tMGC39584\tGene Expression\n+ENSG00000279321\tRP11-555K2.4\tGene Expression\n+ENSG00000279851\tCH507-216K13.2\tGene Expression\n+ENSG00000277693\tAP003900.6\tGene Expression\n+ENSG00000274391\tTPTE\tGene Expression\n+ENSG00000277282\tIGHV1OR21-1\tGene Expression\n+ENSG00000229306\tAP001464.4\tGene Expression\n+ENSG00000280108\tAJ239318.1\tGene Expression\n+ENSG00000228159\tAP001465.5\tGene Expression\n+ENSG00000166351\tPOTED\tGene Expression\n+ENSG00000224922\tAL050303.7\tGene Expression\n+ENSG00000224905\tAP001347.6\tGene Expression\n+ENSG00000188992\tLIPI\tGene Expression\n+ENSG00000185272\tRBM11\tGene Expression\n+ENSG00000155304\tHSPA13\tGene Expression\n+ENSG00000155307\tSAMSN1\tGene Expression\n+ENSG00000223662\tSAMSN1-AS1\tGene Expression\n+ENSG00000243440\tAF165138.7\tGene Expression\n+ENSG00000232884\tAF127936.3\tGene Expression\n+ENSG00000226751\tAF127936.5\tGene Expression\n+ENSG00000235609\tAF127936.9\tGene Expression\n+ENSG00000281903\tAF127936.7\tGene Expression\n+ENSG00000235277\tAF127577.8\tGene Expression\n+ENSG00000180530\tNRIP1\tGene Expression\n+ENSG00000229047\tAF127577.10\tGene Expression\n+ENSG00000231201\tAF127577.11\tGene Expression\n+ENSG00000236471\tAF127577.12\tGene Expression\n+ENSG00000229425\tAJ006998.2\tGene Expression\n+ENSG00000224247\tAJ009632.3\tGene Expression\n+ENSG00000155313\tUSP25\tGene Expression\n+ENSG00000215386\tMIR99AHG\tGene Expression\n+ENSG00000270071\tAP001172.2\tGene Expression\n+ENSG00000270139\tAP001172.3\tGene Expression\n+ENSG00000269950\tAP000962.2\tGene Expression\n+ENSG00000228798\tAP000473.5\tGene Expression\n+ENSG00000270093\tAP000473.8\tGene Expression\n+ENSG00000237735\tAP000473.6\tGene Expression\n+ENSG00000232886\tAF212831.2\tGene Expression\n+ENSG00000232560\tLINC01549\tGene Expression\n+ENSG00000154639\tCXADR\tGene Expression\n+ENSG00000154640\tBTG3\tGene Expression\n+ENSG00000226956\tAP000432.2\tGene Expression\n+ENSG00000240770\tC21orf91-OT1\tGene Expression\n+ENSG00000'..b'ssion\n+ENSG00000237604\tAP001056.1\tGene Expression\n+ENSG00000232124\tAP001057.1\tGene Expression\n+ENSG00000232698\tAP001058.3\tGene Expression\n+ENSG00000160223\tICOSLG\tGene Expression\n+ENSG00000278158\tAP001059.6\tGene Expression\n+ENSG00000275799\tAP001059.7\tGene Expression\n+ENSG00000142182\tDNMT3L\tGene Expression\n+ENSG00000232010\tAP001059.5\tGene Expression\n+ENSG00000160224\tAIRE\tGene Expression\n+ENSG00000141959\tPFKL\tGene Expression\n+ENSG00000160226\tC21orf2\tGene Expression\n+ENSG00000184441\tAP001062.7\tGene Expression\n+ENSG00000232969\tAP001062.9\tGene Expression\n+ENSG00000260256\tAP001063.1\tGene Expression\n+ENSG00000142185\tTRPM2\tGene Expression\n+ENSG00000230061\tTRPM2-AS\tGene Expression\n+ENSG00000229356\tLRRC3-AS1\tGene Expression\n+ENSG00000160233\tLRRC3\tGene Expression\n+ENSG00000274225\tKB-68A7.1\tGene Expression\n+ENSG00000228709\tAP001065.15\tGene Expression\n+ENSG00000277352\tKB-68A7.2\tGene Expression\n+ENSG00000175894\tTSPEAR\tGene Expression\n+ENSG00000235890\tTSPEAR-AS1\tGene Expression\n+ENSG00000182912\tTSPEAR-AS2\tGene Expression\n+ENSG00000215455\tKRTAP10-1\tGene Expression\n+ENSG00000205445\tKRTAP10-2\tGene Expression\n+ENSG00000212935\tKRTAP10-3\tGene Expression\n+ENSG00000215454\tKRTAP10-4\tGene Expression\n+ENSG00000241123\tKRTAP10-5\tGene Expression\n+ENSG00000188155\tKRTAP10-6\tGene Expression\n+ENSG00000272804\tKRTAP10-7\tGene Expression\n+ENSG00000187766\tKRTAP10-8\tGene Expression\n+ENSG00000221837\tKRTAP10-9\tGene Expression\n+ENSG00000221859\tKRTAP10-10\tGene Expression\n+ENSG00000243489\tKRTAP10-11\tGene Expression\n+ENSG00000205439\tKRTAP12-3\tGene Expression\n+ENSG00000212933\tKRTAP12-4\tGene Expression\n+ENSG00000221864\tKRTAP12-2\tGene Expression\n+ENSG00000187175\tKRTAP12-1\tGene Expression\n+ENSG00000189169\tKRTAP10-12\tGene Expression\n+ENSG00000184787\tUBE2G2\tGene Expression\n+ENSG00000236519\tLINC01424\tGene Expression\n+ENSG00000184900\tSUMO3\tGene Expression\n+ENSG00000183255\tPTTG1IP\tGene Expression\n+ENSG00000160255\tITGB2\tGene Expression\n+ENSG00000227039\tITGB2-AS1\tGene Expression\n+ENSG00000183250\tLINC01547\tGene Expression\n+ENSG00000272825\tLL21NC02-1C16.2\tGene Expression\n+ENSG00000160256\tFAM207A\tGene Expression\n+ENSG00000276529\tAP001505.10\tGene Expression\n+ENSG00000234880\tLINC00163\tGene Expression\n+ENSG00000261706\tLINC00165\tGene Expression\n+ENSG00000275874\tLINC00162\tGene Expression\n+ENSG00000197381\tADARB1\tGene Expression\n+ENSG00000267857\tRP5-1023B21.1\tGene Expression\n+ENSG00000182586\tLINC00334\tGene Expression\n+ENSG00000186866\tPOFUT2\tGene Expression\n+ENSG00000223768\tLINC00205\tGene Expression\n+ENSG00000184274\tLINC00315\tGene Expression\n+ENSG00000229382\tBX322557.13\tGene Expression\n+ENSG00000237664\tLINC00316\tGene Expression\n+ENSG00000228355\tBX322559.3\tGene Expression\n+ENSG00000273796\tLL21NC02-21A1.1\tGene Expression\n+ENSG00000182871\tCOL18A1\tGene Expression\n+ENSG00000224574\tCOL18A1-AS2\tGene Expression\n+ENSG00000183535\tCOL18A1-AS1\tGene Expression\n+ENSG00000173638\tSLC19A1\tGene Expression\n+ENSG00000233922\tAL133493.2\tGene Expression\n+ENSG00000183570\tPCBP3\tGene Expression\n+ENSG00000275139\tRP1-101D8.1\tGene Expression\n+ENSG00000205424\tAL592528.1\tGene Expression\n+ENSG00000274248\tAJ011932.1\tGene Expression\n+ENSG00000142156\tCOL6A1\tGene Expression\n+ENSG00000224413\tAP001476.2\tGene Expression\n+ENSG00000228235\tAP001476.4\tGene Expression\n+ENSG00000226115\tAP001476.3\tGene Expression\n+ENSG00000227438\tAP001471.1\tGene Expression\n+ENSG00000142173\tCOL6A2\tGene Expression\n+ENSG00000160282\tFTCD\tGene Expression\n+ENSG00000237338\tFTCD-AS1\tGene Expression\n+ENSG00000160284\tSPATC1L\tGene Expression\n+ENSG00000228404\tAP001468.58\tGene Expression\n+ENSG00000160285\tLSS\tGene Expression\n+ENSG00000223901\tAP001469.5\tGene Expression\n+ENSG00000215424\tMCM3AP-AS1\tGene Expression\n+ENSG00000160294\tMCM3AP\tGene Expression\n+ENSG00000228137\tAP001469.7\tGene Expression\n+ENSG00000239415\tAP001469.9\tGene Expression\n+ENSG00000182362\tYBEY\tGene Expression\n+ENSG00000160298\tC21orf58\tGene Expression\n+ENSG00000160299\tPCNT\tGene Expression\n+ENSG00000160305\tDIP2A\tGene Expression\n+ENSG00000160307\tS100B\tGene Expression\n+ENSG00000160310\tPRMT2\tGene Expression\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/finallayer.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/finallayer.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,9 @@
+900.0 901.0 902.0 903.0 904.0 905.0 906.0 907.0 908.0 909.0 910.0 911.0 912.0 913.0 914.0 915.0 916.0 917.0 918.0 919.0 920.0 921.0 922.0 923.0 924.0 925.0 926.0 927.0 928.0 929.0 930.0 931.0 932.0 933.0 934.0 935.0 936.0 937.0 938.0 939.0 940.0 941.0 942.0 943.0 944.0 945.0 946.0 947.0 948.0 949.0 950.0 951.0 952.0 953.0 954.0 955.0 956.0 957.0 958.0 959.0 960.0 961.0 962.0 963.0 964.0 965.0 966.0 967.0 968.0 969.0 970.0 971.0 972.0 973.0 974.0 975.0 976.0 977.0 978.0 979.0 980.0 981.0 982.0 983.0 984.0 985.0 986.0 987.0 988.0 989.0 990.0 991.0 992.0 993.0 994.0 995.0 996.0 997.0 998.0 999.0
+1000.0 1001.0 1002.0 1003.0 1004.0 1005.0 1006.0 1007.0 1008.0 1009.0 1010.0 1011.0 1012.0 1013.0 1014.0 1015.0 1016.0 1017.0 1018.0 1019.0 1020.0 1021.0 1022.0 1023.0 1024.0 1025.0 1026.0 1027.0 1028.0 1029.0 1030.0 1031.0 1032.0 1033.0 1034.0 1035.0 1036.0 1037.0 1038.0 1039.0 1040.0 1041.0 1042.0 1043.0 1044.0 1045.0 1046.0 1047.0 1048.0 1049.0 1050.0 1051.0 1052.0 1053.0 1054.0 1055.0 1056.0 1057.0 1058.0 1059.0 1060.0 1061.0 1062.0 1063.0 1064.0 1065.0 1066.0 1067.0 1068.0 1069.0 1070.0 1071.0 1072.0 1073.0 1074.0 1075.0 1076.0 1077.0 1078.0 1079.0 1080.0 1081.0 1082.0 1083.0 1084.0 1085.0 1086.0 1087.0 1088.0 1089.0 1090.0 1091.0 1092.0 1093.0 1094.0 1095.0 1096.0 1097.0 1098.0 1099.0
+1100.0 1101.0 1102.0 1103.0 1104.0 1105.0 1106.0 1107.0 1108.0 1109.0 1110.0 1111.0 1112.0 1113.0 1114.0 1115.0 1116.0 1117.0 1118.0 1119.0 1120.0 1121.0 1122.0 1123.0 1124.0 1125.0 1126.0 1127.0 1128.0 1129.0 1130.0 1131.0 1132.0 1133.0 1134.0 1135.0 1136.0 1137.0 1138.0 1139.0 1140.0 1141.0 1142.0 1143.0 1144.0 1145.0 1146.0 1147.0 1148.0 1149.0 1150.0 1151.0 1152.0 1153.0 1154.0 1155.0 1156.0 1157.0 1158.0 1159.0 1160.0 1161.0 1162.0 1163.0 1164.0 1165.0 1166.0 1167.0 1168.0 1169.0 1170.0 1171.0 1172.0 1173.0 1174.0 1175.0 1176.0 1177.0 1178.0 1179.0 1180.0 1181.0 1182.0 1183.0 1184.0 1185.0 1186.0 1187.0 1188.0 1189.0 1190.0 1191.0 1192.0 1193.0 1194.0 1195.0 1196.0 1197.0 1198.0 1199.0
+1200.0 1201.0 1202.0 1203.0 1204.0 1205.0 1206.0 1207.0 1208.0 1209.0 1210.0 1211.0 1212.0 1213.0 1214.0 1215.0 1216.0 1217.0 1218.0 1219.0 1220.0 1221.0 1222.0 1223.0 1224.0 1225.0 1226.0 1227.0 1228.0 1229.0 1230.0 1231.0 1232.0 1233.0 1234.0 1235.0 1236.0 1237.0 1238.0 1239.0 1240.0 1241.0 1242.0 1243.0 1244.0 1245.0 1246.0 1247.0 1248.0 1249.0 1250.0 1251.0 1252.0 1253.0 1254.0 1255.0 1256.0 1257.0 1258.0 1259.0 1260.0 1261.0 1262.0 1263.0 1264.0 1265.0 1266.0 1267.0 1268.0 1269.0 1270.0 1271.0 1272.0 1273.0 1274.0 1275.0 1276.0 1277.0 1278.0 1279.0 1280.0 1281.0 1282.0 1283.0 1284.0 1285.0 1286.0 1287.0 1288.0 1289.0 1290.0 1291.0 1292.0 1293.0 1294.0 1295.0 1296.0 1297.0 1298.0 1299.0
+1300.0 1301.0 1302.0 1303.0 1304.0 1305.0 1306.0 1307.0 1308.0 1309.0 1310.0 1311.0 1312.0 1313.0 1314.0 1315.0 1316.0 1317.0 1318.0 1319.0 1320.0 1321.0 1322.0 1323.0 1324.0 1325.0 1326.0 1327.0 1328.0 1329.0 1330.0 1331.0 1332.0 1333.0 1334.0 1335.0 1336.0 1337.0 1338.0 1339.0 1340.0 1341.0 1342.0 1343.0 1344.0 1345.0 1346.0 1347.0 1348.0 1349.0 1350.0 1351.0 1352.0 1353.0 1354.0 1355.0 1356.0 1357.0 1358.0 1359.0 1360.0 1361.0 1362.0 1363.0 1364.0 1365.0 1366.0 1367.0 1368.0 1369.0 1370.0 1371.0 1372.0 1373.0 1374.0 1375.0 1376.0 1377.0 1378.0 1379.0 1380.0 1381.0 1382.0 1383.0 1384.0 1385.0 1386.0 1387.0 1388.0 1389.0 1390.0 1391.0 1392.0 1393.0 1394.0 1395.0 1396.0 1397.0 1398.0 1399.0
+1400.0 1401.0 1402.0 1403.0 1404.0 1405.0 1406.0 1407.0 1408.0 1409.0 1410.0 1411.0 1412.0 1413.0 1414.0 1415.0 1416.0 1417.0 1418.0 1419.0 1420.0 1421.0 1422.0 1423.0 1424.0 1425.0 1426.0 1427.0 1428.0 1429.0 1430.0 1431.0 1432.0 1433.0 1434.0 1435.0 1436.0 1437.0 1438.0 1439.0 1440.0 1441.0 1442.0 1443.0 1444.0 1445.0 1446.0 1447.0 1448.0 1449.0 1450.0 1451.0 1452.0 1453.0 1454.0 1455.0 1456.0 1457.0 1458.0 1459.0 1460.0 1461.0 1462.0 1463.0 1464.0 1465.0 1466.0 1467.0 1468.0 1469.0 1470.0 1471.0 1472.0 1473.0 1474.0 1475.0 1476.0 1477.0 1478.0 1479.0 1480.0 1481.0 1482.0 1483.0 1484.0 1485.0 1486.0 1487.0 1488.0 1489.0 1490.0 1491.0 1492.0 1493.0 1494.0 1495.0 1496.0 1497.0 1498.0 1499.0
+1500.0 1501.0 1502.0 1503.0 1504.0 1505.0 1506.0 1507.0 1508.0 1509.0 1510.0 1511.0 1512.0 1513.0 1514.0 1515.0 1516.0 1517.0 1518.0 1519.0 1520.0 1521.0 1522.0 1523.0 1524.0 1525.0 1526.0 1527.0 1528.0 1529.0 1530.0 1531.0 1532.0 1533.0 1534.0 1535.0 1536.0 1537.0 1538.0 1539.0 1540.0 1541.0 1542.0 1543.0 1544.0 1545.0 1546.0 1547.0 1548.0 1549.0 1550.0 1551.0 1552.0 1553.0 1554.0 1555.0 1556.0 1557.0 1558.0 1559.0 1560.0 1561.0 1562.0 1563.0 1564.0 1565.0 1566.0 1567.0 1568.0 1569.0 1570.0 1571.0 1572.0 1573.0 1574.0 1575.0 1576.0 1577.0 1578.0 1579.0 1580.0 1581.0 1582.0 1583.0 1584.0 1585.0 1586.0 1587.0 1588.0 1589.0 1590.0 1591.0 1592.0 1593.0 1594.0 1595.0 1596.0 1597.0 1598.0 1599.0
+1600.0 1601.0 1602.0 1603.0 1604.0 1605.0 1606.0 1607.0 1608.0 1609.0 1610.0 1611.0 1612.0 1613.0 1614.0 1615.0 1616.0 1617.0 1618.0 1619.0 1620.0 1621.0 1622.0 1623.0 1624.0 1625.0 1626.0 1627.0 1628.0 1629.0 1630.0 1631.0 1632.0 1633.0 1634.0 1635.0 1636.0 1637.0 1638.0 1639.0 1640.0 1641.0 1642.0 1643.0 1644.0 1645.0 1646.0 1647.0 1648.0 1649.0 1650.0 1651.0 1652.0 1653.0 1654.0 1655.0 1656.0 1657.0 1658.0 1659.0 1660.0 1661.0 1662.0 1663.0 1664.0 1665.0 1666.0 1667.0 1668.0 1669.0 1670.0 1671.0 1672.0 1673.0 1674.0 1675.0 1676.0 1677.0 1678.0 1679.0 1680.0 1681.0 1682.0 1683.0 1684.0 1685.0 1686.0 1687.0 1688.0 1689.0 1690.0 1691.0 1692.0 1693.0 1694.0 1695.0 1696.0 1697.0 1698.0 1699.0
+1700.0 1701.0 1702.0 1703.0 1704.0 1705.0 1706.0 1707.0 1708.0 1709.0 1710.0 1711.0 1712.0 1713.0 1714.0 1715.0 1716.0 1717.0 1718.0 1719.0 1720.0 1721.0 1722.0 1723.0 1724.0 1725.0 1726.0 1727.0 1728.0 1729.0 1730.0 1731.0 1732.0 1733.0 1734.0 1735.0 1736.0 1737.0 1738.0 1739.0 1740.0 1741.0 1742.0 1743.0 1744.0 1745.0 1746.0 1747.0 1748.0 1749.0 1750.0 1751.0 1752.0 1753.0 1754.0 1755.0 1756.0 1757.0 1758.0 1759.0 1760.0 1761.0 1762.0 1763.0 1764.0 1765.0 1766.0 1767.0 1768.0 1769.0 1770.0 1771.0 1772.0 1773.0 1774.0 1775.0 1776.0 1777.0 1778.0 1779.0 1780.0 1781.0 1782.0 1783.0 1784.0 1785.0 1786.0 1787.0 1788.0 1789.0 1790.0 1791.0 1792.0 1793.0 1794.0 1795.0 1796.0 1797.0 1798.0 1799.0

