def parseGetorfOutput(content):
"""
Parse getorf output file(handle), returns dictionaty with orfs
@type content: open filehandle
@param content: filehandle of a EMBOSS getorf output fasta file
@rtype: dictionary
@return: dictionary with keys (original fastaheader, orf-start, orf-stop) and sequence as values
@attention: content can be: sys.stdin.readlines()
@attention: content can be: fh.readlines()
"""
orfs = {}
for header, sequence in parseFasta(content).iteritems():
# below 3 lines retrieves start coordinates from getorf output
(fref,whatever)= header.split("_",1)
(start,stop) = header.split(" ",1)[-1][1:-1].split(" - ")
(start,stop) = (int(start),int(stop))
name = (fref,start,stop)
orfs[name] = sequence
# return fasta dictionary with openreadingframe info
return orfs
def parse_cexpander(cexpanderdata, fname_fasta):
"""
Parse the cexpander_dr output file into a CexpanderOutput class object
@type fname_cexpander: string
@param fname_cexpander: (absolute) path to cexpander_dr output file
@type fname_fasta: string
@param fname_fasta: (absolute) path to fasta input file
@rtype: CexpanderOutput object
@return: CexpanderOutput object
"""
# open file to txt string and initialize empty CexpanderOutput object
cxpOut = CexpanderOutput()
cxpOut.sequences = parseFasta(open(fname_fasta).readlines())
data = cexpanderdata.split("\n\n")[0:-1]
# generate header list; omit first 5 lines (cexpander STDOUT messages)
headers = data.pop(0)
headers = [
line.split("\t")[2].replace(">", "")
for line in headers.split("\n")[5:]
]
# loop over the `transfer blocks` in the file
for pos in range(0, len(data)):
cxpTrfblck = CexpanderTransferBlock()
if not set([
line.split("\t")[1] for line in data[pos][1:].split("\n")[1:]
]).difference(['0', '1']):
# cexpander in binary mode
# single-line string of zeros (0) and ones (1)
#cxpTrfblck.binarystring = ''.join( [ line.split("\t")[1] for line in data[pos][1:].split("\n")[1:] ] )
mode = "binary"
cxpTrfblck.binarystring = ""
for line in data[pos][1:].split("\n")[1:]:
for cell in line.strip().split("\t")[1:]:
cxpTrfblck.binarystring += cell
else:
# cexpander in float mode
mode = "float"
cxpTrfblck.binarystring = []
for line in data[pos][1:].split("\n")[1:]:
for cell in line.strip().split("\t")[1:]:
cxpTrfblck.binarystring.append(float(cell))
cxpTrfblck.header = headers[pos]
cxpTrfblck.sequence = cxpOut.sequences[cxpTrfblck.header]
cxpTrfblck.positions = len(cxpTrfblck.sequence)
cxpTrfblck.uniform = cxpTrfblck.get_uniform_positions()
cxpTrfblck.score = len(cxpTrfblck.uniform)
cxpTrfblck.ratio = cxpTrfblck._binarystring2matchratio(
cxpTrfblck.binarystring)
cxpTrfblck.mode = mode
if cxpTrfblck.positions != len(cxpTrfblck.binarystring):
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.positions, "!=", len(
cxpTrfblck.binarystring)
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.header, mode
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.sequence
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.binarystring
print "#" * 40
print "".join(data[pos])
print "#" * 40
# add CexpanderTransferBlock to CexpanderOutput object
cxpOut.add_transferblock(cxpTrfblck)
# return the created object
return cxpOut
import unittest
import sys
from os.path import join, abspath, dirname
LOCAL_DIR = abspath(dirname(__file__))
sys.path.append(abspath(join(LOCAL_DIR, '..')))
import MOODS
import fasta
DIST_DIR = abspath(dirname(dirname(LOCAL_DIR)))
print(DIST_DIR)
fasta_filepath = join(DIST_DIR, "examples/data/sequence/dnaACGT.txt")
records = fasta.parseFasta(fasta_filepath)
seq = records[0][1]
matrix1 = [ [0,1,0,0,0,0,0,1,1,0],
[1,0,0,0,0,0,0,0,0,0],
[0,0,0,0,0,0,0,0,0,0],
[0,0,1,1,1,1,1,0,0,1]
]
matrix2 = [ [10,0,10,3,5,5],
[0,5,0,3,5,0,5],
[0,1,0,3,0,5,0],
[0,4,0,1,0,0,5]
]
results = MOODS.search(seq, [matrix1, matrix2], 0.011)
import unittest
import sys
from os.path import join, abspath, dirname
LOCAL_DIR = abspath(dirname(__file__))
sys.path.append(abspath(join(LOCAL_DIR, '..')))
