msp_sr_bowtie_parser: smRtools.py annotate

annotate smRtools.py @ 1:ca3845fb0b31 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09

author	drosofff
date	Mon, 18 Apr 2016 10:09:08 -0400
parents	b996480cd604
children

rev	line source
0 b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	1 #!/usr/bin/python
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	2 # version 1 7-5-2012 unification of the SmRNAwindow class
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	3
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	4 import sys, subprocess
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	5 from collections import defaultdict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	6 from numpy import mean, median, std
1 ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09 drosofff parents: 0 diff changeset	7 ##Disable scipy import temporarily, as no working scipy on toolshed.
ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09 drosofff parents: 0 diff changeset	8 ##from scipy import stats
0 b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	9
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	10 def get_fasta (index="/home/galaxy/galaxy-dist/bowtie/5.37_Dmel/5.37_Dmel"):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	11 '''This function will return a dictionary containing fasta identifiers as keys and the
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	12 sequence as values. Index must be the path to a fasta file.'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	13 p = subprocess.Popen(args=["bowtie-inspect","-a", "0", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	14 outputlines = p.stdout.readlines()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	15 p.wait()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	16 item_dic = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	17 for line in outputlines:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	18 if (line[0] == ">"):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	19 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	20 item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	21 except: pass
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	22 current_item = line[1:].rstrip().split()[0] #take the first word before space because bowtie splits headers !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	23 item_dic[current_item] = ""
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	24 stringlist=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	25 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	26 stringlist.append(line.rstrip() )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	27 item_dic[current_item] = "".join(stringlist) # for the last item
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	28 return item_dic
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	29
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	30 def get_fasta_headers (index):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	31 p = subprocess.Popen(args=["bowtie-inspect","-n", index], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) # bowtie-inspect outputs sequences on single lines
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	32 outputlines = p.stdout.readlines()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	33 p.wait()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	34 item_dic = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	35 for line in outputlines:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	36 header = line.rstrip().split()[0] #take the first word before space because bowtie splits headers !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	37 item_dic[header] = 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	38 return item_dic
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	39
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	40
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	41 def get_file_sample (file, numberoflines):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	42 '''import random to use this function'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	43 F=open(file)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	44 fullfile = F.read().splitlines()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	45 F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	46 if len(fullfile) < numberoflines:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	47 return "sample size exceeds file size"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	48 return random.sample(fullfile, numberoflines)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	49
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	50 def get_fasta_from_history (file):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	51 F = open (file, "r")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	52 item_dic = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	53 for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	54 if (line[0] == ">"):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	55 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	56 item_dic[current_item] = "".join(stringlist) # to dump the sequence of the previous item - try because of the keyerror of the first item
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	57 except: pass
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	58 current_item = line[1:-1].split()[0] #take the first word before space because bowtie splits headers !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	59 item_dic[current_item] = ""
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	60 stringlist=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	61 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	62 stringlist.append(line[:-1])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	63 item_dic[current_item] = "".join(stringlist) # for the last item
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	64 return item_dic
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	65
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	66 def antipara (sequence):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	67 antidict = {"A":"T", "T":"A", "G":"C", "C":"G", "N":"N"}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	68 revseq = sequence[::-1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	69 return "".join([antidict[i] for i in revseq])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	70
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	71 def RNAtranslate (sequence):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	72 return "".join([i if i in "AGCN" else "U" for i in sequence])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	73 def DNAtranslate (sequence):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	74 return "".join([i if i in "AGCN" else "T" for i in sequence])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	75
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	76 def RNAfold (sequence_list):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	77 thestring= "\n".join(sequence_list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	78 p = subprocess.Popen(args=["RNAfold","--noPS"], stdin= subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	79 output=p.communicate(thestring)[0]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	80 p.wait()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	81 output=output.split("\n")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	82 if not output[-1]: output = output[:-1] # nasty patch to remove last empty line
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	83 buffer=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	84 for line in output:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	85 if line[0] in ["N","A","T","U","G","C"]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	86 buffer.append(DNAtranslate(line))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	87 if line[0] in ["(",".",")"]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	88 fields=line.split("(")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	89 energy= fields[-1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	90 energy = energy[:-1] # remove the ) parenthesis
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	91 energy=float(energy)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	92 buffer.append(str(energy))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	93 return dict(zip(buffer[::2], buffer[1::2]))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	94
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	95 def extractsubinstance (start, end, instance):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	96 ''' Testing whether this can be an function external to the class to save memory'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	97 subinstance = SmRNAwindow (instance.gene, instance.sequence[start-1:end], start)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	98 subinstance.gene = "%s %s %s" % (subinstance.gene, subinstance.windowoffset, subinstance.windowoffset + subinstance.size - 1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	99 upcoordinate = [i for i in range(start,end+1) if instance.readDict.has_key(i) ]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	100 downcoordinate = [-i for i in range(start,end+1) if instance.readDict.has_key(-i) ]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	101 for i in upcoordinate:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	102 subinstance.readDict[i]=instance.readDict[i]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	103 for i in downcoordinate:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	104 subinstance.readDict[i]=instance.readDict[i]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	105 return subinstance
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	106
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	107 class HandleSmRNAwindows:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	108 def __init__(self, alignmentFile="~", alignmentFileFormat="tabular", genomeRefFile="~", genomeRefFormat="bowtieIndex", biosample="undetermined", size_inf=None, size_sup=1000, norm=1.0):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	109 self.biosample = biosample
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	110 self.alignmentFile = alignmentFile
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	111 self.alignmentFileFormat = alignmentFileFormat # can be "tabular" or "sam"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	112 self.genomeRefFile = genomeRefFile
