From d562cf09af75c67b327d880f358efaa0ccb5655e Mon Sep 17 00:00:00 2001
From: baer0006 <max.baer@unibas.ch>
Date: Thu, 1 Dec 2022 11:23:33 +0100
Subject: [PATCH] First unclead version able to generate GTF output file
---
primingsitepredictor/createtranscript.py | 12 ++++++++++++
primingsitepredictor/output_transcripts_df.txt | 3 +++
2 files changed, 15 insertions(+)
create mode 100644 primingsitepredictor/output_transcripts_df.txt
diff --git a/primingsitepredictor/createtranscript.py b/primingsitepredictor/createtranscript.py
index 4466d92..dddeb1f 100644
--- a/primingsitepredictor/createtranscript.py
+++ b/primingsitepredictor/createtranscript.py
@@ -62,7 +62,19 @@ class CreateTranscript():
return self.df
+
+
transcripts = CreateTranscript()
interaction_df = transcripts.generate_interaction_df()
+#print line by line to file and then you're done
+
+output = str()
+for i in interaction_df.index:
+ #print(interaction_df[3][i]+'\t' + 'RIBlast' + '\t' + 'Priming_site' + '\t' + interaction_df[13][i] + '\t' + interaction_df[12][i] + '\t' + '.' + '\t' + '+' + '\t' + '.' + '\t' + f'Accessibility_Energy "{interaction_df["Interaction Energy"][i]}"')
+ output = output + str(interaction_df[3][i]+'\t' + 'RIBlast' + '\t' + 'Priming_site' + '\t' + interaction_df[13][i] + '\t' + interaction_df[12][i] + '\t' + '.' + '\t' + '+' + '\t' + '.' + '\t' + f'Accessibility_Energy "{interaction_df["Interaction Energy"][i]}"' + '\n')
+
+print(output)
+with open('output_transcripts_df.txt', 'w') as f:
+ f.write(output)
diff --git a/primingsitepredictor/output_transcripts_df.txt b/primingsitepredictor/output_transcripts_df.txt
new file mode 100644
index 0000000..bb43f20
--- /dev/null
+++ b/primingsitepredictor/output_transcripts_df.txt
@@ -0,0 +1,3 @@
+Transcript_1 RIBlast Priming_site 2974 2988 . + . Accessibility_Energy "0.08051396365277928"
+Transcript_1 RIBlast Priming_site 4 18 . + . Accessibility_Energy "0.17770481173297115"
+Transcript_2 RIBlast Priming_site 1270 1284 . + . Accessibility_Energy "0.6445369481689498"
--
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