Galaxy |

Changeset 0:69e2275406fd (2019-04-10)

Next changeset 1:a61350ab6563 (2019-10-16)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da

added:
import.xml
macros.xml
test-data/adata.csv
test-data/adata.tsv
test-data/barcodes_10x_v1.2.0.tsv
test-data/barcodes_10x_v3.0.0.tsv
test-data/export.krumsiek11.X.tabular
test-data/export.krumsiek11.loom
test-data/export.krumsiek11.obs.tabular
test-data/export.krumsiek11.obsm.tabular
test-data/export.krumsiek11.var.tabular
test-data/export.krumsiek11.varm.tabular
test-data/export_csv_X.csv
test-data/export_csv_obs.csv
test-data/export_csv_obsm.csv
test-data/export_csv_var.csv
test-data/export_csv_varm.csv
test-data/features_10x_v3.0.0.tsv
test-data/genes_10x_v1.2.0.tsv
test-data/import.csv.h5ad
test-data/import.loom.krumsiek11.h5ad
test-data/import.mtx.legacy_10x.h5ad
test-data/import.mtx.no_10x.h5ad
test-data/import.mtx.v3_10x.h5ad
test-data/import.tsv.h5ad
test-data/import.umi_tools.h5ad
test-data/inspect.X.tabular
test-data/inspect.chunk_X.specified.tabular
test-data/inspect.general.txt
test-data/inspect.obs.tabular
test-data/inspect.var.tabular
test-data/krumsiek11.h5ad
test-data/krumsiek11.loom
test-data/manipulate.concatenate.h5ad
test-data/manipulate.obs_names_make_unique.h5ad
test-data/manipulate.rename_categories.h5ad
test-data/manipulate.strings_to_categoricals.h5ad
test-data/manipulate.transpose.h5ad
test-data/manipulate.var_names_make_unique.h5ad
test-data/matrix_10x_v1.2.0.mtx
test-data/matrix_10x_v3.0.0.mtx
test-data/umi_tools.tsv

diff -r 000000000000 -r 69e2275406fd import.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/import.xml Wed Apr 10 03:23:36 2019 -0400

[

b'@@ -0,0 +1,244 @@\n+<tool id="anndata_import" name="Import AnnData" version="@VERSION@+@GALAXY_VERSION@">\n+ <description>from different format</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <xml name="params_10x">\n+ <param name="barcodes" type="data" format="tabular,txt" label="Barcodes"/>\n+ <param name="var_names" type="select" label="Variables index">\n+ <option value="gene_symbols">gene_symbols</option>\n+ <option value="gene_ids">gene_ids</option>\n+ </param>\n+ <param name="make_unique" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Make the variable index unique by appending \'-1\', \'-2\'?"/>\n+ <param name="gex_only" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Keep only \'Gene Expression\' data and ignore other feature types?"/>\n+ </xml>\n+ </macros>\n+ <expand macro="requirements">\n+\n+ </expand>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+#if $in.adata_format == \'mtx\'\n+mkdir mtx\n+ #if $in.tenx.use == \'legacy_10x\'\n+&& cp \'$in.matrix\' \'mtx/matrix.mtx\'\n+&& cp \'$in.tenx.genes\' \'mtx/genes.tsv\'\n+&& cp \'$in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n+ #else if $in.tenx.use == \'v3_10x\'\n+&& cp \'$in.matrix\' \'mtx/matrix.mtx\'\n+&& gzip \'mtx/matrix.mtx\'\n+&& cp \'$in.tenx.features\' \'mtx/features.tsv\'\n+&& gzip \'mtx/features.tsv\'\n+&& cp \'$in.tenx.barcodes\' \'mtx/barcodes.tsv\'\n+&& gzip \'mtx/barcodes.tsv\'\n+ #end if\n+&&\n+#else if $in.adata_format == \'umi_tools\'\n+gzip \'$in.input\'\n+&&\n+#end if\n+\n+@CMD@\n+\n+#if $in.adata_format == \'mtx\'\n+&& rm -rf mtx\n+#end if\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+@CMD_imports@\n+#if $in.adata_format == \'loom\'\n+adata = ad.read_loom(\n+ \'$in.input\',\n+ sparse=$in.sparse,\n+ cleanup=$in.cleanup,\n+ X_name=\'$in.x_name\',\n+ obs_names=\'$in.obs_names\',\n+ var_names=\'$in.var_names\')\n+\n+#else if $in.adata_format == \'tabular\'\n+ #set delimiter=$in.input.metadata.delimiter\n+ #if $delimiter != \',\'\n+ #set delimiter=\'\\\\t\'\n+ #end if\n+adata = ad.read_csv(\n+ \'$in.input\',\n+ delimiter=\'$delimiter\',\n+ first_column_names=$in.first_column_names)\n+\n+#else if $in.adata_format == \'mtx\'\n+ #if $in.tenx.use == \'no\'\n+adata = ad.read_mtx(filename=\'$in.matrix\')\n+ #else\n+import scanpy as sc\n+adata = sc.read_10x_mtx(\n+ \'mtx\',\n+ var_names=\'$in.tenx.var_names\',\n+ make_unique=$in.tenx.make_unique,\n+ cache=False,\n+ gex_only=$in.tenx.gex_only)\n+ #end if\n+\n+#else if $in.adata_format == \'umi_tools\'\n+adata = ad.read_umi_tools(\'${in.input}.gz\')\n+\n+#end if\n+\n+adata.write(\'anndata.h5ad\')\n+]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <conditional name="in">\n+ <param name="adata_format" type="select" label="Format for the annotated data matrix">\n+ <option value="loom">Loom</option>\n+ <option value="tabular">Tabular, CSV, TSV</option>\n+ <option value="mtx">Matrix Market (mtx), from Cell ranger or not</option>\n+ <option value="umi_tools">UMI tools</option>\n+ </param>\n+ <when value="loom">\n+ <param name="input" type="data" format="loom" label="Annotated data matrix"/>\n+ <param name="sparse" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Is the data matrix to read sparse?"/>\n+ <param name="cleanup" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cleanup?"/>\n+ <param name="x_name" type="text" value="spliced" label="X_name"/>\n+ <param name="obs_names" type="text" value="CellID" label="obs_names"/>\n+ <param name="var_names" type="text" value="Gene" label="var_names"/>\n+ </when>\n+ <when value="tabular">\n+ <param name="input" type="data" format="tabular,csv'..b'<has_text_matching expression="ad.read_csv"/>\n+ <has_text_matching expression="delimiter=\',\'"/>\n+ <has_text_matching expression="first_column_names=True"/>\n+ </assert_stdout>\n+ <output name="anndata" value="import.csv.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <conditional name="in">\n+ <param name="adata_format" value="tabular"/>\n+ <param name="input" value="adata.tsv"/>\n+ <param name="first_column_names" value="true"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="ad.read_csv"/>\n+ <has_text_matching expression="delimiter=\'\\\\t\'"/>\n+ <has_text_matching expression="first_column_names=True"/>\n+ </assert_stdout>\n+ <output name="anndata" value="import.tsv.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ \n+ <test>\n+ <conditional name="in">\n+ <param name="adata_format" value="umi_tools"/>\n+ <param name="input" value="umi_tools.tsv"/>\n+ </conditional>\n+ <output name="anndata" value="import.umi_tools.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+This tool creates an AnnData dataset from several input types:\n+\n+- Loom (`read_loom method <https://anndata.readthedocs.io/en/latest/anndata.read_loom.html>`__) \n+- Tabular (`read_csv method <https://anndata.readthedocs.io/en/latest/anndata.read_csv.html>`__) \n+- Matrix Market (mtx), from Cell ranger or not (`read_mtx method <https://anndata.readthedocs.io/en/latest/anndata.read_mtx.html>`__) \n+- UMI tools (`read_umi_tools method <https://anndata.readthedocs.io/en/latest/anndata.read_umi_tools.html>`__) \n+\n+@HELP@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n'

diff -r 000000000000 -r 69e2275406fd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Apr 10 03:23:36 2019 -0400

