From 259bfe5a1552f460ce9509f69572229583d071c4 Mon Sep 17 00:00:00 2001
From: rwnull <65666230+rwnull@users.noreply.github.com>
Date: Wed, 3 Jun 2020 16:09:20 -0400
Subject: [PATCH] Add files via upload

---
 HCRProbeMaker2_7_v2.py | 24 ++++++++++++------------
 HCRProbeMaker3_7_v2.py | 17 ++++++++---------
 2 files changed, 20 insertions(+), 21 deletions(-)

diff --git a/HCRProbeMaker2_7_v2.py b/HCRProbeMaker2_7_v2.py
index 2747dcb..1e45b4b 100644
--- a/HCRProbeMaker2_7_v2.py
+++ b/HCRProbeMaker2_7_v2.py
@@ -6,7 +6,7 @@
 __copyright__ = "Copyright 2019-2020, The Ozpolat Lab (http://bduyguozpolat.org/)"
 __credits__ = ["B. Duygu Ozpolat"]
 __license__ = "GPL 3.0"
-__version__ = "2020_2.0"
+__version__ = "2020_0.2.0"
 
 
 
@@ -93,7 +93,7 @@ def amp(ampl):
 
 print ""
 print ""
-print "HCR3.0_Probe_Maker_Output"
+print "HCR3.0 Probe Maker Output"
 print ""
 print ""
 
@@ -105,7 +105,7 @@ def amp(ampl):
 print "Figure Layout:"
 print ""
 print str(amplifier+"_"+str(name)+"_"+str(count))							# Name based on inputs
-print "Pair#\t1st_Half_of_Initiator_I1\tSpacer\tProbe\t\tProbe\tSpacer\t2nd_Half_of_Initiator_I1"	# HEADER of Output
+print "Pair#,1st Half of Initiator I1,Spacer,Probe,,Probe,Spacer,2nd Half of Initiator I1"	# HEADER of Output
 
 
 position=cdna-pause     										# This controls how far from the 5'end of the mRNA probes begin 
@@ -116,11 +116,11 @@ def amp(ampl):
 while position>52: 											# 52 is the cutoff for fitting an entire pair at the end of the gene. the program will cycle back over the RNA if not limited like this
     downstream=str(fullseq[position-25:position])
     upstream=str(fullseq[position-52:position-27])
-    pairlib[pair]=str(str(pair)+"\t"+str(cdna-position+25)+"\t"+str(fullseq[position-25:position])+"\t"+str(cdna-position)+"\t\t"+str(cdna-position+52)+"\t"+str(fullseq[position-52:position-27])+"\t"+str(cdna-position+27))
-    idtlibu[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+"\t"+upinit+uspc+upstream)   		# This is a library used for IDT output
-    idtlibd[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+"\t"+downstream+dspc+dninit)
+    pairlib[pair]=str(str(pair)+","+str(cdna-position+25)+","+str(fullseq[position-25:position])+","+str(cdna-position)+",,"+str(cdna-position+52)+","+str(fullseq[position-52:position-27])+","+str(cdna-position+27))
+    idtlibu[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+","+upinit+uspc+upstream)   		# This is a library used for IDT output
+    idtlibd[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+","+downstream+dspc+dninit)
     position-=54      											# 54 is the number of bases covered by one probe set (25bp probe 1, 2bp spacer, 25bp probe 2, 2bp spacer). 
-    print str(pair)+"\t"+upinit+"\t"+uspc+"\t"+upstream+"\t\t"+downstream+"\t"+dspc+"\t"+dninit
+    print str(pair)+","+upinit+","+uspc+","+upstream+",,"+downstream+","+dspc+","+dninit
     if pair<count:
         pair+=1
     else:
@@ -134,10 +134,10 @@ def amp(ampl):
 print ""
 print "Below are the hybridizing sequences and where they align to the cDNA:"
 print ""
-print "Pair#\tcDNAcoord\tProbe\tcDNAcoord\t\tcDNAcoord\tProbe\tcDNAcoord"				# Header for Output
+print "Pair#,cDNAcoord,Probe,cDNAcoord,,cDNAcoord,Probe,cDNAcoord"				# Header for Output
 i=1
 while i <= pair:
-    print(pairlib[i])
+    print pairlib[i]
     i+=1
 