diff -r 000000000000 -r c8e4d0b9ae8c test-data/firstlayer.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/firstlayer.tsv Mon Jan 06 13:43:38 2020 -0500

diff -r 000000000000 -r c8e4d0b9ae8c test-data/genes_10x_v1.2.0.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes_10x_v1.2.0.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,343 @@
+DSCAM DSCAM
+MIR99AHG MIR99AHG
+APP APP
+USP16 USP16
+ADAMTS5 ADAMTS5
+TIAM1 TIAM1
+LOC339622 LOC339622
+IFNAR2 IFNAR2
+DYRK1A DYRK1A
+MORC3 MORC3
+ERG ERG
+RRP1B RRP1B
+TEKT4P2 TEKT4P2
+ANKRD30BP2 ANKRD30BP2
+RBM11 RBM11
+ANKRD20A11P ANKRD20A11P
+SAMSN1 SAMSN1
+NRIP1 NRIP1
+LOC388813 LOC388813
+USP25 USP25
+CHODL CHODL
+TMPRSS15 TMPRSS15
+MIR548XHG MIR548XHG
+NCAM2 NCAM2
+LINC00320 LINC00320
+LOC101927843 LOC101927843
+LOC101927869 LOC101927869
+GABPA GABPA
+CYYR1 CYYR1
+MIR5009 MIR5009
+LINC00113 LINC00113
+LOC284825 LOC284825
+LOC101927973 LOC101927973
+GRIK1 GRIK1
+MAP3K7CL MAP3K7CL
+CLDN8 CLDN8
+HUNK HUNK
+SYNJ1 SYNJ1
+URB1 URB1
+TCP10L TCP10L
+EVA1C EVA1C
+MRAP MRAP
+ITSN1 ITSN1
+CRYZL1 CRYZL1
+RUNX1 RUNX1
+RCAN1 RCAN1
+CLIC6 CLIC6
+DOPEY2 DOPEY2
+LOC100506403 LOC100506403
+LOC100133286 LOC100133286
+LOC101928269 LOC101928269
+CLDN14 CLDN14
+TTC3 TTC3
+HLCS HLCS
+DSCR4 DSCR4
+KCNJ6 KCNJ6
+LINC01423 LINC01423
+BRWD1 BRWD1
+WRB WRB
+B3GALT5 B3GALT5
+PCP4 PCP4
+IGSF5 IGSF5
+FAM3B FAM3B
+TMPRSS2 TMPRSS2
+BACE2 BACE2
+UMODL1 UMODL1
+PRDM15 PRDM15
+ABCG1 ABCG1
+RSPH1 RSPH1
+PDE9A PDE9A
+PKNOX1 PKNOX1
+HSF2BP HSF2BP
+AGPAT3 AGPAT3
+TRAPPC10 TRAPPC10
+TSPEAR TSPEAR
+PFKL PFKL
+RRP1 RRP1
+ADARB1 ADARB1
+COL18A1 COL18A1
+YBEY YBEY
+PCBP3 PCBP3
+DIP2A DIP2A
+PCNT PCNT
+MIR3648-1 MIR3648-1
+MIR3687-1 MIR3687-1
+MIR3648-2 MIR3648-2
+MIR3687-2 MIR3687-2
+TPTE TPTE
+BAGE BAGE
+BAGE4 BAGE4
+BAGE3 BAGE3
+BAGE5 BAGE5
+BAGE2 BAGE2
+MIR3156-3 MIR3156-3
+LOC102724188 LOC102724188
+MIR3118-1 MIR3118-1
+POTED POTED
+MIR8069-1 MIR8069-1
+MIR8069-2 MIR8069-2
+CYP4F29P CYP4F29P
+LIPI LIPI
+ABCC13 ABCC13
+HSPA13 HSPA13
+SAMSN1-AS1 SAMSN1-AS1
+MIR99A MIR99A
+MIRLET7C MIRLET7C
+MIR125B2 MIR125B2
+LINC01549 LINC01549
+CXADR CXADR
+BTG3 BTG3
+C21orf91 C21orf91
+CHODL-AS1 CHODL-AS1
+C21orf91-OT1 C21orf91-OT1
+LINC00317 LINC00317
+LINC01425 LINC01425
+LINC00308 LINC00308
+D21S2088E D21S2088E
+LINC00158 LINC00158
+MRPL39 MRPL39
+LINC00515 LINC00515
+MIR155 MIR155
+MIR155HG MIR155HG
+ATP5J ATP5J
+JAM2 JAM2
+ADAMTS1 ADAMTS1
+MIR4759 MIR4759
+LINC00314 LINC00314
+LINC00161 LINC00161
+N6AMT1 N6AMT1
+LTN1 LTN1
+RWDD2B RWDD2B
+CCT8 CCT8
+LINC00189 LINC00189
+BACH1 BACH1
+BACH1-IT2 BACH1-IT2
+GRIK1-AS2 GRIK1-AS2
+GRIK1-AS1 GRIK1-AS1
+CLDN17 CLDN17
+LINC00307 LINC00307
+KRTAP27-1 KRTAP27-1
+KRTAP25-1 KRTAP25-1
+KRTAP24-1 KRTAP24-1
+KRTAP26-1 KRTAP26-1
+KRTAP13-4 KRTAP13-4
+KRTAP15-1 KRTAP15-1
+KRTAP13-3 KRTAP13-3
+MIR4327 MIR4327
+KRTAP13-1 KRTAP13-1
+KRTAP23-1 KRTAP23-1
+KRTAP13-2 KRTAP13-2
+KRTAP6-2 KRTAP6-2
+KRTAP19-7 KRTAP19-7
+KRTAP19-5 KRTAP19-5
+KRTAP19-4 KRTAP19-4
+KRTAP19-3 KRTAP19-3
+KRTAP19-2 KRTAP19-2
+KRTAP19-6 KRTAP19-6
+KRTAP22-2 KRTAP22-2
+KRTAP6-3 KRTAP6-3
+KRTAP22-1 KRTAP22-1
+KRTAP19-1 KRTAP19-1
+KRTAP6-1 KRTAP6-1
+KRTAP20-2 KRTAP20-2
+KRTAP20-1 KRTAP20-1
+KRTAP20-4 KRTAP20-4
+KRTAP20-3 KRTAP20-3
+KRTAP21-3 KRTAP21-3
+KRTAP21-1 KRTAP21-1
+KRTAP21-2 KRTAP21-2
+KRTAP8-1 KRTAP8-1
+KRTAP7-1 KRTAP7-1
+KRTAP11-1 KRTAP11-1
+KRTAP19-8 KRTAP19-8
+SCAF4 SCAF4
+SOD1 SOD1
+LINC00159 LINC00159
+MIS18A MIS18A
+URB1-AS1 URB1-AS1
+SNORA80A SNORA80A
+C21orf59 C21orf59
+PAXBP1 PAXBP1
+C21orf62 C21orf62
+C21orf62-AS1 C21orf62-AS1
+PAXBP1-AS1 PAXBP1-AS1
+OLIG1 OLIG1
+OLIG2 OLIG2
+LINC00945 LINC00945
+LINC01548 LINC01548
+LOC101928107 LOC101928107
+IFNAR1 IFNAR1
+IL10RB IL10RB
+IL10RB-AS1 IL10RB-AS1
+DNAJC28 DNAJC28
+TMEM50B TMEM50B
+IFNGR2 IFNGR2
+GART GART
+SON SON
+DONSON DONSON
+MIR6501 MIR6501
+ATP5O ATP5O
+LINC00649 LINC00649
+MRPS6 MRPS6
+SLC5A3 SLC5A3
+LINC00310 LINC00310
+KCNE2 KCNE2
+C21orf140 C21orf140
+SMIM11A SMIM11A
+SMIM11B SMIM11B
+KCNE1 KCNE1
+LINC00160 LINC00160
+LINC01426 LINC01426
+RUNX1-IT1 RUNX1-IT1
+MIR802 MIR802
+SETD4 SETD4
+CBR1 CBR1
+LINC01436 LINC01436
+CBR3 CBR3
+CBR3-AS1 CBR3-AS1
+CHAF1B CHAF1B
+SIM2 SIM2
+RIPPLY3 RIPPLY3
+PIGP PIGP
+LOC105372795 LOC105372795
+DSCR3 DSCR3
+DSCR9 DSCR9
+DSCR10 DSCR10
+DSCR8 DSCR8
+KCNJ15 KCNJ15
+ETS2 ETS2
+LOC101928398 LOC101928398
+LINC00114 LINC00114
+LOC101928435 LOC101928435
+LOC400867 LOC400867
+PSMG1 PSMG1
+BRWD1-AS1 BRWD1-AS1
+HMGN1 HMGN1
+BRWD1-IT2 BRWD1-IT2
+LCA5L LCA5L
+SH3BGR SH3BGR
+MIR6508 MIR6508
+B3GALT5-AS1 B3GALT5-AS1
+MIR4760 MIR4760
+DSCAM-AS1 DSCAM-AS1
+DSCAM-IT1 DSCAM-IT1
+MIR3197 MIR3197
+LINC00323 LINC00323
+PLAC4 PLAC4
+MX2 MX2
+MX1 MX1
+LINC00111 LINC00111
+RIPK4 RIPK4
+MIR6814 MIR6814
+LINC00112 LINC00112
+LINC00479 LINC00479
+C2CD2 C2CD2
+SNORA91 SNORA91
+ZBTB21 ZBTB21
+ZNF295-AS1 ZNF295-AS1
+UMODL1-AS1 UMODL1-AS1
+TFF3 TFF3
+TFF2 TFF2
+UBASH3A UBASH3A
+TMPRSS3 TMPRSS3
+TFF1 TFF1
+SLC37A1 SLC37A1
+LOC101928233 LOC101928233
+WDR4 WDR4
+NDUFV3 NDUFV3
+ERVH48-1 ERVH48-1
+U2AF1 U2AF1
+CBS CBS
+FRGCA FRGCA
+LOC106780825 LOC106780825
+LOC102724652 LOC102724652
+CRYAA CRYAA
+LINC00322 LINC00322
+TCONS_00029157 TCONS_00029157
+SIK1 SIK1
+LINC00313 LINC00313
+LINC00319 LINC00319
+MIR6070 MIR6070
+PDXK PDXK
+CSTB CSTB
+AATBC AATBC
+C21orf33 C21orf33
+PWP2 PWP2
+ICOSLG ICOSLG
+DNMT3L DNMT3L
+AIRE AIRE
+C21orf2 C21orf2
+TRPM2 TRPM2
+TRPM2-AS TRPM2-AS
+LRRC3-AS1 LRRC3-AS1
+TSPEAR-AS1 TSPEAR-AS1
+KRTAP10-3 KRTAP10-3
+KRTAP10-1 KRTAP10-1
+LRRC3 LRRC3
+TSPEAR-AS2 TSPEAR-AS2
+KRTAP10-4 KRTAP10-4
+KRTAP10-5 KRTAP10-5
+KRTAP10-2 KRTAP10-2
+KRTAP10-12 KRTAP10-12
+KRTAP12-4 KRTAP12-4
+KRTAP12-3 KRTAP12-3
+KRTAP10-7 KRTAP10-7
+KRTAP12-1 KRTAP12-1
+KRTAP10-8 KRTAP10-8
+KRTAP10-11 KRTAP10-11
+KRTAP10-9 KRTAP10-9
+KRTAP12-2 KRTAP12-2
+KRTAP10-10 KRTAP10-10
+KRTAP10-6 KRTAP10-6
+SUMO3 SUMO3
+UBE2G2 UBE2G2
+LINC01424 LINC01424
+FAM207A FAM207A
+ITGB2 ITGB2
+PTTG1IP PTTG1IP
+LINC01547 LINC01547
+ITGB2-AS1 ITGB2-AS1
+SSR4P1 SSR4P1
+LINC00163 LINC00163
+LINC00162 LINC00162
+POFUT2 POFUT2
+LINC00316 LINC00316
+LOC642852 LOC642852
+COL18A1-AS1 COL18A1-AS1
+COL18A1-AS2 COL18A1-AS2
+MIR6815 MIR6815
+SLC19A1 SLC19A1
+LOC100129027 LOC100129027
+LOC101928796 LOC101928796
+COL6A1 COL6A1
+FTCD FTCD
+COL6A2 COL6A2
+SPATC1L SPATC1L
+LSS LSS
+MCM3AP-AS1 MCM3AP-AS1
+MCM3AP MCM3AP
+C21orf58 C21orf58
+DIP2A-IT1 DIP2A-IT1
+PRMT2 PRMT2
+S100B S100B

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.csv.h5ad

Binary file test-data/import.csv.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.loom.krumsiek11.h5ad

Binary file test-data/import.loom.krumsiek11.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.mtx.legacy_10x.h5ad

Binary file test-data/import.mtx.legacy_10x.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.mtx.no_10x.h5ad

Binary file test-data/import.mtx.no_10x.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.mtx.v3_10x.h5ad

Binary file test-data/import.mtx.v3_10x.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.tsv.h5ad

Binary file test-data/import.tsv.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/import.umi_tools.h5ad

Binary file test-data/import.umi_tools.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/inspect.X.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.X.tabular Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,641 @@\n+index\tGata2\tGata1\tFog1\tEKLF\tFli1\tSCL\tCebpa\tPu.1\tcJun\tEgrNab\tGfi1\n+0\t0.8032\t-0.0005\t-1e-04\t0.0003\t0.0013\t0.0011\t0.7997\t0.8017\t0.0006\t0.0009\t0.0002\n+1\t0.7239\t0.0016\t-0.0003\t-0.001\t0.0011\t0.0022\t0.8195\t0.7256\t0.0784\t0.0077\t0.0941\n+2\t0.6578\t0.0013\t-0.001\t-0.0027\t0.0025\t0.0011\t0.8358\t0.6624\t0.1105\t0.0239\t0.1497\n+3\t0.5972\t0.0038\t-0.0009\t-0.0064\t0.0007\t-0.0036\t0.8534\t0.5992\t0.1271\t0.0311\t0.1702\n+4\t0.5396\t0.0071\t-0.0029\t-0.0063\t0.0011\t-0.007\t0.8656\t0.547\t0.1385\t0.0379\t0.1752\n+5\t0.4897\t0.011\t-0.0023\t-0.0061\t0.0013\t-0.0034\t0.8759\t0.4998\t0.1496\t0.0459\t0.1747\n+6\t0.4449\t0.0153\t-0.002\t-0.0089\t0.0003\t-0.0057\t0.8854\t0.4516\t0.1569\t0.0489\t0.1727\n+7\t0.4078\t0.0131\t-0.0013\t-0.0121\t-0.0024\t-0.0076\t0.8986\t0.4096\t0.1666\t0.0556\t0.1661\n+8\t0.3719\t0.0156\t0.0021\t-0.0105\t-0.0007\t-0.0066\t0.9062\t0.3742\t0.1731\t0.0631\t0.1623\n+9\t0.3424\t0.0175\t0.0027\t-0.0083\t-0.0045\t-0.0017\t0.9135\t0.3433\t0.1781\t0.0698\t0.1565\n+10\t0.3143\t0.0179\t-1e-04\t-0.01\t-0.0042\t-0.0039\t0.9191\t0.3175\t0.1891\t0.0785\t0.1473\n+11\t0.29\t0.0215\t-0.0007\t-0.0069\t-0.0034\t-0.0018\t0.928\t0.2934\t0.1988\t0.0844\t0.1371\n+12\t0.2674\t0.0255\t-0.002\t-0.0074\t-0.003\t-0.0013\t0.9373\t0.2749\t0.2103\t0.0942\t0.1301\n+13\t0.2519\t0.0284\t-0.0011\t-0.0029\t-0.0037\t-0.0022\t0.9424\t0.26\t0.2211\t0.102\t0.1193\n+14\t0.2353\t0.0371\t0.0009\t-0.0017\t-0.0018\t0.0\t0.9492\t0.2439\t0.2336\t0.1114\t0.1089\n+15\t0.221\t0.0413\t0.0009\t-0.0028\t0.0019\t0.0025\t0.9503\t0.2353\t0.2473\t0.1219\t0.1018\n+16\t0.2077\t0.0423\t0.0003\t-0.0016\t0.0047\t0.0057\t0.9527\t0.2248\t0.2645\t0.1389\t0.0915\n+17\t0.1986\t0.0464\t-0.0005\t0.0012\t0.0025\t0.0081\t0.9551\t0.2187\t0.2866\t0.1572\t0.0846\n+18\t0.1914\t0.0531\t0.002\t0.0035\t0.0022\t0.0143\t0.9573\t0.2117\t0.3103\t0.1756\t0.0761\n+19\t0.1818\t0.0613\t0.0037\t0.0063\t0.0018\t0.0179\t0.9579\t0.2034\t0.3332\t0.2\t0.0722\n+20\t0.1734\t0.0666\t0.0069\t0.0066\t0.0053\t0.0218\t0.9585\t0.2051\t0.3505\t0.2227\t0.0672\n+21\t0.172\t0.0715\t0.0052\t0.0112\t0.0066\t0.026\t0.9586\t0.2025\t0.3742\t0.2433\t0.0567\n+22\t0.1638\t0.0762\t0.0084\t0.0177\t0.0096\t0.0289\t0.9655\t0.1981\t0.3971\t0.2726\t0.0492\n+23\t0.1556\t0.0826\t0.009\t0.0151\t0.0125\t0.0374\t0.9661\t0.1974\t0.4208\t0.2965\t0.0461\n+24\t0.1515\t0.0831\t0.0117\t0.0169\t0.0101\t0.0385\t0.9724\t0.1936\t0.445\t0.3236\t0.0395\n+25\t0.1475\t0.0821\t0.0123\t0.0174\t0.015\t0.0429\t0.9757\t0.1898\t0.4697\t0.3503\t0.0346\n+26\t0.148\t0.0842\t0.0137\t0.0186\t0.0133\t0.0468\t0.9751\t0.19\t0.4953\t0.3773\t0.0297\n+27\t0.144\t0.087\t0.0101\t0.0184\t0.0152\t0.0544\t0.9734\t0.1893\t0.5165\t0.4037\t0.0264\n+28\t0.1463\t0.0892\t0.009\t0.0231\t0.0156\t0.0551\t0.976\t0.1906\t0.532\t0.4323\t0.0203\n+29\t0.1413\t0.0919\t0.0085\t0.0255\t0.0193\t0.0594\t0.9795\t0.1887\t0.5534\t0.4581\t0.0198\n+30\t0.1415\t0.0919\t0.0067\t0.0273\t0.0218\t0.0629\t0.9853\t0.1891\t0.568\t0.4826\t0.0224\n+31\t0.1385\t0.0952\t0.0072\t0.0306\t0.0209\t0.0687\t0.9866\t0.1904\t0.5856\t0.5025\t0.0213\n+32\t0.1386\t0.0993\t0.0075\t0.0265\t0.0268\t0.073\t0.9878\t0.1916\t0.6031\t0.5224\t0.0198\n+33\t0.1337\t0.1011\t0.0061\t0.0237\t0.0242\t0.0751\t0.9897\t0.1885\t0.619\t0.5403\t0.0177\n+34\t0.1318\t0.1009\t0.0046\t0.0278\t0.0267\t0.0793\t0.9925\t0.1892\t0.6339\t0.5546\t0.0173\n+35\t0.1295\t0.1035\t0.0074\t0.03\t0.0266\t0.0817\t0.9967\t0.1855\t0.6451\t0.5754\t0.0171\n+36\t0.1284\t0.1001\t0.0063\t0.0299\t0.0293\t0.0868\t0.9949\t0.1841\t0.6546\t0.5917\t0.0112\n+37\t0.1246\t0.1018\t0.0112\t0.0354\t0.0264\t0.0901\t0.9949\t0.1886\t0.6651\t0.6068\t0.0119\n+38\t0.123\t0.1057\t0.0079\t0.0353\t0.03\t0.0972\t0.989\t0.1858\t0.6758\t0.621\t0.0118\n+39\t0.1184\t0.104\t0.0087\t0.0357\t0.0303\t0.0996\t0.9889\t0.1861\t0.6811\t0.63\t0.0092\n+40\t0.1191\t0.1036\t0.0092\t0.0322\t0.0303\t0.1016\t0.9881\t0.1853\t0.6913\t0.6417\t0.0084\n+41\t0.1198\t0.1035\t0.0052\t0.0332\t0.0306\t0.1001\t0.9874\t0.187\t0.7005\t0.6513\t0.0069\n+42\t0.1171\t0.1055\t0.0055\t0.0339\t0.0303\t0.1041\t0.9877\t0.1889\t0.7091\t0.659\t0.0077\n+43\t0.1157\t0.1066\t0.0084\t0.0349\t0.0303\t0.1031\t0.9882\t0.1905\t0.7142\t0.6705\t0.0064\n+44\t0.116\t0.1097\t0.0087\t0.0341\t0.0321\t0.1078\t0.9902\t0.1886\t0.7201\t0.6802\t0.0046\n+45\t0.1141\t0.1096\t0.0116\t0.0362\t0.0363\t0.1088\t0.9904\t0.1884\t0.7225\t0.6883\t0.0035\n+46\t0.1185\t0.1081\t0.0096\t0.0351\t0.0363\t0.1055\t0.9888\t0.1909\t0.7314\t0.6989\t0.0051\n+47\t0.1174\t0.1046\t0.0098\t0.037\t0.0369\t0.1061\t0.989\t0.1883\t0.7348\t0.7054\t0.0022\n+48\t0.1135\t0.1022\t0.011\t0.0408\t0.033\t0.1091\t0'..b'-0.0012\t1.001\t1.0015\t0.0203\t0.0063\t0.9264\n+113\t0.0024\t-0.0035\t-0.0028\t0.0016\t-0.0004\t-0.0013\t1.0027\t1.0006\t0.0214\t0.0027\t0.9278\n+114\t0.0036\t-0.0006\t-0.0018\t0.0002\t-0.001\t0.0011\t1.0038\t1.0032\t0.0185\t0.0014\t0.9326\n+115\t0.0036\t-0.0017\t-0.0026\t0.0049\t-0.0051\t0.0024\t1.0048\t1.0039\t0.0179\t-0.0011\t0.9367\n+116\t0.0036\t-0.0032\t-0.0034\t0.0032\t-0.0023\t0.0036\t1.0062\t1.0058\t0.0195\t-0.0015\t0.9401\n+117\t0.0018\t-0.0049\t1e-04\t0.001\t0.0\t0.0044\t1.0066\t1.0055\t0.0204\t-0.0021\t0.9432\n+118\t-0.0\t-0.0055\t-0.0014\t-0.0013\t-0.0025\t0.002\t1.0021\t1.0051\t0.0189\t-0.0044\t0.9453\n+119\t-0.0035\t-0.004\t-0.0032\t-0.0007\t-0.0018\t-0.0\t1.0024\t1.0047\t0.0187\t-0.0066\t0.9389\n+120\t-0.0071\t-0.0056\t-0.0025\t0.0002\t-0.002\t-0.004\t1.0032\t1.0047\t0.0155\t-0.0102\t0.9278\n+121\t-0.0053\t-0.0073\t-0.0031\t0.0033\t0.0006\t-0.0011\t1.0012\t1.0025\t0.0137\t-0.0045\t0.9215\n+122\t-0.001\t-0.0068\t-0.0031\t0.0045\t-0.0015\t-0.0032\t0.9998\t1.0044\t0.0113\t-0.0052\t0.9236\n+123\t-0.0017\t-0.0023\t-0.0046\t0.0052\t0.0033\t-0.0023\t0.9987\t1.0078\t0.0105\t-0.007\t0.9217\n+124\t-0.0025\t0.0006\t-1e-04\t0.0069\t0.0048\t-0.0008\t0.9951\t1.005\t0.0144\t-0.0072\t0.9174\n+125\t-0.0014\t0.0029\t-0.0026\t0.0083\t0.003\t0.0\t0.9967\t1.0052\t0.013\t-0.0051\t0.9144\n+126\t1e-04\t0.0038\t-0.0015\t0.0065\t0.0026\t0.0015\t0.9945\t1.0036\t0.0144\t-0.003\t0.9207\n+127\t0.0019\t0.002\t0.0014\t0.0059\t0.0048\t0.0008\t0.9966\t1.007\t0.0151\t-0.0008\t0.9236\n+128\t0.0013\t0.0018\t-0.0016\t0.0077\t0.0045\t-0.0\t0.9966\t1.0074\t0.0135\t-0.0022\t0.9318\n+129\t0.0014\t-0.0\t-0.0017\t0.006\t0.0053\t0.0002\t0.989\t1.0061\t0.014\t-0.0034\t0.9351\n+130\t0.0012\t0.0023\t0.0008\t0.0046\t0.0053\t0.0032\t0.9867\t1.0054\t0.0131\t-0.0067\t0.938\n+131\t0.0045\t0.0011\t0.0021\t0.0024\t0.007\t0.0006\t0.9872\t1.004\t0.0125\t-0.0076\t0.9325\n+132\t0.0077\t0.0017\t0.0034\t0.0055\t0.0049\t-0.001\t0.9914\t1.0053\t0.0113\t-0.0099\t0.92\n+133\t0.0061\t-0.0006\t0.0036\t0.0096\t0.0063\t-0.0023\t0.9914\t1.0067\t0.0126\t-0.0062\t0.9187\n+134\t0.0046\t-0.0029\t0.0047\t0.0083\t0.0047\t-0.0058\t0.9915\t1.0034\t0.0144\t-0.0047\t0.9198\n+135\t0.0025\t-0.002\t0.0026\t0.0064\t0.0047\t-0.0078\t0.9926\t1.003\t0.0153\t-0.0054\t0.9198\n+136\t-0.0023\t-0.0027\t0.0013\t0.0059\t0.0014\t-0.0077\t0.9938\t1.0012\t0.0143\t-0.0046\t0.9246\n+137\t0.0004\t-0.0045\t0.0011\t0.0046\t0.0035\t-0.0082\t0.9927\t1.0007\t0.0133\t-0.0049\t0.9222\n+138\t-0.0006\t-0.0044\t0.001\t0.0071\t0.0049\t-0.0112\t0.9953\t1.0034\t0.0123\t-0.0061\t0.9246\n+139\t-0.0025\t-0.0051\t-0.0003\t0.0076\t0.003\t-0.0067\t0.9932\t1.0029\t0.014\t-0.0055\t0.9267\n+140\t-0.0038\t-0.0068\t0.0007\t0.0066\t-0.0003\t-0.0066\t0.9921\t1.0051\t0.013\t-0.0046\t0.9243\n+141\t-0.0023\t-0.0119\t0.0046\t0.0063\t0.0037\t-0.0059\t0.9913\t1.004\t0.0146\t-0.0022\t0.9326\n+142\t-0.0034\t-0.0117\t0.002\t0.0028\t0.003\t-0.0026\t0.9923\t1.0021\t0.0158\t-0.0021\t0.9364\n+143\t-0.0047\t-0.0134\t0.0031\t0.0018\t0.0046\t-0.0006\t0.9908\t0.9996\t0.0136\t-0.0015\t0.9376\n+144\t-0.0035\t-0.0163\t0.0017\t0.0016\t0.0035\t-0.0008\t0.9938\t0.9976\t0.013\t0.0009\t0.9446\n+145\t-0.002\t-0.0149\t-0.0009\t0.0021\t0.0013\t-0.0018\t0.9938\t0.9941\t0.015\t-0.0055\t0.9497\n+146\t-0.0036\t-0.0151\t0.0024\t-0.0013\t0.0012\t0.0004\t0.9976\t0.9917\t0.0123\t-0.0032\t0.9441\n+147\t-0.0032\t-0.0116\t0.001\t0.0008\t-0.0024\t0.0006\t1.001\t0.9934\t0.0108\t-0.0065\t0.9492\n+148\t-0.0023\t-0.0083\t0.0027\t0.0005\t0.0006\t-0.0014\t1.0014\t0.9927\t0.0136\t-0.0067\t0.94\n+149\t-0.001\t-0.006\t0.0022\t0.0034\t-0.0011\t-0.0018\t0.9997\t0.9933\t0.0132\t-0.0049\t0.9404\n+150\t-0.0024\t-0.0073\t-0.0011\t0.0036\t-0.0024\t-0.0008\t0.9975\t0.9958\t0.0165\t-0.0064\t0.9398\n+151\t0.0007\t-0.0051\t0.0008\t0.0036\t-0.003\t-0.0012\t1.0006\t0.9932\t0.0161\t-0.0076\t0.9372\n+152\t-0.0008\t-0.0076\t0.0025\t0.0028\t-0.0048\t-0.0003\t1.0016\t0.992\t0.015\t-0.0095\t0.9325\n+153\t-0.0029\t-0.0045\t0.0027\t0.0051\t-0.0046\t-0.0039\t0.9989\t0.9913\t0.0177\t-0.0087\t0.9232\n+154\t0.0002\t-0.002\t0.0061\t0.0048\t-0.0043\t-0.0016\t0.9989\t0.9911\t0.0152\t-0.0072\t0.916\n+155\t-0.001\t-0.002\t0.0015\t0.0029\t-0.0055\t-0.0004\t0.999\t0.9915\t0.0107\t-0.0076\t0.9119\n+156\t0.0028\t-0.003\t0.0009\t0.0049\t-0.0073\t0.002\t1.0\t0.9946\t0.0127\t-0.0082\t0.9095\n+157\t0.003\t-0.0035\t0.0008\t0.0052\t-0.0066\t1e-04\t1.0014\t0.9977\t0.0125\t-0.0046\t0.9069\n+158\t0.0063\t-0.0023\t-0.0005\t0.0081\t-0.0046\t-0.0006\t0.9983\t0.997\t0.0109\t-0.003\t0.9118\n+159\t0.0049\t0.0002\t-0.0013\t0.0054\t-0.0036\t0.0009\t1.0011\t0.9967\t0.0066\t-0.0033\t0.9177\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/inspect.chunk_X.specified.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.chunk_X.specified.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,4 @@
+ 0 1 2 3 4 5 6 7 8 9 10
+0 0.5972 0.0038 -0.0009 -0.0064 0.0007 -0.0036 0.8534 0.5992 0.1271 0.0311 0.1702
+1 0.4897 0.011 -0.0023 -0.0061 0.0013 -0.0034 0.8759 0.4998 0.1496 0.0459 0.1747
+2 0.3719 0.0156 0.0021 -0.0105 -0.0007 -0.0066 0.9062 0.3742 0.1731 0.0631 0.1623

