From 1368ccf7bc32d3b4d1bf4a7e64f610efd7323bcc Mon Sep 17 00:00:00 2001
From: Jakob Rien <jakobj.rien@stud.unibas.ch>
Date: Tue, 20 Dec 2022 08:42:55 +0000
Subject: [PATCH] Replace find_representative_transcripts.py
---
scripts/find_representative_transcripts.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/scripts/find_representative_transcripts.py b/scripts/find_representative_transcripts.py
index 6fc2efd..8921db3 100644
--- a/scripts/find_representative_transcripts.py
+++ b/scripts/find_representative_transcripts.py
@@ -1,5 +1,5 @@
#### Find representative transcripts ####
-"""Version 1.0.0"""
+"""Version 1.0.1"""
### Imports ###
import argparse
@@ -36,7 +36,7 @@ def find_in_attributs (attributs,look_for):
index = attributs.index(look_for)+1
return attributs[index]
except:
- #print("No",look_for,"in the entry the return was set to NA\n",attributs)
+ print("No",look_for,"in the entry the return was set to NA\n",attributs)
return "NA"
def exon_length(entry):
@@ -108,10 +108,10 @@ def get_rep_trans(file_name = "test"):
if ignor_trans:
continue
elif cur_gID != attributs[1]:
- print("ERROR exon from an unexpected Gen")
+ raise ValueError("ERROR exon from an unexpected Gen")
continue
elif find_in_attributs (attributs,"transcript_id") != cur_tID:
- print("ERROR exon from an unexpected transcript")
+ raise ValueError("exon from an unexpected transcript")
continue
#calculating exon_length and adding it to the appropriat list and chackin for changes in best transcript
@@ -129,7 +129,7 @@ def get_rep_trans(file_name = "test"):
#varryfi that the gen is correct
if cur_gID != attributs[1]:
- print("ERROR transcript from an unexpected Gen")
+ raise ValueError("ERROR transcript from an unexpected Gen")
continue
#finding the transcript id and the support level
@@ -175,7 +175,7 @@ def get_rep_trans(file_name = "test"):
#raises an error for unidentifyable entrys
else:
- print("This entry could not be identified\n",entry)
+ raise ValueError("This entry could not be identified\n",entry)
del rep_trans[""]
rep_transcripts = _re_format(rep_trans)
--
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