import MOODS
import fasta
DIST_DIR = abspath(dirname(dirname(LOCAL_DIR)))
print(DIST_DIR)
fasta_filepath = join(DIST_DIR, "examples/data/sequence/dnaACGT.txt")
records = fasta.parseFasta(fasta_filepath)
seq = records[0][1]
matrix1 = [[0, 1, 0, 0, 0, 0, 0, 1, 1, 0], [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 1, 1, 1, 1, 1, 0, 0, 1]]
matrix2 = [[10, 0, 10, 3, 5, 5], [0, 5, 0, 3, 5, 0, 5], [0, 1, 0, 3, 0, 5, 0],
[0, 4, 0, 1, 0, 0, 5]]
results = MOODS.search(seq, [matrix1, matrix2], 0.011)
print("Matrix 1 results: " + str(len(results[0])))
print("Matrix 2 results: " + str(len(results[1])))
matrices = [matrix1, matrix2]
thresholds = [0.011, 0.011]
bg = MOODS.bg_from_sequence(seq, 0.1)
def parse_cexpander(cexpanderdata,fname_fasta):
"""
Parse the cexpander_dr output file into a CexpanderOutput class object
@type fname_cexpander: string
@param fname_cexpander: (absolute) path to cexpander_dr output file
@type fname_fasta: string
@param fname_fasta: (absolute) path to fasta input file
@rtype: CexpanderOutput object
@return: CexpanderOutput object
"""
# open file to txt string and initialize empty CexpanderOutput object
cxpOut = CexpanderOutput()
cxpOut.sequences = parseFasta(open(fname_fasta).readlines())
data = cexpanderdata.split("\n\n")[0:-1]
# generate header list; omit first 5 lines (cexpander STDOUT messages)
headers = data.pop(0)
headers = [ line.split("\t")[2].replace(">","") for line in headers.split("\n")[5:] ]
# loop over the `transfer blocks` in the file
for pos in range(0,len(data)):
cxpTrfblck = CexpanderTransferBlock()
if not set([ line.split("\t")[1] for line in data[pos][1:].split("\n")[1:] ]).difference(['0','1']):
# cexpander in binary mode
# single-line string of zeros (0) and ones (1)
#cxpTrfblck.binarystring = ''.join( [ line.split("\t")[1] for line in data[pos][1:].split("\n")[1:] ] )
mode = "binary"
cxpTrfblck.binarystring = ""
for line in data[pos][1:].split("\n")[1:]:
for cell in line.strip().split("\t")[1:]:
cxpTrfblck.binarystring+=cell
else:
# cexpander in float mode
mode = "float"
cxpTrfblck.binarystring = []
for line in data[pos][1:].split("\n")[1:]:
for cell in line.strip().split("\t")[1:]:
cxpTrfblck.binarystring.append(float(cell))
cxpTrfblck.header = headers[pos]
cxpTrfblck.sequence = cxpOut.sequences[cxpTrfblck.header]
cxpTrfblck.positions = len(cxpTrfblck.sequence)
cxpTrfblck.uniform = cxpTrfblck.get_uniform_positions()
cxpTrfblck.score = len(cxpTrfblck.uniform)
cxpTrfblck.ratio = cxpTrfblck._binarystring2matchratio(cxpTrfblck.binarystring)
cxpTrfblck.mode = mode
if cxpTrfblck.positions != len(cxpTrfblck.binarystring):
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.positions, "!=", len(cxpTrfblck.binarystring)
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.header, mode
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.sequence
print "CEXPANDER-PARSE-ERROR:", cxpTrfblck.binarystring
print "#"*40
print "".join(data[pos])
print "#"*40
# add CexpanderTransferBlock to CexpanderOutput object
cxpOut.add_transferblock(cxpTrfblck)
# return the created object
return cxpOut
