updated docs

GoekeLab · Nov 20, 2020 · a3acb73 · a3acb73
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diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -23,6 +23,7 @@ Contents
 
    installation
    quickstart
+   outputtable
    configuration
    preparation
    scripts

diff --git a/docs/source/outputtable.rst b/docs/source/outputtable.rst
@@ -0,0 +1,22 @@
+.. _outputtable:
+
+Output table description
+=========================
+
+=============                               ==============
+Column name                                 Description
+=============                               ==============
+id                                          transcript or gene id
+position                                    transcript or gene position
+kmer                                        5-mer where modified base sits in the middle if modified
+diff_mod_rate_<condition1>_vs_<condition2>  differential modification rate between condition1 and condition2 (modification rate of condition1 - modification rate of condition2)
+z_score_<condition1>_vs_<condition2>        z score obtained from z-test of the differential modification rate
+pval_<condition1>_vs_<condition2>           significance level from z-test of the differential modification rate
+mod_rate_<condition>-<replicate>            modification rate of a replicate in the condition
+mu_unmod                                    inferred mean of the unmodified RNAs distribution
+mu_mod                                      inferred mean of the modified RNAs distribution
+sigma2_unmod                                inferred sigma^2 of the unmodified RNAs distribution
+sigma2_mod                                  inferred sigma^2 of the modified RNAs distribution
+conf_mu_unmod                               confidence level of mu_unmod compared to the unmodified reference signal
+conf_mu_mod                                 confidence level of mu_unmod compared to the unmodified reference signal
+mod_assignment                              lower if mu_mod < mu_unmod and higher if mu_mod > mu_unmod
diff --git a/xpore/scripts/dataprep.py b/xpore/scripts/dataprep.py
@@ -514,6 +514,36 @@ def preprocess_tx(tx_id,data_dict,out_paths,locks):  # todo
         f.write(log_str + '\n')
 
 
+def index_nanopolish(eventalign_filepath,summary_filepath,out_dir,n_processes):
+    with helper.EventalignFile(eventalign_filepath) as eventalign_file, open(summary_filepath,'r') as summary_file:
+
+#         reader_summary = csv.DictReader(summary_file, delimiter="\t")
+#         reader_eventalign = csv.DictReader(eventalign_file, delimiter="\t")
+
+#         row_summary = next(reader_summary)
+#         read_name = row_summary['read_name']
+#         read_index = row_summary['read_index']
+#         eventalign_per_read = []
+#         for row_eventalign in reader_eventalign:
+#             if (row_eventalign['read_index'] == read_index):
+#                 eventalign_per_read += [row_eventalign]
+#             else: 
+#                 # Load a read info to the task queue.
+#                 if read_name not in read_names_done:
+#                     task_queue.put((read_name,eventalign_per_read,out_paths))
+#                 # Next read.
+#                 try:
+#                     row_summary = next(reader_summary)
+#                 except StopIteration: # no more read.
+#                     break
+#                 else:
+#                     read_index = row_summary['read_index']
+#                     read_name = row_summary['read_name']
+#                     assert row_eventalign['read_index'] == read_index 
+#                     eventalign_per_read = [row_eventalign]
+
+
+
 def main():
     args = get_args()
     #