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Scripts/supermatrix.py
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#!/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() |