 print ""
@@ -150,11 +150,11 @@ def amp(ampl):
 print "Below is in IDT oPool submission format."
 print "Copy and Paste this into an XLSX file for submission to IDT."
 print ""
-print "Pool name\tsequence"										#Header for output
+print "Pool name,sequence"										#Header for output
 i=1
 while i <= pair:
-    print(str(idtlibu[i])
-    print(str(idtlibd[i])
+    print str(idtlibu[i])
+    print str(idtlibd[i])
     i+=1
 
     
diff --git a/HCRProbeMaker3_7_v2.py b/HCRProbeMaker3_7_v2.py
index c57c71c..7762930 100644
--- a/HCRProbeMaker3_7_v2.py
+++ b/HCRProbeMaker3_7_v2.py
@@ -5,7 +5,7 @@
 __copyright__ = "Copyright 2019-2020, The Ozpolat Lab (http://bduyguozpolat.org/)"
 __credits__ = ["B. Duygu Ozpolat"]
 __license__ = "GPL 3.0"
-__version__ = "2020_2.0"
+__version__ = "2020_0.2.0"
 
 
 
@@ -105,7 +105,7 @@ def amp(ampl):
 print("Figure Layout:")
 print("")
 print(str(amplifier+"_"+str(name)+"_"+str(count)))							# Name based on inputs
-print("Pair#\t1st_Half_of_Initiator_I1\tSpacer\tProbe\t\tProbe\tSpacer\t2nd_Half_of_Initiator_I1")	# HEADER of Output
+print("Pair#,1st Half of Initiator I1,Spacer,Probe,,Probe,Spacer,2nd Half of Initiator I1")	# HEADER of Output
 
 
 position=cdna-pause     										# This controls how far from the 5'end of the mRNA probes begin 
@@ -116,11 +116,11 @@ def amp(ampl):
 while position>52: 											#52 is the cutoff for fitting an entire pair at the end of the gene. the program will cycle back over the RNA if not limited like this
     downstream=str(fullseq[position-25:position])
     upstream=str(fullseq[position-52:position-27])
-    pairlib[pair]=str(str(pair)+"\t"+str(cdna-position+25)+"\t"+str(fullseq[position-25:position])+"\t"+str(cdna-position)+"\t\t"+str(cdna-position+52)+"\t"+str(fullseq[position-52:position-27])+"\t"+str(cdna-position+27))
-    idtlibu[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+"\t"+upinit+uspc+upstream)   		# This is a library used for IDT output
-    idtlibd[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+"\t"+downstream+dspc+dninit)
+    pairlib[pair]=str(str(pair)+","+str(cdna-position+25)+","+str(fullseq[position-25:position])+","+str(cdna-position)+",,"+str(cdna-position+52)+","+str(fullseq[position-52:position-27])+","+str(cdna-position+27))
+    idtlibu[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+","+upinit+uspc+upstream)   		# This is a library used for IDT output
+    idtlibd[pair]=str(amplifier+"_"+str(name)+"_"+str(count)+","+downstream+dspc+dninit)
     position-=54      											# 54 is the number of bases covered by one probe set (25bp probe 1, 2bp spacer, 25bp probe 2, 2bp spacer). 
-    print(str(pair)+"\t"+upinit+"\t"+uspc+"\t"+upstream+"\t\t"+downstream+"\t"+dspc+"\t"+dninit)
+    print(str(pair)+","+upinit+","+uspc+","+upstream+",,"+downstream+","+dspc+","+dninit)
     if pair<count:
         pair+=1
     else:
@@ -134,7 +134,7 @@ def amp(ampl):
 print("")
 print("Below are the hybridizing sequences and where they align to the cDNA:")
 print("")
-print("Pair#\tcDNAcoord\tProbe\tcDNAcoord\t\tcDNAcoord\tProbe\tcDNAcoord")				# Header for Output
+print("Pair#,cDNAcoord,Probe,cDNAcoord,,cDNAcoord,Probe,cDNAcoord")				# Header for Output
 i=1
 while i <= pair:
     print(pairlib[i])
@@ -150,7 +150,7 @@ def amp(ampl):
 print("Below is in IDT oPool submission_format.")
 print("Copy and Paste this into an XLSX file for submission to IDT.")
 print("")
-print("Pool_name\tsequence")										#Header for output
+print("Pool name,sequence")										#Header for output
 i=1
 while i <= pair:
     print(str(idtlibu[i]))
@@ -171,7 +171,6 @@ def amp(ampl):
 print(fullseq)
 
 
-# In[ ]: