v0.3.1

docs/locale/zh_CN/LC_MESSAGES/api.po

@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: scglue 0.2.3\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2022-08-12 12:19+0800\n"
+"POT-Creation-Date: 2022-08-22 14:24+0800\n"
 "Last-Translator: Pei-Wen Ji <[email protected]>\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=utf-8\n"
@@ -144,7 +144,7 @@ msgstr ""
 msgid "Check whether certain dependencies are installed"
 msgstr ""
 
-#: ../../api/scglue.check.rst:25 ../../api/scglue.genomics.rst:37
+#: ../../api/scglue.check.rst:25 ../../api/scglue.genomics.rst:38
 #: ../../api/scglue.models.base.rst:17 ../../api/scglue.models.data.rst:17
 #: ../../api/scglue.models.glue.rst:17 ../../api/scglue.models.nn.rst:27
 #: ../../api/scglue.models.plugins.rst:17 ../../api/scglue.models.prob.rst:17
@@ -440,7 +440,8 @@ msgstr ""
 #: scglue.genomics.ens_trim_version scglue.genomics.get_chr_len_from_fai
 #: scglue.genomics.interval_dist scglue.genomics.read_ctx_grn
 #: scglue.genomics.regulatory_inference
-#: scglue.genomics.rna_anchored_guidance_graph scglue.genomics.window_graph
+#: scglue.genomics.rna_anchored_guidance_graph
+#: scglue.genomics.rna_anchored_prior_graph scglue.genomics.window_graph
 #: scglue.genomics.write_links scglue.genomics.write_scenic_feather
 #: scglue.graph.check_graph scglue.graph.collapse_multigraph
 #: scglue.graph.compose_multigraph scglue.graph.reachable_vertices
@@ -1244,144 +1245,155 @@ msgstr ""
 msgid "scglue.genomics"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`cis_regulatory_ranking <scglue.genomics.cis_regulatory_ranking>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.cis_regulatory_ranking:1
 msgid "Generate cis-regulatory ranking between genes and transcription factors"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`dist_power_decay <scglue.genomics.dist_power_decay>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.dist_power_decay:1
 msgid ""
 "Distance-based power decay weight, computed as :math:`w = {\\left( \\frac"
 " {d + 1000} {1000} \\right)} ^ {-0.75}`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`ens_trim_version <scglue.genomics.ens_trim_version>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.ens_trim_version:1
 msgid "Trim version suffix from Ensembl ID"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`get_chr_len_from_fai <scglue.genomics.get_chr_len_from_fai>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.get_chr_len_from_fai:1
 msgid "Get chromosome length information from fasta index file"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`interval_dist <scglue.genomics.interval_dist>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.interval_dist:1
 msgid "Compute distance and relative position between two bed intervals"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`read_bed <scglue.genomics.read_bed>`"
 msgstr ""
 
 #: ../../api/scglue.genomics.Bed.rst:30:<autosummary>:1
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.Bed.read_bed:1
 msgid "Read BED file"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`read_ctx_grn <scglue.genomics.read_ctx_grn>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.read_ctx_grn:1
 msgid "Read pruned TF-target GRN as generated by ``pyscenic ctx``"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`read_gtf <scglue.genomics.read_gtf>`"
 msgstr ""
 
