Merge pull request #5 from stjude/update

Update
stjude · Jun 10, 2020 · c081fb8 · c081fb8
2 parents 833bde9 + 5b866f3
commit c081fb8
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Showing 82 changed files with 41 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -126,3 +126,5 @@ dmypy.json
 # End of https://www.gitignore.io/api/python
 #vscode
 .vscode
+
+.DS_Store
diff --git a/.travis.yml b/.travis.yml
diff --git a/Changelog.md b/Changelog.md
@@ -0,0 +1,23 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+
+## [1.0.2] - 2020-02-21
+### Added
+- Changelog file to keep track of changes to this project.
+
+### Fixed
+- Fixed bug with outputting to an user-specified output directory.
+- Fixed bug in `find_islands_in_pr` so that empty island lists do not trigger `IndexError`. 
+
+## [1.0.1] - 2019-12-28
+### Fixed
+- Fixed issue with calling BEDTools using `subprocess.call`. Instead, use `subprocess.Popen` to enable piping.
+- Fixed method for getting CPU count
+
+## [1.0.0] - 2019-06-14
+### Added
+- New version of SICER for improved user-friendliness and parallelization support
+- Multiprocessing based on chromosomes
+- RECOGNICER algorithm added
+- Uses BEDTools to convert BAM file to BED automatically
diff --git a/LICENSE b/LICENSE
diff --git a/README.md b/README.md
diff --git a/bin/recognicer b/bin/recognicer
@@ -219,6 +219,9 @@ def main():
         except:
             sys.exit("Output directory (%s) could not be created. Terminating program." % args.output_directory)
 
+    if not(os.path.isabs(args.output_directory)):
+        args.output_directory = os.path.join(curr_path, args.output_directory)
+
     if args.cpu > cpu_available:
         args.cpu = cpu_available
         warnings.warn("The number of CPU cores entered is greater than the number of cores available for this process. Executing SICER with the maximum number of cores available.\n")

diff --git a/bin/recognicer_df b/bin/recognicer_df
@@ -210,6 +210,9 @@ def main():
         except:
             sys.exit("Output directory (%s) could not be created. Terminating program.\n" % args.output_directory)
 
+    if not(os.path.isabs(args.output_directory)):
+        args.output_directory = os.path.join(curr_path, args.output_directory)
+
     if (args.control_file is not None):
         if (len(args.control_file) > 2):
             sys.stderr.write("Error: Too many control file inputs. RECOGNICER accepts at max two files.\n")

diff --git a/bin/sicer b/bin/sicer
@@ -218,6 +218,9 @@ def main():
             sys.stderr.write("Error: Gap size is not a multiple of window size.\n" % args.output_directory)
             sys.exit(1)
 
+    if not(os.path.isabs(args.output_directory)):
+        args.output_directory = os.path.join(curr_path, args.output_directory)
+
     if args.cpu > cpu_available:
         args.cpu = cpu_available
         warnings.warn("The number of CPU cores entered is greater than the number of cores available for this process. Executing SICER with the maximum number of cores available.\n")

diff --git a/bin/sicer_df b/bin/sicer_df
@@ -209,6 +209,9 @@ def main():
         except:
             sys.exit("Output directory (%s) could not be created. Terminating program.\n" % args.output_directory)
 
+    if not(os.path.isabs(args.output_directory)):
+        args.output_directory = os.path.join(curr_path, args.output_directory)
+
     if (args.control_file is not None):
         if (len(args.control_file) > 2):
             sys.stderr.write("Error: Too many control file inputs. SICER accepts at max two files.\n")

diff --git a/docs/contact.md b/docs/contact.md
diff --git a/docs/img/sicer2_workflow.png b/docs/img/sicer2_workflow.png
diff --git a/docs/index.md b/docs/index.md
diff --git a/docs/sicer2_output.md b/docs/sicer2_output.md
diff --git a/docs/workflow.md b/docs/workflow.md
diff --git a/mkdocs.yml b/mkdocs.yml
diff --git a/setup.py b/setup.py
@@ -14,7 +14,7 @@
 
 setup(
     name='SICER2',
-    version='1.0.1',
+    version='1.0.2',
     description = 'SICER2, a redesigned and improved ChIP-seq broad peak calling tool',
     long_description='Redesigned and improved version of the original ChIP-seq broad peak calling tool SICER. Also contains Coarse-graining Approach for Identifying Broad Domains from ChIP-Enriched Regions (RECOGNICER)',
     url = 'http://zanglab.github.io/SICER2 ',

diff --git a/sicer/__init__.py b/sicer/__init__.py
diff --git a/sicer/lib/Background_island_probscore_statistics.py b/sicer/lib/Background_island_probscore_statistics.py
diff --git a/sicer/lib/GenomeData.py b/sicer/lib/GenomeData.py
diff --git a/sicer/lib/Utility.py b/sicer/lib/Utility.py
diff --git a/sicer/lib/__init__.py b/sicer/lib/__init__.py
diff --git a/sicer/lib/associate_tags_with_regions.py b/sicer/lib/associate_tags_with_regions.py
diff --git a/sicer/main/run_RECOGNICER.py b/sicer/main/run_RECOGNICER.py
diff --git a/sicer/main/run_RECOGNICER_df.py b/sicer/main/run_RECOGNICER_df.py
diff --git a/sicer/main/run_SICER.py b/sicer/main/run_SICER.py
diff --git a/sicer/main/run_SICER_df.py b/sicer/main/run_SICER_df.py
diff --git a/sicer/src/__init__.py b/sicer/src/__init__.py
diff --git a/sicer/src/associate_tags_with_chip_and_control_w_fc_q.py b/sicer/src/associate_tags_with_chip_and_control_w_fc_q.py
diff --git a/sicer/src/coarsegraining.c b/sicer/src/coarsegraining.c
diff --git a/sicer/src/coarsegraining.pyx b/sicer/src/coarsegraining.pyx
diff --git a/sicer/src/compare_two_libraries_on_islands.py b/sicer/src/compare_two_libraries_on_islands.py
diff --git a/sicer/src/filter_islands_by_significance.py b/sicer/src/filter_islands_by_significance.py
diff --git a/sicer/src/filter_raw_tags_by_islands.py b/sicer/src/filter_raw_tags_by_islands.py
diff --git a/sicer/src/find_islands_in_pr.py b/sicer/src/find_islands_in_pr.py
@@ -77,6 +77,9 @@ def combine_proximal_islands(islands, gap, window_size_buffer=3):
     """
 
     proximal_island_dist = gap + window_size_buffer;
+
+    if len(islands) == 0:
+        return []
     final_islands = []
     current_island = islands[0];
 

diff --git a/sicer/src/find_union_islands.py b/sicer/src/find_union_islands.py
diff --git a/sicer/src/make_normalized_wig.py b/sicer/src/make_normalized_wig.py
diff --git a/sicer/src/remove_redundant_reads.py b/sicer/src/remove_redundant_reads.py
diff --git a/sicer/src/run_make_graph_file_by_chrom.py b/sicer/src/run_make_graph_file_by_chrom.py
diff --git a/sicer/utility/__init__.py b/sicer/utility/__init__.py
diff --git a/sicer/utility/calculate_cross_correlation_long_range.py b/sicer/utility/calculate_cross_correlation_long_range.py
diff --git a/sicer/utility/fragment-size-estimation.sh b/sicer/utility/fragment-size-estimation.sh
diff --git a/sicer/utility/make_graph_file.py b/sicer/utility/make_graph_file.py
diff --git a/test/control_1.bed b/test/control_1.bed
diff --git a/test/control_2.bed b/test/control_2.bed
diff --git a/test/test_scripts/__init__.py b/test/test_scripts/__init__.py
diff --git a/test/test_scripts/compare.py b/test/test_scripts/compare.py
diff --git a/test/test_scripts/test.py b/test/test_scripts/test.py
diff --git a/test/travisCI/compare.py b/test/travisCI/compare.py
diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-island.bed
diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_1-W200-FDR0.01-islandfiltered.bed
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-island.bed
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_1-W200-G600-FDR0.01-islandfiltered.bed
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-decreased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-G600-decreased-islands-summary-FDR0.01
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-increased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-G600-increased-islands-summary-FDR0.01
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600-islands-summary b/test/travisCI/expected_output/treatment_1-W200-G600-islands-summary
diff --git a/test/travisCI/expected_output/treatment_1-W200-G600.scoreisland b/test/travisCI/expected_output/treatment_1-W200-G600.scoreisland
diff --git a/test/travisCI/expected_output/treatment_1-W200-cgnormalized.wig b/test/travisCI/expected_output/treatment_1-W200-cgnormalized.wig
diff --git a/test/travisCI/expected_output/treatment_1-W200-decreased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-decreased-islands-summary-FDR0.01
diff --git a/test/travisCI/expected_output/treatment_1-W200-increased-islands-summary-FDR0.01 b/test/travisCI/expected_output/treatment_1-W200-increased-islands-summary-FDR0.01
diff --git a/test/travisCI/expected_output/treatment_1-W200-islands-summary b/test/travisCI/expected_output/treatment_1-W200-islands-summary
diff --git a/test/travisCI/expected_output/treatment_1-W200-normalized.wig b/test/travisCI/expected_output/treatment_1-W200-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_1-W200.cgisland b/test/travisCI/expected_output/treatment_1-W200.cgisland
diff --git a/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-G600-summary b/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-G600-summary
diff --git a/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-summary b/test/travisCI/expected_output/treatment_1-and-treatment_2-W200-summary
diff --git a/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-G600-E1000-union.island b/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-G600-E1000-union.island
diff --git a/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-union.island b/test/travisCI/expected_output/treatment_1-vs-treatment_2-W200-union.island
diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-island.bed
diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_2-W200-FDR0.01-islandfiltered.bed
diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-island.bed b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-island.bed
diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered.bed b/test/travisCI/expected_output/treatment_2-W200-G600-FDR0.01-islandfiltered.bed
diff --git a/test/travisCI/expected_output/treatment_2-W200-G600-islands-summary b/test/travisCI/expected_output/treatment_2-W200-G600-islands-summary
diff --git a/test/travisCI/expected_output/treatment_2-W200-G600.scoreisland b/test/travisCI/expected_output/treatment_2-W200-G600.scoreisland
diff --git a/test/travisCI/expected_output/treatment_2-W200-cgnormalized.wig b/test/travisCI/expected_output/treatment_2-W200-cgnormalized.wig
diff --git a/test/travisCI/expected_output/treatment_2-W200-islands-summary b/test/travisCI/expected_output/treatment_2-W200-islands-summary
diff --git a/test/travisCI/expected_output/treatment_2-W200-normalized.wig b/test/travisCI/expected_output/treatment_2-W200-normalized.wig
diff --git a/test/travisCI/expected_output/treatment_2-W200.cgisland b/test/travisCI/expected_output/treatment_2-W200.cgisland
diff --git a/test/treatment_1.bed b/test/treatment_1.bed
diff --git a/test/treatment_2.bed b/test/treatment_2.bed