diff -r 000000000000 -r c8e4d0b9ae8c test-data/inspect.general.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.general.txt Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,3 @@
+AnnData object with n_obs × n_vars = 640 × 11
+ obs: 'cell_type'
+ uns: 'cell_type_colors', 'highlights', 'iroot'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/inspect.obs.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.obs.tabular Mon Jan 06 13:43:38 2020 -0500

diff -r 000000000000 -r c8e4d0b9ae8c test-data/inspect.var.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.var.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+index
+Gata2
+Gata1
+Fog1
+EKLF
+Fli1
+SCL
+Cebpa
+Pu.1
+cJun
+EgrNab
+Gfi1

diff -r 000000000000 -r c8e4d0b9ae8c test-data/krumsiek11.h5ad

Binary file test-data/krumsiek11.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/krumsiek11.loom

Binary file test-data/krumsiek11.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/loomtest.loom

Binary file test-data/loomtest.loom has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.add_annotation_obs.h5ad

Binary file test-data/manipulate.add_annotation_obs.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.add_annotation_var.h5ad

Binary file test-data/manipulate.add_annotation_var.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.concatenate.h5ad

Binary file test-data/manipulate.concatenate.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.filter_obs_key.h5ad

Binary file test-data/manipulate.filter_obs_key.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.filter_var_index.h5ad

Binary file test-data/manipulate.filter_var_index.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.obs_names_make_unique.h5ad

Binary file test-data/manipulate.obs_names_make_unique.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.rename_categories.h5ad

Binary file test-data/manipulate.rename_categories.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.save_raw.h5ad

Binary file test-data/manipulate.save_raw.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.strings_to_categoricals.h5ad

Binary file test-data/manipulate.strings_to_categoricals.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.transpose.h5ad

Binary file test-data/manipulate.transpose.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/manipulate.var_names_make_unique.h5ad

Binary file test-data/manipulate.var_names_make_unique.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/matrix_10x_v1.2.0.mtx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_10x_v1.2.0.mtx Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,15 @@
+%%MatrixMarket matrix coordinate integer general
+%
+343 12 12
+201 1 1
+123 2 1
+283 3 1
+318 4 1
+175 5 1
+12 6 1
+132 7 1
+197 8 1
+222 9 1
+236 10 1
+317 11 1
+127 12 1
\ No newline at end of file

diff -r 000000000000 -r c8e4d0b9ae8c test-data/matrix_10x_v3.0.0.mtx
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_10x_v3.0.0.mtx Mon Jan 06 13:43:38 2020 -0500

