From 80021b95d5a0fa5092371a20cbda6c1424afe1c0 Mon Sep 17 00:00:00 2001
From: Yutian Feng <yutian.feng@uconn.edu>
Date: Thu, 18 Oct 2018 17:47:48 -0400
Subject: [PATCH] Delete supermatrix.py

---
 supermatrix.py | 106 -------------------------------------------------
 1 file changed, 106 deletions(-)
 delete mode 100644 supermatrix.py

diff --git a/supermatrix.py b/supermatrix.py
deleted file mode 100644
index 5fe71e0..0000000
--- a/supermatrix.py
+++ /dev/null
@@ -1,106 +0,0 @@
-#!/usr/bin/env python
-
-import sys
-import os
-import textwrap
-
-InFile1 = sys.argv[1]
-InFile2 = sys.argv[2]
-InFile3 = sys.argv[3]
-
-OInFile1 = open(InFile1, 'rU')
-OInFile2 = open(InFile2, 'rU')
-OutFile1 = open(InFile3, 'w')
-
-Concatdict1 = {}
-TaxaList = []
-for Line in OInFile1:
-	Line = Line.strip("\n")
-	if Line[0] == ">":
-		TaxaList.append(Line)
-		Concatdict1[Line] = []
-	else:
-		Concatdict1[TaxaList[len(TaxaList)-1]].append(Line)
-
-Concatdict2 = {}
-TaxaList2 = []
-for Line in OInFile2:
-	Line = Line.strip("\n")
-	if Line[0] == ">":
-		TaxaList2.append(Line)
-		Concatdict2[Line] = []
-	else:
-		Concatdict2[TaxaList2[len(TaxaList2)-1]].append(Line)
-
-MissingSeqs2 = frozenset(Concatdict1.keys()) - frozenset(Concatdict2.keys()) #Keys in 1 but not 2
-MissingSeqs1 = frozenset(Concatdict2.keys()) - frozenset(Concatdict1.keys()) #Keys in 2 but not 1
-
-print MissingSeqs1
-print MissingSeqs2
-
-SeqLengthFile1 = []
-
-X = 1
-for Element in Concatdict1:
-	ValueStr = "".join(Concatdict1[Element])
-	SeqLengthFile1.append(len(ValueStr))
-	X = X + 1
-	if X > 1:
-		break
-#print SeqLengthFile1
-
-EmptySeq1 = "-" * SeqLengthFile1[0]
-
-
-SeqLengthFile2 = []
-X = 1
-for Element in Concatdict2:
-	ValueStr2 = "".join(Concatdict2[Element])
-	SeqLengthFile2.append(len(ValueStr2))
-	X = X + 1
-	if X > 1:
-		break
-#print SeqLengthFile2
-
-EmptySeq2 = "-" * SeqLengthFile2[0]
-
-
-for Elements in MissingSeqs1:
-	Concatdict1[Elements] = list(EmptySeq1)
-for Elements in MissingSeqs2:
-	Concatdict2[Elements] = list(EmptySeq2)
-	
-for Element in Concatdict2:
-	SeqStr = "".join(Concatdict2[Element])
-	Concatdict1[Element].append(SeqStr)
-
-for Key in Concatdict1:
-	print Key
-	OutFile1.write(Key + "\n")
-	SeqStr = "".join(Concatdict1[Key])
-	OutFile1.write(SeqStr + "\n")
-	#OutFile1.write(textwrap.fill(SeqStr, width=60) + "\n")
-	print SeqStr
-	#print len(SeqStr)
-
-OInFile1.close()
-OInFile2.close()	
-OutFile1.close()
-
-OutFile2 = "MissingSeqs.list_" + InFile3	
-OpenOutFile2 = open(OutFile2, 'w')
-OpenOutFile2.write("Missing sequences in " + InFile1 + " are: " + "\n")
-for Element in MissingSeqs1:
-	OpenOutFile2.write(Element + "\n")
-OpenOutFile2.write("Missing sequences in " + InFile2 + " are: " + "\n")
-for Element in MissingSeqs2:
-	OpenOutFile2.write(Element + "\n")
-OpenOutFile2.close()
-
-OutFile3 = "Partition.list_" + InFile3
-openOutFile3 = open(OutFile3, 'w')
-openOutFile3.write(InFile1 + " = 1 - " + str(SeqLengthFile1[0]) + "\n")
-first_value = SeqLengthFile1[0] + 1
-second_value = SeqLengthFile1[0] + SeqLengthFile2[0]
-openOutFile3.write(InFile2 + " = " + str(first_value) + " - " + str(second_value) + "\n")
-openOutFile3.close()