[

@@ -0,0 +1,62 @@
+<macros>
+    <token name="@VERSION@">0.6.19</token>
+    <token name="@GALAXY_VERSION@">galaxy0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">anndata</requirement>
+            <requirement type="package" version="1.4">scanpy</requirement>
+            <requirement type="package" version="2.0.17">loompy</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__)"]]></version_command>
+    </xml>
+    <token name="@CMD@"><![CDATA[
+cat '$script_file' &&
+python '$script_file'
+    ]]>
+    </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>`__
+    ]]>
+    </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 69e2275406fd test-data/adata.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adata.csv Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd test-data/adata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adata.tsv Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

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 69e2275406fd test-data/export.krumsiek11.X.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.X.tabular Wed Apr 10 03:23:36 2019 -0400

b'@@ -0,0 +1,640 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diff -r 000000000000 -r 69e2275406fd test-data/export.krumsiek11.loom

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

diff -r 000000000000 -r 69e2275406fd test-data/export.krumsiek11.obs.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.obs.tabular Wed Apr 10 03:23:36 2019 -0400

@@ -0,0 +1,641 @@
+index cell_type
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+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
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diff -r 000000000000 -r 69e2275406fd test-data/export.krumsiek11.obsm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.obsm.tabular Wed Apr 10 03:23:36 2019 -0400

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diff -r 000000000000 -r 69e2275406fd test-data/export.krumsiek11.var.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.var.tabular Wed Apr 10 03:23:36 2019 -0400

@@ -0,0 +1,12 @@
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diff -r 000000000000 -r 69e2275406fd test-data/export.krumsiek11.varm.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export.krumsiek11.varm.tabular Wed Apr 10 03:23:36 2019 -0400

@@ -0,0 +1,12 @@
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diff -r 000000000000 -r 69e2275406fd test-data/export_csv_X.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_X.csv Wed Apr 10 03:23:36 2019 -0400

diff -r 000000000000 -r 69e2275406fd test-data/export_csv_obs.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_obs.csv Wed Apr 10 03:23:36 2019 -0400

diff -r 000000000000 -r 69e2275406fd test-data/export_csv_obsm.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_obsm.csv Wed Apr 10 03:23:36 2019 -0400

diff -r 000000000000 -r 69e2275406fd test-data/export_csv_var.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_var.csv Wed Apr 10 03:23:36 2019 -0400

@@ -0,0 +1,12 @@
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diff -r 000000000000 -r 69e2275406fd test-data/export_csv_varm.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/export_csv_varm.csv Wed Apr 10 03:23:36 2019 -0400

@@ -0,0 +1,12 @@
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diff -r 000000000000 -r 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

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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 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd test-data/import.csv.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.loom.krumsiek11.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.mtx.legacy_10x.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.mtx.no_10x.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.mtx.v3_10x.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.tsv.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/import.umi_tools.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/inspect.X.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.X.tabular Wed Apr 10 03:23:36 2019 -0400

b'@@ -0,0 +1,641 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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 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd test-data/inspect.general.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.general.txt Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd test-data/inspect.obs.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.obs.tabular Wed Apr 10 03:23:36 2019 -0400

diff -r 000000000000 -r 69e2275406fd test-data/inspect.var.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/inspect.var.tabular Wed Apr 10 03:23:36 2019 -0400

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

diff -r 000000000000 -r 69e2275406fd test-data/krumsiek11.h5ad

Binary file test-data/krumsiek11.h5ad has changed

diff -r 000000000000 -r 69e2275406fd test-data/krumsiek11.loom

Binary file test-data/krumsiek11.loom has changed

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.concatenate.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.obs_names_make_unique.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.rename_categories.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.strings_to_categoricals.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.transpose.h5ad

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

diff -r 000000000000 -r 69e2275406fd test-data/manipulate.var_names_make_unique.h5ad

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

diff -r 000000000000 -r 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

@@ -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 69e2275406fd 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 Wed Apr 10 03:23:36 2019 -0400

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 69e2275406fd test-data/umi_tools.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/umi_tools.tsv Wed Apr 10 03:23:36 2019 -0400

@@ -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