| Next changeset 1:19592ec717ef (2019-10-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da |
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added:
macros.xml manipulate.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 |
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| diff -r 000000000000 -r 0ef28c0963c8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 10 03:25:05 2019 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r 0ef28c0963c8 manipulate.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/manipulate.xml Wed Apr 10 03:25:05 2019 -0400 |
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| b'@@ -0,0 +1,217 @@\n+<tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@">\n+ <description>object</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <xml name="param_join">\n+ <param name="join" type="select" label="The connecting string between name and integer">\n+ <option value="-">-</option>\n+ <option value="_">_</option>\n+ <option value=" "> </option>\n+ <option value="/">/</option>\n+ </param>\n+ </xml>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+@CMD@\n+ ]]></command>\n+ <configfiles>\n+ <configfile name="script_file"><![CDATA[\n+@CMD_imports@\n+\n+adata = ad.read(\'$input\')\n+\n+#if $manipulate.function == \'concatenate\'\n+ #for i, filepath in enumerate($manipulate.other_adatas)\n+adata_$i = ad.read(\'$filepath\')\n+ #end for\n+adata.concatenate(\n+ #for i, filepath in enumerate($manipulate.other_adatas)\n+ adata_$i,\n+ #end for\n+ join=\'$manipulate.join\',\n+ #if str($manipulate.index_unique) != \'\'\n+ index_unique=\'$manipulate.index_unique\',\n+ #else\n+ index_unique=None,\n+ #end if\n+ batch_key=\'$manipulate.batch_key\')\n+\n+#else if $manipulate.function == \'var_names_make_unique\'\n+adata.var_names_make_unique(join=\'$manipulate.join\')\n+\n+#else if $manipulate.function == \'obs_names_make_unique\'\n+adata.obs_names_make_unique(join=\'$manipulate.join\')\n+\n+#else if $manipulate.function == \'rename_categories\'\n+ #set $categories = [x.strip() for x in str($manipulate.categories).split(\',\')]\n+adata.rename_categories(\n+ key=\'$manipulate.key\',\n+ categories=$categories)\n+\n+#else if $manipulate.function == \'transpose\'\n+adata.transpose()\n+\n+#else if $manipulate.function == \'strings_to_categoricals\'\n+adata.strings_to_categoricals()\n+#end if\n+\n+adata.write(\'anndata.h5ad\')\n+]]></configfile>\n+ </configfiles>\n+ <inputs>\n+ <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>\n+ <conditional name="manipulate">\n+ <param name="function" type="select" label="Function of manipulate the object">\n+ <option value="concatenate">Concatenate along the observations axis</option>\n+ <option value="obs_names_make_unique">Makes the obs index unique by appending \'1\', \'2\', etc</option>\n+ <option value="var_names_make_unique">Makes the var index unique by appending \'1\', \'2\', etc</option>\n+ <option value="rename_categories">Rename categories of annotation</option>\n+ <option value="strings_to_categoricals">Transform string annotations to categoricals</option>\n+ <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>\n+ </param>\n+ <when value="concatenate">\n+ <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>\n+ <param name="join" type="select" label="Join method">\n+ <option value="inner">Intersection of variables</option>\n+ <option value="outer">Union of variables</option>\n+ </param>\n+ <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>\n+ <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices">\n+ <option value="-">-</option>\n+ <option value="_">_</option>\n+ <option value=" "> </option>\n+ <option value="/">/</option>\n+ </param>\n+ </when>\n+ <when value="obs_names_make_unique">\n+ <expand macro="param_join"/>\n+ </when>\n+ '..b' </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.var_names_make_unique\\(join=\'-\'\\)"/>\n+ </assert_stdout>\n+ <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="rename_categories"/>\n+ <param name="key" value="cell_type"/>\n+ <param name="categories" value="Er,Ml,Mt, Ne, pr"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.rename_categories"/>\n+ <has_text_matching expression="key=\'cell_type\'"/>\n+ <has_text_matching expression="categories=\\[\'Er\', \'Ml\', \'Mt\', \'Ne\', \'pr\'\\]"/>\n+ </assert_stdout>\n+ <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="strings_to_categoricals"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.strings_to_categoricals"/>\n+ </assert_stdout>\n+ <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ <test>\n+ <param name="input" value="krumsiek11.h5ad"/>\n+ <conditional name="manipulate">\n+ <param name="function" value="transpose"/>\n+ </conditional>\n+ <assert_stdout>\n+ <has_text_matching expression="adata.transpose"/>\n+ </assert_stdout>\n+ <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+This tool takes a AnnData dataset, manipulates it and returns it. \n+\n+The possible manipulations are: \n+\n+- Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__) \n+\n+ The `uns`, `varm` and `obsm` attributes are ignored.