b'@@ -0,0 +1,23869 @@\n+%%MatrixMarket matrix coordinate integer general\n+%metadata_json: {"format_version": 2, "software_version": "4009.30.5"}\n+507 1107 23866\n+458 1 3\n+456 1 1\n+409 1 1\n+406 1 2\n+391 1 2\n+386 1 1\n+376 1 1\n+314 1 1\n+295 1 2\n+293 1 1\n+289 1 2\n+263 1 1\n+262 1 1\n+258 1 1\n+257 1 1\n+253 1 2\n+250 1 1\n+217 1 1\n+216 1 1\n+215 1 1\n+169 1 3\n+166 1 2\n+162 1 1\n+141 1 1\n+140 1 1\n+139 1 1\n+499 2 1\n+470 2 1\n+418 2 1\n+406 2 1\n+391 2 1\n+385 2 1\n+353 2 1\n+352 2 1\n+336 2 2\n+314 2 1\n+307 2 1\n+303 2 1\n+263 2 3\n+258 2 2\n+253 2 2\n+252 2 1\n+235 2 1\n+215 2 1\n+61 2 1\n+458 3 5\n+406 3 1\n+404 3 1\n+336 3 1\n+332 3 1\n+314 3 1\n+306 3 1\n+289 3 1\n+282 3 1\n+263 3 1\n+261 3 1\n+247 3 1\n+232 3 1\n+215 3 2\n+162 3 1\n+139 3 1\n+76 3 1\n+70 3 1\n+507 4 1\n+499 4 1\n+336 4 1\n+311 4 1\n+263 4 1\n+258 4 1\n+254 4 1\n+232 4 1\n+215 4 2\n+165 4 1\n+139 4 1\n+507 5 2\n+458 5 4\n+405 5 1\n+404 5 1\n+352 5 1\n+336 5 2\n+314 5 1\n+311 5 1\n+307 5 3\n+295 5 1\n+258 5 2\n+254 5 1\n+237 5 2\n+215 5 1\n+166 5 3\n+139 5 4\n+90 5 1\n+62 5 1\n+462 6 1\n+458 6 1\n+456 6 1\n+423 6 1\n+417 6 1\n+406 6 3\n+404 6 1\n+386 6 1\n+376 6 1\n+348 6 1\n+336 6 2\n+311 6 1\n+295 6 1\n+293 6 2\n+263 6 2\n+257 6 1\n+253 6 2\n+252 6 1\n+215 6 1\n+166 6 1\n+165 6 1\n+139 6 3\n+87 6 1\n+499 7 1\n+406 7 2\n+348 7 1\n+336 7 3\n+332 7 1\n+307 7 2\n+258 7 1\n+254 7 1\n+253 7 1\n+249 7 1\n+232 7 1\n+215 7 2\n+139 7 1\n+137 7 1\n+507 8 1\n+499 8 1\n+480 8 2\n+477 8 1\n+458 8 19\n+457 8 1\n+456 8 3\n+454 8 1\n+423 8 2\n+411 8 1\n+410 8 1\n+406 8 6\n+405 8 2\n+391 8 2\n+366 8 1\n+336 8 1\n+323 8 2\n+307 8 1\n+306 8 1\n+289 8 1\n+282 8 1\n+263 8 1\n+258 8 2\n+254 8 1\n+253 8 1\n+252 8 2\n+250 8 1\n+215 8 2\n+212 8 2\n+169 8 1\n+165 8 2\n+141 8 1\n+139 8 2\n+502 9 1\n+480 9 2\n+462 9 1\n+458 9 12\n+457 9 2\n+456 9 1\n+454 9 1\n+423 9 3\n+410 9 1\n+409 9 1\n+406 9 1\n+405 9 1\n+404 9 1\n+391 9 2\n+386 9 1\n+352 9 3\n+336 9 5\n+323 9 3\n+307 9 1\n+303 9 3\n+282 9 1\n+277 9 1\n+263 9 3\n+261 9 1\n+258 9 3\n+253 9 4\n+229 9 2\n+217 9 1\n+212 9 1\n+169 9 1\n+165 9 2\n+141 9 1\n+139 9 5\n+137 9 1\n+61 9 1\n+507 10 4\n+505 10 1\n+458 10 2\n+353 10 1\n+352 10 1\n+336 10 4\n+311 10 2\n+306 10 1\n+263 10 2\n+258 10 2\n+253 10 1\n+217 10 1\n+215 10 1\n+166 10 1\n+165 10 1\n+141 10 1\n+60 10 1\n+389 11 1\n+336 11 3\n+266 11 1\n+258 11 1\n+215 11 5\n+162 11 2\n+90 11 1\n+87 11 1\n+507 12 3\n+470 12 1\n+458 12 8\n+457 12 1\n+456 12 2\n+412 12 1\n+409 12 2\n+406 12 7\n+391 12 1\n+386 12 1\n+352 12 1\n+336 12 3\n+323 12 1\n+307 12 2\n+306 12 1\n+303 12 2\n+289 12 1\n+263 12 2\n+262 12 1\n+258 12 4\n+257 12 2\n+253 12 2\n+252 12 1\n+250 12 2\n+217 12 1\n+215 12 1\n+169 12 1\n+166 12 3\n+141 12 2\n+140 12 2\n+139 12 2\n+76 12 1\n+507 13 4\n+494 13 1\n+458 13 1\n+454 13 1\n+353 13 1\n+336 13 1\n+264 13 1\n+263 13 1\n+258 13 2\n+215 13 1\n+165 13 1\n+139 13 1\n+6 13 1\n+502 14 1\n+467 14 1\n+462 14 1\n+458 14 2\n+457 14 1\n+454 14 1\n+409 14 1\n+406 14 1\n+391 14 1\n+385 14 1\n+337 14 2\n+336 14 6\n+331 14 2\n+307 14 1\n+293 14 2\n+289 14 2\n+282 14 2\n+267 14 1\n+263 14 3\n+258 14 3\n+257 14 1\n+253 14 2\n+252 14 1\n+215 14 1\n+167 14 2\n+165 14 1\n+141 14 1\n+139 14 2\n+135 14 1\n+87 14 1\n+505 15 3\n+502 15 1\n+467 15 1\n+462 15 1\n+458 15 3\n+412 15 1\n+410 15 1\n+406 15 1\n+405 15 1\n+391 15 1\n+307 15 1\n+282 15 2\n+263 15 1\n+257 15 1\n+252 15 1\n+250 15 1\n+217 15 1\n+215 15 2\n+166 15 2\n+162 15 1\n+140 15 1\n+139 15 2\n+507 16 1\n+502 16 1\n+458 16 13\n+456 16 4\n+423 16 2\n+412 16 2\n+409 16 1\n+408 16 1\n+407 16 1\n+406 16 3\n+405 16 1\n+391 16 2\n+386 16 2\n+366 16 1\n+352 16 1\n+332 16 3\n+311 16 1\n+307 16 1\n+306 16 2\n+295 16 1\n+289 16 1\n+267 16 2\n+266 16 1\n+263 16 6\n+261 16 2\n+258 16 2\n+254 16 1\n+253 16 4\n+250 16 1\n+235 16 1\n+232 16 2\n+217 16 1\n+216 16 1\n+169 16 2\n+165 16 2\n+161 16 1\n+139 16 4\n+70 16 1\n+507 17 5\n+505 17 1\n+480 17 1\n+462 17 1\n+458 17 9\n+457 17 1\n+456 17 4\n+407 17 1\n+405 17 1\n+386 17 1\n+337 17 1\n+336 17 5\n+331 17 1\n+323 17 2\n+311 17 1\n+307 17 4\n+293 17 1\n+287 17 1\n+266 17 1\n+263 17 3\n+261 17 1\n+254 17 1\n+217 17 1\n+215 17 2\n+169 17 2\n+166 17 2\n+165 17 1\n+141 17 1\n+139 17 1\n+76 17 1\n+507 18 6\n+502 18 2\n+496 18 2\n+486 18 1\n+467 18 1\n+462 18 1\n+459 18 1\n+458 18 15\n+456 18 4\n+423 18 3\n+409 18 2\n+406 18 10\n+405 18 1\n+404 18 2\n+386 18 2\n+374 18 2\n+369 18 1\n+366 18 1'..b'1091 1\n+267 1091 1\n+264 1091 2\n+263 1091 6\n+261 1091 1\n+259 1091 1\n+258 1091 4\n+257 1091 2\n+254 1091 3\n+253 1091 1\n+250 1091 1\n+247 1091 1\n+215 1091 2\n+169 1091 1\n+166 1091 5\n+148 1091 1\n+141 1091 1\n+139 1091 7\n+137 1091 1\n+76 1091 1\n+70 1091 1\n+61 1091 1\n+20 1091 1\n+507 1092 2\n+505 1092 1\n+496 1092 1\n+480 1092 1\n+470 1092 1\n+458 1092 7\n+457 1092 3\n+456 1092 3\n+454 1092 1\n+424 1092 1\n+409 1092 2\n+406 1092 6\n+391 1092 1\n+386 1092 1\n+337 1092 1\n+336 1092 1\n+332 1092 2\n+307 1092 1\n+282 1092 2\n+266 1092 1\n+263 1092 3\n+258 1092 5\n+252 1092 1\n+250 1092 1\n+243 1092 1\n+215 1092 3\n+212 1092 1\n+169 1092 1\n+166 1092 2\n+141 1092 2\n+90 1092 1\n+70 1092 1\n+62 1092 2\n+499 1093 1\n+459 1093 1\n+458 1093 1\n+456 1093 1\n+391 1093 1\n+332 1093 1\n+323 1093 2\n+282 1093 1\n+247 1093 1\n+173 1093 1\n+162 1093 1\n+141 1093 1\n+505 1094 1\n+458 1094 1\n+409 1094 1\n+336 1094 2\n+307 1094 1\n+295 1094 1\n+264 1094 1\n+263 1094 1\n+261 1094 1\n+258 1094 2\n+257 1094 1\n+215 1094 1\n+137 1094 1\n+480 1095 1\n+477 1095 1\n+428 1095 1\n+391 1095 1\n+389 1095 1\n+318 1095 1\n+311 1095 1\n+307 1095 1\n+289 1095 1\n+263 1095 1\n+254 1095 1\n+140 1095 1\n+139 1095 1\n+499 1096 2\n+458 1096 1\n+353 1096 2\n+336 1096 1\n+307 1096 1\n+258 1096 1\n+217 1096 2\n+167 1096 2\n+165 1096 1\n+507 1097 2\n+506 1097 2\n+459 1097 2\n+458 1097 4\n+456 1097 1\n+454 1097 1\n+406 1097 3\n+404 1097 1\n+336 1097 4\n+314 1097 1\n+306 1097 1\n+295 1097 1\n+282 1097 1\n+267 1097 1\n+266 1097 2\n+263 1097 3\n+258 1097 2\n+250 1097 1\n+235 1097 1\n+215 1097 2\n+170 1097 1\n+166 1097 1\n+165 1097 1\n+139 1097 1\n+62 1097 1\n+458 1098 1\n+423 1098 1\n+417 1098 1\n+406 1098 2\n+398 1098 1\n+391 1098 1\n+363 1098 1\n+348 1098 1\n+336 1098 5\n+314 1098 1\n+295 1098 1\n+293 1098 1\n+266 1098 2\n+258 1098 1\n+254 1098 2\n+252 1098 1\n+247 1098 1\n+215 1098 2\n+161 1098 1\n+139 1098 1\n+62 1098 1\n+507 1099 1\n+458 1099 1\n+456 1099 1\n+423 1099 1\n+418 1099 1\n+410 1099 1\n+391 1099 1\n+385 1099 1\n+352 1099 1\n+348 1099 1\n+307 1099 2\n+263 1099 2\n+253 1099 1\n+232 1099 1\n+215 1099 1\n+166 1099 1\n+62 1099 1\n+459 1100 1\n+458 1100 2\n+406 1100 1\n+376 1100 1\n+352 1100 1\n+336 1100 2\n+331 1100 1\n+287 1100 1\n+263 1100 2\n+215 1100 1\n+167 1100 1\n+165 1100 2\n+140 1100 1\n+139 1100 2\n+70 1100 1\n+504 1101 1\n+499 1101 1\n+458 1101 4\n+457 1101 2\n+456 1101 1\n+454 1101 1\n+423 1101 1\n+386 1101 1\n+352 1101 1\n+336 1101 1\n+307 1101 2\n+295 1101 1\n+287 1101 1\n+266 1101 2\n+263 1101 3\n+253 1101 3\n+235 1101 1\n+215 1101 1\n+169 1101 2\n+165 1101 1\n+141 1101 1\n+139 1101 2\n+507 1102 1\n+458 1102 2\n+424 1102 1\n+423 1102 1\n+336 1102 2\n+306 1102 1\n+258 1102 1\n+216 1102 1\n+169 1102 1\n+141 1102 1\n+140 1102 1\n+499 1103 2\n+458 1103 5\n+454 1103 1\n+410 1103 1\n+406 1103 2\n+389 1103 1\n+385 1103 1\n+374 1103 1\n+369 1103 1\n+311 1103 1\n+282 1103 1\n+266 1103 1\n+263 1103 1\n+261 1103 1\n+258 1103 3\n+257 1103 2\n+252 1103 1\n+247 1103 1\n+215 1103 3\n+166 1103 2\n+162 1103 1\n+61 1103 1\n+507 1104 2\n+504 1104 2\n+499 1104 1\n+463 1104 1\n+458 1104 8\n+456 1104 2\n+423 1104 4\n+412 1104 1\n+410 1104 1\n+406 1104 6\n+391 1104 1\n+386 1104 1\n+353 1104 1\n+336 1104 2\n+332 1104 1\n+307 1104 2\n+306 1104 1\n+295 1104 1\n+289 1104 1\n+282 1104 1\n+267 1104 1\n+263 1104 1\n+258 1104 3\n+257 1104 1\n+254 1104 2\n+253 1104 2\n+252 1104 2\n+250 1104 1\n+247 1104 1\n+235 1104 1\n+232 1104 1\n+215 1104 2\n+212 1104 1\n+169 1104 2\n+165 1104 1\n+139 1104 3\n+70 1104 1\n+62 1104 2\n+491 1105 1\n+458 1105 1\n+406 1105 2\n+404 1105 1\n+374 1105 1\n+336 1105 2\n+332 1105 1\n+314 1105 1\n+295 1105 1\n+287 1105 1\n+263 1105 1\n+258 1105 3\n+254 1105 1\n+253 1105 1\n+252 1105 1\n+235 1105 2\n+232 1105 1\n+215 1105 1\n+212 1105 1\n+166 1105 1\n+139 1105 1\n+87 1105 1\n+458 1106 2\n+454 1106 2\n+409 1106 1\n+391 1106 2\n+389 1106 1\n+386 1106 1\n+336 1106 2\n+332 1106 1\n+307 1106 2\n+264 1106 2\n+258 1106 1\n+254 1106 1\n+250 1106 1\n+215 1106 1\n+139 1106 1\n+505 1107 1\n+461 1107 1\n+458 1107 6\n+457 1107 1\n+456 1107 1\n+454 1107 1\n+423 1107 1\n+413 1107 1\n+406 1107 2\n+405 1107 1\n+332 1107 1\n+293 1107 1\n+263 1107 1\n+262 1107 1\n+258 1107 2\n+253 1107 1\n+252 1107 1\n+250 1107 1\n+247 1107 1\n+215 1107 1\n+165 1107 3\n+141 1107 1\n+139 1107 2\n+62 1107 1\n'

