Merge pull request #71 from SATAY-LL/release_1.1.4

Release 1.1.4

CHANGELOG.md

@@ -4,6 +4,15 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.1.4] - 2022-01-25
+
+### Modified
+
+- Fix the file in the transposonmapper module inside the exporting submodule: save_as_wig.py
+- The change is related to save the wig file as the standard convention which requires a lower case letter instead of a capital one that was the case of previous versions. Specifically, the change of the `VariableStep` line to `variableStep`. 
+- This change is not affecting the functionality of the code.
+- Fix the 10% first truncation of the gene calculation. Basically redefine`N10percent` to `int(len(N_reads) * 0.1)`
+
 ## [1.1.3] - 2021-11-23
 
 ### Added

CITATION.cff

@@ -26,5 +26,5 @@ message: "If you use this software, please cite it using these metadata."
 repository-code: "https://github.com/SATAY-LL/Transposonmapper"
 title: transposonmapper
 doi: 10.5281/zenodo.4636301
-version: 1.1.3
+version: 1.1.4
 ...

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.3
+current_version = 1.1.4
 
 [bumpversion:file:transposonmapper/__version__.py]
 search = __version__ = "{current_version}"

transposonmapper/__version__.py

@@ -1 +1 @@
-__version__ = "1.1.3"
+__version__ = "1.1.4"

transposonmapper/data_files/files4test/SRR062634.filt_trimmed.sorted.bam.wig

@@ -1,5 +1,5 @@
 track type=wiggle_0 ,maxheightPixels=60 name=SRR062634.filt_trimmed.sorted.bam
-VariableStep chrom=chrref|NC_001133|
+variableStep chrom=chrref|NC_001133|
 23708 1
 23719 1
 31487 1
@@ -8,7 +8,7 @@ VariableStep chrom=chrref|NC_001133|
 120156 1
 120186 1
 126867 2
-VariableStep chrom=chrref|NC_001134|
+variableStep chrom=chrref|NC_001134|
 68281 1
 68324 2
 72368 1
@@ -39,7 +39,7 @@ VariableStep chrom=chrref|NC_001134|
 681992 2
 682025 1
 682029 2
-VariableStep chrom=chrref|NC_001135|
+variableStep chrom=chrref|NC_001135|
 42004 1
 57049 1
 57086 1
@@ -49,7 +49,7 @@ VariableStep chrom=chrref|NC_001135|
 247924 2
 247930 1
 247952 3
-VariableStep chrom=chrref|NC_001136|
+variableStep chrom=chrref|NC_001136|
 133 1
 33361 1
 57025 1
@@ -100,10 +100,10 @@ VariableStep chrom=chrref|NC_001136|
 1357513 4
 1412423 3
 1412424 1
-VariableStep chrom=chrref|NC_001137|
+variableStep chrom=chrref|NC_001137|
 79258 1
 86481 3
-VariableStep chrom=chrref|NC_001138|
+variableStep chrom=chrref|NC_001138|
 210337 1
 210344 5
 210350 4
@@ -113,7 +113,7 @@ VariableStep chrom=chrref|NC_001138|
 210372 1
 210396 43
 210412 1
-VariableStep chrom=chrref|NC_001139|
+variableStep chrom=chrref|NC_001139|
 69350 8
 69357 5
 69383 1
@@ -164,7 +164,7 @@ VariableStep chrom=chrref|NC_001139|
 808415 1
 1010880 1
 1010911 2
-VariableStep chrom=chrref|NC_001140|
+variableStep chrom=chrref|NC_001140|
 81890 1
 81893 2
 111561 1
@@ -186,7 +186,7 @@ VariableStep chrom=chrref|NC_001140|
 549757 2
 549762 3
 549764 1
-VariableStep chrom=chrref|NC_001141|
+variableStep chrom=chrref|NC_001141|
 105779 1
 105789 1
 128704 1
@@ -195,7 +195,7 @@ VariableStep chrom=chrref|NC_001141|
 154019 1
 163218 1
 254921 2
-VariableStep chrom=chrref|NC_001142|
+variableStep chrom=chrref|NC_001142|
 141069 1
 470174 1
 519258 1
@@ -214,7 +214,7 @@ VariableStep chrom=chrref|NC_001142|
 701728 1
 701747 5
 701767 2
-VariableStep chrom=chrref|NC_001143|
+variableStep chrom=chrref|NC_001143|
 22037 2
 22040 2
 22079 1
@@ -231,7 +231,7 @@ VariableStep chrom=chrref|NC_001143|
 518141 1
 613752 1
 635450 2
-VariableStep chrom=chrref|NC_001144|
+variableStep chrom=chrref|NC_001144|
 41219 1
 41265 1
 48856 1
@@ -266,7 +266,7 @@ VariableStep chrom=chrref|NC_001144|
 829458 1
 873640 1
 873669 2
-VariableStep chrom=chrref|NC_001145|
+variableStep chrom=chrref|NC_001145|
 40166 2
 87027 1
 87060 2
@@ -279,7 +279,7 @@ VariableStep chrom=chrref|NC_001145|
 822618 1
 822626 16
 822628 1
-VariableStep chrom=chrref|NC_001146|
+variableStep chrom=chrref|NC_001146|
 135871 1
 357010 4
 359341 26
@@ -309,7 +309,7 @@ VariableStep chrom=chrref|NC_001146|
 772656 1
 784227 1
 784259 2
-VariableStep chrom=chrref|NC_001147|
+variableStep chrom=chrref|NC_001147|
 13998 1
 45693 4
 63057 1
@@ -338,7 +338,7 @@ VariableStep chrom=chrref|NC_001147|
 944460 1
 954134 4
 954135 1
-VariableStep chrom=chrref|NC_001148|
+variableStep chrom=chrref|NC_001148|
 9540 1
 138286 1
 138292 1
@@ -352,7 +352,7 @@ VariableStep chrom=chrref|NC_001148|
 536772 1
 536777 1
 536780 2
-VariableStep chrom=chrref|NC_001224|
+variableStep chrom=chrref|NC_001224|
 1212 1
 2847 1
 3267 1

transposonmapper/exporting/save_as_wig.py

@@ -73,7 +73,7 @@ def save_as_wig(wigfile, tncoordinates_array, ref_tid, readnumb_array):
         filename = os.path.splitext(base)[0]
         f.write("track type=wiggle_0 ,maxheightPixels=60 name=" + filename + "\n")
         for kk in ref_names:
-            f.write("VariableStep chrom=chr" + kk + "\n")
+            f.write("variableStep chrom=chr" + kk + "\n")
 
             index = np.where(
                 tncoordinateswig_duplicatesremoved_array[:, 0] == int(ref_tid[kk] + 1)

transposonmapper/processing/dna_features_helpers.py

@@ -463,7 +463,7 @@ def build_dataframe(dna_dict,start_chr,end_chr,insrt_in_chrom_list,reads_in_chro
             N_reads_list_true.append(np.array(N_reads,dtype=float))
             N_insrt_list.append(len([ins for ins in N_reads if not ins == 0]))
             if not f_type == None and f_type.startswith('Gene'):
-                N10percent = 100#int(len(N_reads) * 0.1) #TRUNCATED GENE DEFINITION
+                N10percent = int(len(N_reads) * 0.1) #TRUNCATED GENE DEFINITION 100
                 N_reads_truncatedgene_list.append(sum(N_reads[N10percent:-N10percent]))
                 N_insrt_truncatedgene_list.append(len([ins for ins in N_reads[N10percent:-N10percent] if not ins == 0]))
             else: