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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import sys
import os
import random
from xml.dom.minidom import parse, getDOMImplementation
def getInputData(finName):
fin = open(finName)
data = []
line = fin.readline()
while line:
data.append(line.strip())
line = fin.readline()
fin.close()
return data
def getAllChunkNames(data):
names = []
for string in data:
for ltr in string:
if ltr != "+" and ltr != "-":
names.append(ltr)
return set(names)
def generateRandomSequence(seqLen):
seq = ""
nucl = ["A", "C", "G", "T"]
for x in range(seqLen):
i = random.randint(0, 3)
seq += nucl[i]
return seq
def getChunkSequences(longChunkLen, shortChunkLen, chunkNames):
seqs = {}
for name in chunkNames:
assert len(name) == 1
lenToGen = longChunkLen
if name.islower():
lenToGen = shortChunkLen
seqs[name] = generateRandomSequence(lenToGen)
return seqs
def getReverseComplement(seq):
revNucl = {"A" : "T", "T" : "A", "C" : "G", "G" : "C"}
revSeq = ""
for x in reversed(seq):
revSeq += revNucl[x]
return revSeq
def getSequenceByChunkString(chunkString, chunkSeqs):
seq = ""
for i in range(0, len(chunkString)-1, 2):
ltr = chunkString[i]
chunkName = chunkString[i+1]
if ltr == "+":
seq += chunkSeqs[chunkName]
elif ltr == "-":
seq += getReverseComplement(chunkSeqs[chunkName])
return seq
def getAllContigData(contigNodes):
data = []
for contigNode in contigNodes:
for node in contigNode.childNodes:
if node.nodeType == node.TEXT_NODE:
data.append(node.data)
return data
if __name__ == "__main__":
random.seed(239)
if len(sys.argv) < 5:
print("Usage: " + sys.argv[0] + " <name of input file> <output format xml/fasta> <name of output file> <length of chunk> (<length of chunk for lower case>)")
sys.exit()
#random.seed()
chunkLen = int(sys.argv[4])
shortChunkLen = chunkLen
if len(sys.argv) > 5:
shortChunkLen = int(sys.argv[5])
dom = parse(sys.argv[1])
contigNodes = dom.getElementsByTagName("contig")
chunkNames = getAllChunkNames(getAllContigData(contigNodes))
chunkSeqs = getChunkSequences(chunkLen, shortChunkLen, chunkNames)
for node in contigNodes:
for child in node.childNodes:
child.data = getSequenceByChunkString(child.data, chunkSeqs)
assert sys.argv[2] == "xml" or sys.argv[2] == "fasta";
if sys.argv[2] == "xml":
fout = open(sys.argv[3], "w")
dom.writexml(fout+".xml")
fout.close()
else:
if not os.path.exists(sys.argv[3]):
os.makedirs(sys.argv[3])
exampleNodes = dom.getElementsByTagName("example")
for example in exampleNodes:
folder = sys.argv[3] + "/example_" + example.attributes["n"].value + "/"
if not os.path.exists(folder):
os.makedirs(folder)
genome_cnt = 1
for genome in example.getElementsByTagName("genome"):
filename = folder + "genome_" + str(genome_cnt) + ".fasta"
fout = open(filename, "w")
contig_cnt = 1
for contig in genome.getElementsByTagName("contig"):
fout.write(">contig_" + str(contig_cnt) + "\n")
for node in contig.childNodes:
fout.write(node.data + "\n")
contig_cnt = contig_cnt + 1
fout.close()
genome_cnt = genome_cnt + 1;
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