From 97c526d60f039f3c10c29e7f395c6851852b5352 Mon Sep 17 00:00:00 2001 From: basti Date: Thu, 10 Jan 2019 17:51:01 +0100 Subject: [PATCH] Fix for #51 --- .../Modules/Ensembl/ActivityCategorizer.py | 10 ++++++---- bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py | 5 ++++- bin/3.1_create_gtf/config/celltypes_homo_sapiens.json | 2 +- 3 files changed, 11 insertions(+), 6 deletions(-) diff --git a/bin/3.1_create_gtf/Modules/Ensembl/ActivityCategorizer.py b/bin/3.1_create_gtf/Modules/Ensembl/ActivityCategorizer.py index 78f1826..eb201dd 100644 --- a/bin/3.1_create_gtf/Modules/Ensembl/ActivityCategorizer.py +++ b/bin/3.1_create_gtf/Modules/Ensembl/ActivityCategorizer.py @@ -122,8 +122,9 @@ def activity_comparator(self, aliaslist): concatenated_array = bytearray([]) length = len(self.activity[aliaslist[0]]) input_arrays = [self.activity[index] for index in aliaslist] - try: - for x in range(length): + for x in range(length): + # This try-catch block is needed because of inconsistency in file-lengths in Ensembl-release-95 + try: if any(y[x] == 0 for y in input_arrays): concatenated_array.append(0) elif any(y[x] == 1 for y in input_arrays): @@ -134,8 +135,9 @@ def activity_comparator(self, aliaslist): concatenated_array.append(3) elif any(y[x] == 4 for y in input_arrays): concatenated_array.append(4) - except IndexError: - print("Indexerror occured") + except IndexError: + concatenated_array.append(4) + return concatenated_array diff --git a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py index cad1451..22914b6 100644 --- a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py +++ b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py @@ -107,10 +107,13 @@ def generate_activity_list(self, activity, index): activity_list = [] for key, value in activity.items(): + # if no index is found the key will be annotated as "NA" + # this is needed due to an inconsistency in ensembl-release-95 + # some activity-files contain less entries than others try: activity_list.append(key+">"+self.value_map[value[index]]) except IndexError: - pass + activity_list.append(key+">NA") return activity_list def get_gtf(self, release, activity): diff --git a/bin/3.1_create_gtf/config/celltypes_homo_sapiens.json b/bin/3.1_create_gtf/config/celltypes_homo_sapiens.json index d10135b..776d83e 100644 --- a/bin/3.1_create_gtf/config/celltypes_homo_sapiens.json +++ b/bin/3.1_create_gtf/config/celltypes_homo_sapiens.json @@ -129,7 +129,7 @@ { "type": "Heart", "alias_ucsc": ["heart"], - "alias_ensembl": ["Right_Atrium", "Left_Ventricle", "cardiac_muscle_cell", "heart_right_ventricle"] + "alias_ensembl": ["Right_Atrium", "Left_Ventricle", "cardiac_muscle_cell", "heart_right_ventricle", "heart"] }, { "type": "Osteoblast",