diff -r 000000000000 -r c8e4d0b9ae8c test-data/obs_add_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/obs_add_annotation.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,641 @@
+annot1 annot2
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Mo
+81 Mo
+82 Mo
+83 Mo
+84 Mo
+85 Mo
+86 Mo
+87 Mo
+88 Mo
+89 Mo
+90 Mo
+91 Mo
+92 Mo
+93 Mo
+94 Mo
+95 Mo
+96 Mo
+97 Mo
+98 Mo
+99 Mo
+100 Mo
+101 Mo
+102 Mo
+103 Mo
+104 Mo
+105 Mo
+106 Mo
+107 Mo
+108 Mo
+109 Mo
+110 Mo
+111 Mo
+112 Mo
+113 Mo
+114 Mo
+115 Mo
+116 Mo
+117 Mo
+118 Mo
+119 Mo
+120 Mo
+121 Mo
+122 Mo
+123 Mo
+124 Mo
+125 Mo
+126 Mo
+127 Mo
+128 Mo
+129 Mo
+130 Mo
+131 Mo
+132 Mo
+133 Mo
+134 Mo
+135 Mo
+136 Mo
+137 Mo
+138 Mo
+139 Mo
+140 Mo
+141 Mo
+142 Mo
+143 Mo
+144 Mo
+145 Mo
+146 Mo
+147 Mo
+148 Mo
+149 Mo
+150 Mo
+151 Mo
+152 Mo
+153 Mo
+154 Mo
+155 Mo
+156 Mo
+157 Mo
+158 Mo
+159 Mo
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Ery
+81 Ery
+82 Ery
+83 Ery
+84 Ery
+85 Ery
+86 Ery
+87 Ery
+88 Ery
+89 Ery
+90 Ery
+91 Ery
+92 Ery
+93 Ery
+94 Ery
+95 Ery
+96 Ery
+97 Ery
+98 Ery
+99 Ery
+100 Ery
+101 Ery
+102 Ery
+103 Ery
+104 Ery
+105 Ery
+106 Ery
+107 Ery
+108 Ery
+109 Ery
+110 Ery
+111 Ery
+112 Ery
+113 Ery
+114 Ery
+115 Ery
+116 Ery
+117 Ery
+118 Ery
+119 Ery
+120 Ery
+121 Ery
+122 Ery
+123 Ery
+124 Ery
+125 Ery
+126 Ery
+127 Ery
+128 Ery
+129 Ery
+130 Ery
+131 Ery
+132 Ery
+133 Ery
+134 Ery
+135 Ery
+136 Ery
+137 Ery
+138 Ery
+139 Ery
+140 Ery
+141 Ery
+142 Ery
+143 Ery
+144 Ery
+145 Ery
+146 Ery
+147 Ery
+148 Ery
+149 Ery
+150 Ery
+151 Ery
+152 Ery
+153 Ery
+154 Ery
+155 Ery
+156 Ery
+157 Ery
+158 Ery
+159 Ery
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Mk
+81 Mk
+82 Mk
+83 Mk
+84 Mk
+85 Mk
+86 Mk
+87 Mk
+88 Mk
+89 Mk
+90 Mk
+91 Mk
+92 Mk
+93 Mk
+94 Mk
+95 Mk
+96 Mk
+97 Mk
+98 Mk
+99 Mk
+100 Mk
+101 Mk
+102 Mk
+103 Mk
+104 Mk
+105 Mk
+106 Mk
+107 Mk
+108 Mk
+109 Mk
+110 Mk
+111 Mk
+112 Mk
+113 Mk
+114 Mk
+115 Mk
+116 Mk
+117 Mk
+118 Mk
+119 Mk
+120 Mk
+121 Mk
+122 Mk
+123 Mk
+124 Mk
+125 Mk
+126 Mk
+127 Mk
+128 Mk
+129 Mk
+130 Mk
+131 Mk
+132 Mk
+133 Mk
+134 Mk
+135 Mk
+136 Mk
+137 Mk
+138 Mk
+139 Mk
+140 Mk
+141 Mk
+142 Mk
+143 Mk
+144 Mk
+145 Mk
+146 Mk
+147 Mk
+148 Mk
+149 Mk
+150 Mk
+151 Mk
+152 Mk
+153 Mk
+154 Mk
+155 Mk
+156 Mk
+157 Mk
+158 Mk
+159 Mk
+0 progenitor
+1 progenitor
+2 progenitor
+3 progenitor
+4 progenitor
+5 progenitor
+6 progenitor
+7 progenitor
+8 progenitor
+9 progenitor
+10 progenitor
+11 progenitor
+12 progenitor
+13 progenitor
+14 progenitor
+15 progenitor
+16 progenitor
+17 progenitor
+18 progenitor
+19 progenitor
+20 progenitor
+21 progenitor
+22 progenitor
+23 progenitor
+24 progenitor
+25 progenitor
+26 progenitor
+27 progenitor
+28 progenitor
+29 progenitor
+30 progenitor
+31 progenitor
+32 progenitor
+33 progenitor
+34 progenitor
+35 progenitor
+36 progenitor
+37 progenitor
+38 progenitor
+39 progenitor
+40 progenitor
+41 progenitor
+42 progenitor
+43 progenitor
+44 progenitor
+45 progenitor
+46 progenitor
+47 progenitor
+48 progenitor
+49 progenitor
+50 progenitor
+51 progenitor
+52 progenitor
+53 progenitor
+54 progenitor
+55 progenitor
+56 progenitor
+57 progenitor
+58 progenitor
+59 progenitor
+60 progenitor
+61 progenitor
+62 progenitor
+63 progenitor
+64 progenitor
+65 progenitor
+66 progenitor
+67 progenitor
+68 progenitor
+69 progenitor
+70 progenitor
+71 progenitor
+72 progenitor
+73 progenitor
+74 progenitor
+75 progenitor
+76 progenitor
+77 progenitor
+78 progenitor
+79 progenitor
+80 Neu
+81 Neu
+82 Neu
+83 Neu
+84 Neu
+85 Neu
+86 Neu
+87 Neu
+88 Neu
+89 Neu
+90 Neu
+91 Neu
+92 Neu
+93 Neu
+94 Neu
+95 Neu
+96 Neu
+97 Neu
+98 Neu
+99 Neu
+100 Neu
+101 Neu
+102 Neu
+103 Neu
+104 Neu
+105 Neu
+106 Neu
+107 Neu
+108 Neu
+109 Neu
+110 Neu
+111 Neu
+112 Neu
+113 Neu
+114 Neu
+115 Neu
+116 Neu
+117 Neu
+118 Neu
+119 Neu
+120 Neu
+121 Neu
+122 Neu
+123 Neu
+124 Neu
+125 Neu
+126 Neu
+127 Neu
+128 Neu
+129 Neu
+130 Neu
+131 Neu
+132 Neu
+133 Neu
+134 Neu
+135 Neu
+136 Neu
+137 Neu
+138 Neu
+139 Neu
+140 Neu
+141 Neu
+142 Neu
+143 Neu
+144 Neu
+145 Neu
+146 Neu
+147 Neu
+148 Neu
+149 Neu
+150 Neu
+151 Neu
+152 Neu
+153 Neu
+154 Neu
+155 Neu
+156 Neu
+157 Neu
+158 Neu
+159 Neu

diff -r 000000000000 -r c8e4d0b9ae8c test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad

Binary file test-data/pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/pp.pca.krumsiek11.h5ad

Binary file test-data/pp.pca.krumsiek11.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/rows.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rows.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,10 @@
+Gene Protein Testing Testing2
+0 0 3 15
+1 1 4 16
+2 2 5 17
+3 3 6 18
+4 4 7 19
+5 5 8 20
+6 6 9 21
+7 7 10 22
+8 8 11 23

diff -r 000000000000 -r c8e4d0b9ae8c test-data/secondlayer.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/secondlayer.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,9 @@
+0.0 1.0 2.0 3.0 4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 18.0 19.0 20.0 21.0 22.0 23.0 24.0 25.0 26.0 27.0 28.0 29.0 30.0 31.0 32.0 33.0 34.0 35.0 36.0 37.0 38.0 39.0 40.0 41.0 42.0 43.0 44.0 45.0 46.0 47.0 48.0 49.0 50.0 51.0 52.0 53.0 54.0 55.0 56.0 57.0 58.0 59.0 60.0 61.0 62.0 63.0 64.0 65.0 66.0 67.0 68.0 69.0 70.0 71.0 72.0 73.0 74.0 75.0 76.0 77.0 78.0 79.0 80.0 81.0 82.0 83.0 84.0 85.0 86.0 87.0 88.0 89.0 90.0 91.0 92.0 93.0 94.0 95.0 96.0 97.0 98.0 99.0
+100.0 101.0 102.0 103.0 104.0 105.0 106.0 107.0 108.0 109.0 110.0 111.0 112.0 113.0 114.0 115.0 116.0 117.0 118.0 119.0 120.0 121.0 122.0 123.0 124.0 125.0 126.0 127.0 128.0 129.0 130.0 131.0 132.0 133.0 134.0 135.0 136.0 137.0 138.0 139.0 140.0 141.0 142.0 143.0 144.0 145.0 146.0 147.0 148.0 149.0 150.0 151.0 152.0 153.0 154.0 155.0 156.0 157.0 158.0 159.0 160.0 161.0 162.0 163.0 164.0 165.0 166.0 167.0 168.0 169.0 170.0 171.0 172.0 173.0 174.0 175.0 176.0 177.0 178.0 179.0 180.0 181.0 182.0 183.0 184.0 185.0 186.0 187.0 188.0 189.0 190.0 191.0 192.0 193.0 194.0 195.0 196.0 197.0 198.0 199.0
+200.0 201.0 202.0 203.0 204.0 205.0 206.0 207.0 208.0 209.0 210.0 211.0 212.0 213.0 214.0 215.0 216.0 217.0 218.0 219.0 220.0 221.0 222.0 223.0 224.0 225.0 226.0 227.0 228.0 229.0 230.0 231.0 232.0 233.0 234.0 235.0 236.0 237.0 238.0 239.0 240.0 241.0 242.0 243.0 244.0 245.0 246.0 247.0 248.0 249.0 250.0 251.0 252.0 253.0 254.0 255.0 256.0 257.0 258.0 259.0 260.0 261.0 262.0 263.0 264.0 265.0 266.0 267.0 268.0 269.0 270.0 271.0 272.0 273.0 274.0 275.0 276.0 277.0 278.0 279.0 280.0 281.0 282.0 283.0 284.0 285.0 286.0 287.0 288.0 289.0 290.0 291.0 292.0 293.0 294.0 295.0 296.0 297.0 298.0 299.0
+300.0 301.0 302.0 303.0 304.0 305.0 306.0 307.0 308.0 309.0 310.0 311.0 312.0 313.0 314.0 315.0 316.0 317.0 318.0 319.0 320.0 321.0 322.0 323.0 324.0 325.0 326.0 327.0 328.0 329.0 330.0 331.0 332.0 333.0 334.0 335.0 336.0 337.0 338.0 339.0 340.0 341.0 342.0 343.0 344.0 345.0 346.0 347.0 348.0 349.0 350.0 351.0 352.0 353.0 354.0 355.0 356.0 357.0 358.0 359.0 360.0 361.0 362.0 363.0 364.0 365.0 366.0 367.0 368.0 369.0 370.0 371.0 372.0 373.0 374.0 375.0 376.0 377.0 378.0 379.0 380.0 381.0 382.0 383.0 384.0 385.0 386.0 387.0 388.0 389.0 390.0 391.0 392.0 393.0 394.0 395.0 396.0 397.0 398.0 399.0
+400.0 401.0 402.0 403.0 404.0 405.0 406.0 407.0 408.0 409.0 410.0 411.0 412.0 413.0 414.0 415.0 416.0 417.0 418.0 419.0 420.0 421.0 422.0 423.0 424.0 425.0 426.0 427.0 428.0 429.0 430.0 431.0 432.0 433.0 434.0 435.0 436.0 437.0 438.0 439.0 440.0 441.0 442.0 443.0 444.0 445.0 446.0 447.0 448.0 449.0 450.0 451.0 452.0 453.0 454.0 455.0 456.0 457.0 458.0 459.0 460.0 461.0 462.0 463.0 464.0 465.0 466.0 467.0 468.0 469.0 470.0 471.0 472.0 473.0 474.0 475.0 476.0 477.0 478.0 479.0 480.0 481.0 482.0 483.0 484.0 485.0 486.0 487.0 488.0 489.0 490.0 491.0 492.0 493.0 494.0 495.0 496.0 497.0 498.0 499.0
+500.0 501.0 502.0 503.0 504.0 505.0 506.0 507.0 508.0 509.0 510.0 511.0 512.0 513.0 514.0 515.0 516.0 517.0 518.0 519.0 520.0 521.0 522.0 523.0 524.0 525.0 526.0 527.0 528.0 529.0 530.0 531.0 532.0 533.0 534.0 535.0 536.0 537.0 538.0 539.0 540.0 541.0 542.0 543.0 544.0 545.0 546.0 547.0 548.0 549.0 550.0 551.0 552.0 553.0 554.0 555.0 556.0 557.0 558.0 559.0 560.0 561.0 562.0 563.0 564.0 565.0 566.0 567.0 568.0 569.0 570.0 571.0 572.0 573.0 574.0 575.0 576.0 577.0 578.0 579.0 580.0 581.0 582.0 583.0 584.0 585.0 586.0 587.0 588.0 589.0 590.0 591.0 592.0 593.0 594.0 595.0 596.0 597.0 598.0 599.0
+600.0 601.0 602.0 603.0 604.0 605.0 606.0 607.0 608.0 609.0 610.0 611.0 612.0 613.0 614.0 615.0 616.0 617.0 618.0 619.0 620.0 621.0 622.0 623.0 624.0 625.0 626.0 627.0 628.0 629.0 630.0 631.0 632.0 633.0 634.0 635.0 636.0 637.0 638.0 639.0 640.0 641.0 642.0 643.0 644.0 645.0 646.0 647.0 648.0 649.0 650.0 651.0 652.0 653.0 654.0 655.0 656.0 657.0 658.0 659.0 660.0 661.0 662.0 663.0 664.0 665.0 666.0 667.0 668.0 669.0 670.0 671.0 672.0 673.0 674.0 675.0 676.0 677.0 678.0 679.0 680.0 681.0 682.0 683.0 684.0 685.0 686.0 687.0 688.0 689.0 690.0 691.0 692.0 693.0 694.0 695.0 696.0 697.0 698.0 699.0
+700.0 701.0 702.0 703.0 704.0 705.0 706.0 707.0 708.0 709.0 710.0 711.0 712.0 713.0 714.0 715.0 716.0 717.0 718.0 719.0 720.0 721.0 722.0 723.0 724.0 725.0 726.0 727.0 728.0 729.0 730.0 731.0 732.0 733.0 734.0 735.0 736.0 737.0 738.0 739.0 740.0 741.0 742.0 743.0 744.0 745.0 746.0 747.0 748.0 749.0 750.0 751.0 752.0 753.0 754.0 755.0 756.0 757.0 758.0 759.0 760.0 761.0 762.0 763.0 764.0 765.0 766.0 767.0 768.0 769.0 770.0 771.0 772.0 773.0 774.0 775.0 776.0 777.0 778.0 779.0 780.0 781.0 782.0 783.0 784.0 785.0 786.0 787.0 788.0 789.0 790.0 791.0 792.0 793.0 794.0 795.0 796.0 797.0 798.0 799.0
+800.0 801.0 802.0 803.0 804.0 805.0 806.0 807.0 808.0 809.0 810.0 811.0 812.0 813.0 814.0 815.0 816.0 817.0 818.0 819.0 820.0 821.0 822.0 823.0 824.0 825.0 826.0 827.0 828.0 829.0 830.0 831.0 832.0 833.0 834.0 835.0 836.0 837.0 838.0 839.0 840.0 841.0 842.0 843.0 844.0 845.0 846.0 847.0 848.0 849.0 850.0 851.0 852.0 853.0 854.0 855.0 856.0 857.0 858.0 859.0 860.0 861.0 862.0 863.0 864.0 865.0 866.0 867.0 868.0 869.0 870.0 871.0 872.0 873.0 874.0 875.0 876.0 877.0 878.0 879.0 880.0 881.0 882.0 883.0 884.0 885.0 886.0 887.0 888.0 889.0 890.0 891.0 892.0 893.0 894.0 895.0 896.0 897.0 898.0 899.0

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.diffmap.h5ad

Binary file test-data/tl.diffmap.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.draw_graph.h5ad

Binary file test-data/tl.draw_graph.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad

Binary file test-data/tl.paga.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.rank_genes_groups.krumsiek11.h5ad

Binary file test-data/tl.rank_genes_groups.krumsiek11.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.tsne.h5ad

Binary file test-data/tl.tsne.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/tl.umap.h5ad

Binary file test-data/tl.umap.h5ad has changed

diff -r 000000000000 -r c8e4d0b9ae8c test-data/umi_tools.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/umi_tools.tsv Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,23 @@
+gene cell count
+ENSG00000011304.18 ACAAGG 33
+ENSG00000011304.18 TTCACG 24
+ENSG00000065268.10 ACAAGG 4
+ENSG00000065268.10 TTCACG 11
+ENSG00000070404.9 TTCACG 1
+ENSG00000070423.17 ACAAGG 2
+ENSG00000070423.17 TTCACG 4
+ENSG00000099804.8 ACAAGG 5
+ENSG00000099804.8 TTCACG 4
+ENSG00000099821.13 ACAAGG 6
+ENSG00000099821.13 TTCACG 1
+ENSG00000099864.17 TTCACG 2
+ENSG00000105556.11 ACAAGG 2
+ENSG00000105556.11 TTCACG 3
+ENSG00000116017.10 ACAAGG 7
+ENSG00000116017.10 TTCACG 18
+ENSG00000172270.18 ACAAGG 9
+ENSG00000172270.18 TTCACG 3
+ENSG00000175221.14 ACAAGG 1
+ENSG00000175221.14 TTCACG 3
+ENSG00000198858.9 ACAAGG 1
+ENSG00000267751.5 TTCACG 1

diff -r 000000000000 -r c8e4d0b9ae8c test-data/var_add_annotation.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/var_add_annotation.tabular Mon Jan 06 13:43:38 2020 -0500

@@ -0,0 +1,12 @@
+annot1 annot2
+1 a
+2 b
+3 c
+4 d
+5 e
+6 f
+7 g
+8 h
+9 i
+10 j
+11 k

diff -r 000000000000 -r c8e4d0b9ae8c tsv_to_loompy.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tsv_to_loompy.py Mon Jan 06 13:43:38 2020 -0500

[

@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+"""This module converts a tsv file into a binary loom file"""
+
+import argparse
+import os
+
+import loompy
+import numpy as np
+
+parser = argparse.ArgumentParser(description="Loompy file converter flags")
+parser.add_argument('--VERSION', action='version', version='%(prog)s 0.1.0',
+                    help="Displays tool version")
+parser.add_argument('--rowfile', '-r', help="File of row attributes & values")
+parser.add_argument('--colfile', '-c',
+                    help="File of column attributes and values")
+parser.add_argument('--output', '-o', help="Output file name")
+parser.add_argument('--files', '-f', nargs='*',
+                    help="Input tsv files. First file becomes main layer.")
+args = parser.parse_args()
+
+colsfile = args.colfile
+rowsfile = args.rowfile
+if args.output:
+    filename = args.output
+else:
+    filename = "converted.loom"
+alldata = args.files
+alayers = []
+layernames = []
+rowdict = {}
+coldict = {}
+
+#  Creates dictionary based on row file
+#  For each attribute:
+#  Attribute: [attribute values]
+with open(rowsfile, "r") as rows:
+    count = 0
+    for line in rows:
+        line = line.strip().split("\t")
+        if count == 0:  # First time through
+            row_attributes = line
+            for x in row_attributes:
+                rowdict[x] = []
+            count += 1
+        else:
+            for x in range(0, len(line)):
+                rowdict[row_attributes[x]].append(line[x])
+#  Same as above, but for columns
+with open(colsfile, "r") as cols:
+    count = 0
+    for line in cols:
+        line = line.replace('\"', "")
+        line = line.replace(' ', "")
+        line = line.strip().split("\t")
+        if count == 0:  # First time through
+            col_attributes = line
+            for x in col_attributes:
+                coldict[x] = []
+            count += 1
+        else:
+            for x in range(0, len(line)):
+                coldict[col_attributes[x]].append(line[x])
+#  Finding dimensions for the loom layers
+rowshape = len(rowdict[list(rowdict.keys())[0]])
+colshape = len(coldict[list(coldict.keys())[0]])
+
+#  Creates a list with each element being entire matrix of
+#  each layer file as floats
+for file in range(0, len(alldata)):
+    layer = alldata[file][:-4]
+    layer = layer.split("/")[-1]
+    if layer == "":
+        raise Exception("Please only use named files")
+    layernames.append(layer)
+    cfile = alldata[file]
+    with open(cfile, "r") as tsv:
+        cmatrix = []
+        for line in tsv:
+            line = line.strip().split("\t")
+            line = [float(i) for i in line]
+            cmatrix += line
+        alayers.append(cmatrix)
+
+#  Loompy cannot overwright existing files. If somehow it finds
+#  a second file with the same name, it must be deleted
+if os.path.isfile(filename):
+    os.remove(filename)
+#  To create the file properly, the first row and column attributes must be
+#  added separately in the form of individual dictionaries
+row_attrs = {row_attributes[0]: np.asarray(rowdict[row_attributes[0]])}
+col_attrs = {col_attributes[0]: np.asarray(coldict[col_attributes[0]])}
+matrix = np.asarray(alayers[0])
+matrix = matrix.astype(float)
+matrix = matrix.reshape(rowshape, colshape)
+#  Creation of initial loom file
+if "loom" not in filename[-5:]:
+    filename = filename + ".loom"
+loompy.create(filename, matrix, row_attrs, col_attrs)
+#  Adding all row and column attributes, then all layers
+with loompy.connect(filename) as loomfile:
+    for x in row_attributes:
+        loomfile.ra[x] = rowdict[x]
+    for y in col_attributes:
+        loomfile.ca[y] = coldict[y]
+    for z in range(1, len(alayers)):
+        matrix = np.asarray(alayers[z])
+        matrix = matrix.astype(float)
+        matrix = matrix.reshape(rowshape, colshape)
+        loomfile[layernames[z]] = matrix