 #: ../../api/scglue.genomics.Gtf.rst:26:<autosummary>:1
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.Gtf.read_gtf:1
 msgid "Read GTF file"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`regulatory_inference <scglue.genomics.regulatory_inference>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.regulatory_inference:1
 msgid "Regulatory inference based on feature embeddings"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ""
 ":py:obj:`rna_anchored_guidance_graph "
 "<scglue.genomics.rna_anchored_guidance_graph>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.rna_anchored_guidance_graph:1
 msgid "Build guidance graph anchored on RNA genes"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
+msgid ""
+":py:obj:`rna_anchored_prior_graph "
+"<scglue.genomics.rna_anchored_prior_graph>`"
+msgstr ""
+
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
+#: scglue.genomics.rna_anchored_prior_graph:1
+msgid "Deprecated, please use :func:`rna_anchored_guidance_graph` instead"
+msgstr ""
+
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`window_graph <scglue.genomics.window_graph>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.window_graph:1
 msgid ""
 "Construct a window graph between two sets of genomic features, where "
 "features pairs within a window size are connected."
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`write_links <scglue.genomics.write_links>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.write_links:1
 msgid "Export regulatory graph into a links file"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1
 msgid ":py:obj:`write_scenic_feather <scglue.genomics.write_scenic_feather>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:35:<autosummary>:1 of
+#: ../../api/scglue.genomics.rst:36:<autosummary>:1 of
 #: scglue.genomics.write_scenic_feather:1
 msgid "Write cis-regulatory ranking to a SCENIC-compatible feather file"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:44:<autosummary>:1
+#: ../../api/scglue.genomics.rst:45:<autosummary>:1
 msgid ":py:obj:`Bed <scglue.genomics.Bed>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:44:<autosummary>:1 of scglue.genomics.Bed:1
+#: ../../api/scglue.genomics.rst:45:<autosummary>:1 of scglue.genomics.Bed:1
 msgid "BED format data frame"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:44:<autosummary>:1
+#: ../../api/scglue.genomics.rst:45:<autosummary>:1
 msgid ":py:obj:`Gtf <scglue.genomics.Gtf>`"
 msgstr ""
 
-#: ../../api/scglue.genomics.rst:44:<autosummary>:1 of scglue.genomics.Gtf:1
+#: ../../api/scglue.genomics.rst:45:<autosummary>:1 of scglue.genomics.Gtf:1
 msgid "GTF format data frame"
 msgstr ""
 
@@ -2000,7 +2012,7 @@ msgid "**CAUTION: DO NOT USE**, only for evaluation purpose"
 msgstr ""
 
 #: of scglue.genomics.rna_anchored_guidance_graph:28
-#: scglue.genomics.window_graph:24
+#: scglue.genomics.rna_anchored_prior_graph:4 scglue.genomics.window_graph:24
 msgid ":py:class:`~networkx.MultiDiGraph`"
 msgstr ""
 
@@ -2015,6 +2027,10 @@ msgid ""
 " guidance graph manually."
 msgstr ""
 
+#: ../../api/scglue.genomics.rna_anchored_prior_graph.rst:2
+msgid "scglue.genomics.rna\\_anchored\\_prior\\_graph"
+msgstr ""
+
 #: ../../api/scglue.genomics.window_graph.rst:2
 msgid "scglue.genomics.window\\_graph"
 msgstr ""

docs/locale/zh_CN/LC_MESSAGES/reginf.po

@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: scglue 0.2.3\n"
 "Report-Msgid-Bugs-To: \n"
-"POT-Creation-Date: 2022-08-12 20:21+0800\n"
+"POT-Creation-Date: 2022-08-22 14:24+0800\n"
 "Last-Translator: Zhi-Jie Cao <[email protected]>\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=utf-8\n"
@@ -183,8 +183,8 @@ msgid ""
 "construction>`__), so the inferred regulatory connections are limited to "
 "the proximal promoter and gene body regions."
 msgstr ""
-"需要注意的是，在本教程中，指导图简单地使用了基因组重叠（请参考 `第一步 <preprocessing.ipynb#图构建>`__），"
-"所以推断的调控关系也仅限于近端启动子和基因本体区。"
+"需要注意的是，在本教程中，指导图简单地使用了基因组重叠（请参考 `第一步 "
+"<preprocessing.ipynb#图构建>`__），所以推断的调控关系也仅限于近端启动子和基因本体区。"
 
 #: ../../reginf.ipynb:424
 msgid ""
@@ -245,45 +245,39 @@ msgid "JASPAR motif hits:"
 msgstr "JASPAR motif结合："
 
 #: ../../reginf.ipynb:446
-msgid "http://download.gao-lab.org/GLUE/cisreg/hg19-JASPAR2022-merged.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-hg19.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:447
-msgid "http://download.gao-lab.org/GLUE/cisreg/hg38-JASPAR2022-merged.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-hg38.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:448
-msgid "http://download.gao-lab.org/GLUE/cisreg/mm9-JASPAR2022-merged.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-mm9.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:449
-msgid "http://download.gao-lab.org/GLUE/cisreg/mm10-JASPAR2022-merged.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/JASPAR2022-mm10.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:451
 msgid "ENCODE TF ChIP-seq:"
 msgstr ""
 
 #: ../../reginf.ipynb:453
-msgid ""
-"http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-combined-"
-"hg38.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-hg38.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:454
-msgid ""
-"http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-combined-"
-"hg19.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-hg19.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:455
-msgid ""
-"http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-combined-"
-"mm10.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-mm10.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:456
-msgid "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-combined-mm9.bed.gz"
+msgid "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-ChIP-mm9.bed.gz"
 msgstr ""
 
 #: ../../reginf.ipynb:458
@@ -321,8 +315,8 @@ msgid ""
 "scRNA-seq data as a ``loom`` file (with only highly-variable genes and "
 "TFs). We also need to save the list of TFs as a separate ``txt`` file."
 msgstr ""
-"由于pySCENIC CLI使用的是 ``loom`` 文件作为输入，我们需要将scRNA-"
-"seq数据保存为一个 ``loom`` 文件（只包含高可变基因和TF），我们也需要将TF列表保存为一个单独的 ``txt`` 文件。"
+"由于pySCENIC CLI使用的是 ``loom`` 文件作为输入，我们需要将scRNA-seq数据保存为一个 ``loom`` "
+"文件（只包含高可变基因和TF），我们也需要将TF列表保存为一个单独的 ``txt`` 文件。"
 
 #: ../../reginf.ipynb:762
 msgid ""
@@ -472,8 +466,8 @@ msgid ""
 "using the pySCENIC command ``pyscenic ctx`` (here ``rank_threshold`` was "
 "scaled down according to the number of highly-variable genes):"
 msgstr ""
-"我们现在可以使用pySCENIC命令 ``pyscenic "
-"ctx`` 来修剪共表达网络（这里 ``rank_threshold`` 根据高可变基因的数量等比缩小）："
+"我们现在可以使用pySCENIC命令 ``pyscenic ctx`` 来修剪共表达网络（这里 ``rank_threshold`` "
+"根据高可变基因的数量等比缩小）："
 
 #: ../../reginf.ipynb:1648
 msgid ""
@@ -498,8 +492,8 @@ msgid ""
 "softwares like `Cytoscape <https://cytoscape.org/>`__ and `Gephi "
 "<https://gephi.org/>`__ for more customization."
 msgstr ""
-"您也可以将此图（比如以 ``graphml`` 格式）导出到诸如 `Cytoscape <https://cytoscape.org/>`__ 和 "
-"`Gephi <https://gephi.org/>`__ 等其他软件以进行更多的自定义调整。"
+"您也可以将此图（比如以 ``graphml`` 格式）导出到诸如 `Cytoscape <https://cytoscape.org/>`__ 和"
+" `Gephi <https://gephi.org/>`__ 等其他软件以进行更多的自定义调整。"
 
 #: ../../reginf.ipynb:1730
 msgid ""
@@ -524,3 +518,35 @@ msgid ""
 "Increase the number of highly-variable genes (e.g., to 4000 or 6000) to "
 "incorporate more genes into the analysis."
 msgstr "增加高可变基因数（比如增加到4000或6000）以将更多基因纳入到分析当中。"
+
+#~ msgid "http://download.gao-lab.org/GLUE/cisreg/hg19-JASPAR2022-merged.bed.gz"
+#~ msgstr ""
+
+#~ msgid "http://download.gao-lab.org/GLUE/cisreg/hg38-JASPAR2022-merged.bed.gz"
+#~ msgstr ""
+
+#~ msgid "http://download.gao-lab.org/GLUE/cisreg/mm9-JASPAR2022-merged.bed.gz"
+#~ msgstr ""
+
+#~ msgid "http://download.gao-lab.org/GLUE/cisreg/mm10-JASPAR2022-merged.bed.gz"
+#~ msgstr ""
+
+#~ msgid ""
+#~ "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-"
+#~ "ChIP-combined-hg38.bed.gz"
+#~ msgstr ""
+
+#~ msgid ""
+#~ "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-"
+#~ "ChIP-combined-hg19.bed.gz"
+#~ msgstr ""
+
+#~ msgid ""
+#~ "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-"
+#~ "ChIP-combined-mm10.bed.gz"
+#~ msgstr ""
+
+#~ msgid ""
+#~ "http://download.gao-lab.org/GLUE/cisreg/ENCODE-TF-"
+#~ "ChIP-combined-mm9.bed.gz"
+#~ msgstr ""