\n+\n+ If you use `join=\'outer\'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN`\n+\n+- Makes the obs index unique by appending \'1\', \'2\', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__) \n+\n+ The first occurance of a non-unique value is ignored.\n+\n+- Makes the var index unique by appending \'1\', \'2\', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__) \n+\n+ The first occurance of a non-unique value is ignored.\n+\n+- Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__) \n+\n+ Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key`\n+\n+- Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__) \n+\n+ Only affects string annotations that lead to less categories than the total number of observations.\n+\n+- Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)\n+\n+ Data matrix is transposed, observations and variables are interchanged.\n+\n+@HELP@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 0ef28c0963c8 test-data/adata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adata.csv Wed Apr 10 03:25:05 2019 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 0ef28c0963c8 test-data/adata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/adata.tsv Wed Apr 10 03:25:05 2019 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
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| 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' |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| b'@@ -0,0 +1,640 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| diff -r 000000000000 -r 0ef28c0963c8 test-data/export.krumsiek11.loom |
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| Binary file test-data/export.krumsiek11.loom has changed |
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| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
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| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +index +Gata2 +Gata1 +Fog1 +EKLF +Fli1 +SCL +Cebpa +Pu.1 +cJun +EgrNab +Gfi1 |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ + + + + + + + + + + + + |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
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|
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,641 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ +index +Gata2 +Gata1 +Fog1 +EKLF +Fli1 +SCL +Cebpa +Pu.1 +cJun +EgrNab +Gfi1 |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,12 @@ + + + + + + + + + + + + |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| 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' |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -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 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| diff -r 000000000000 -r 0ef28c0963c8 test-data/inspect.X.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inspect.X.tabular Wed Apr 10 03:25:05 2019 -0400 |
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| b'@@ -0,0 +1,641 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|
| b |
| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 test-data/inspect.general.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inspect.general.txt Wed Apr 10 03:25:05 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +AnnData object with n_obs × n_vars = 640 × 11 + obs: 'cell_type' + uns: 'cell_type_colors', 'highlights', 'iroot' |
| b |
| diff -r 000000000000 -r 0ef28c0963c8 test-data/inspect.obs.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inspect.obs.tabular Wed Apr 10 03:25:05 2019 -0400 |
| b |
| @@ -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 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| diff -r 000000000000 -r 0ef28c0963c8 test-data/inspect.var.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inspect.var.tabular Wed Apr 10 03:25:05 2019 -0400 |
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| @@ -0,0 +1,12 @@ +index +Gata2 +Gata1 +Fog1 +EKLF +Fli1 +SCL +Cebpa +Pu.1 +cJun +EgrNab +Gfi1 |
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| diff -r 000000000000 -r 0ef28c0963c8 test-data/krumsiek11.h5ad |
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| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r 0ef28c0963c8 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 03:25:05 2019 -0400 |
| b |
| 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 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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' |
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| diff -r 000000000000 -r 0ef28c0963c8 test-data/umi_tools.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/umi_tools.tsv Wed Apr 10 03:25:05 2019 -0400 |
| b |
| @@ -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 |