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	113 self.genomeRefFormat = genomeRefFormat # can be "bowtieIndex" or "fastaSource"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	114 self.alignedReads = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	115 self.instanceDict = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	116 self.size_inf=size_inf
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	117 self.size_sup=size_sup
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	118 self.norm=norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	119 if genomeRefFormat == "bowtieIndex":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	120 self.itemDict = get_fasta (genomeRefFile)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	121 elif genomeRefFormat == "fastaSource":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	122 self.itemDict = get_fasta_from_history (genomeRefFile)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	123 for item in self.itemDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	124 self.instanceDict[item] = SmRNAwindow(item, sequence=self.itemDict[item], windowoffset=1, biosample=self.biosample, norm=self.norm) # create as many instances as there is items
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	125 self.readfile()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	126
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	127 def readfile (self) :
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	128 if self.alignmentFileFormat == "tabular":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	129 F = open (self.alignmentFile, "r")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	130 for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	131 fields = line.split()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	132 polarity = fields[1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	133 gene = fields[2]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	134 offset = int(fields[3])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	135 size = len (fields[4])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	136 if self.size_inf:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	137 if (size>=self.size_inf and size<= self.size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	138 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	139 self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	140 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	141 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	142 self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	143 F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	144 return self.instanceDict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	145 # elif self.alignmentFileFormat == "sam":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	146 # F = open (self.alignmentFile, "r")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	147 # dict = {"0":"+", "16":"-"}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	148 # for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	149 # if line[0]=='@':
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	150 # continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	151 # fields = line.split()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	152 # if fields[2] == "*": continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	153 # polarity = dict[fields[1]]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	154 # gene = fields[2]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	155 # offset = int(fields[3])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	156 # size = len (fields[9])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	157 # if self.size_inf:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	158 # if (size>=self.size_inf and size<= self.size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	159 # self.instanceDict[gene].addread (polarity, offset, size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	160 # self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	161 # else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	162 # self.instanceDict[gene].addread (polarity, offset, size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	163 # self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	164 # F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	165 elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	166 import pysam
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	167 samfile = pysam.Samfile(self.alignmentFile)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	168 for read in samfile:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	169 if read.tid == -1:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	170 continue # filter out unaligned reads
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	171 if read.is_reverse:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	172 polarity="-"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	173 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	174 polarity="+"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	175 gene = samfile.getrname(read.tid)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	176 offset = read.pos
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	177 size = read.qlen
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	178 if self.size_inf:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	179 if (size>=self.size_inf and size<= self.size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	180 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	181 self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	182 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	183 self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	184 self.alignedReads += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	185 return self.instanceDict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	186
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	187 # def size_histogram (self):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	188 # size_dict={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	189 # size_dict['F']= defaultdict (int)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	190 # size_dict['R']= defaultdict (int)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	191 # size_dict['both'] = defaultdict (int)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	192 # for item in self.instanceDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	193 # buffer_dict_F = self.instanceDict[item].size_histogram()['F']
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	194 # buffer_dict_R = self.instanceDict[item].size_histogram()['R']
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	195 # for size in buffer_dict_F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	196 # size_dict['F'][size] += buffer_dict_F[size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	197 # for size in buffer_dict_R:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	198 # size_dict['R'][size] -= buffer_dict_R[size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	199 # allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	200 # for size in allSizeKeys:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	201 # size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	202 # return size_dict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	203 def size_histogram (self): # in HandleSmRNAwindows
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	204 '''refactored on 7-9-2014 to debug size_histogram tool'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	205 size_dict={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	206 size_dict['F']= defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	207 size_dict['R']= defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	208 size_dict['both'] = defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	209 for item in self.instanceDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	210 buffer_dict = self.instanceDict[item].size_histogram()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	211 for polarity in ["F", "R"]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	212 for size in buffer_dict[polarity]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	213 size_dict[polarity][size] += buffer_dict[polarity][size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	214 for size in buffer_dict["both"]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	215 size_dict["both"][size] += buffer_dict["F"][size] - buffer_dict["R"][size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	216 return size_dict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	217
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	218 def CountFeatures (self, GFF3="path/to/file"):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	219 featureDict = defaultdict(int)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	220 F = open (GFF3, "r")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	221 for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	222 if line[0] == "#": continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	223 fields = line[:-1].split()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	224 chrom, feature, leftcoord, rightcoord, polarity = fields[0], fields[2], fields[3], fields[4], fields[6]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	225 featureDict[feature] += self.instanceDict[chrom].readcount(upstream_coord=int(leftcoord), downstream_coord=int(rightcoord), polarity="both", method="destructive")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	226 F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	227 return featureDict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	228
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	229 class SmRNAwindow:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	230
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	231 def __init__(self, gene, sequence="ATGC", windowoffset=1, biosample="Undetermined", norm=1.0):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	232 self.biosample = biosample
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	233 self.sequence = sequence
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	234 self.gene = gene
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	235 self.windowoffset = windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	236 self.size = len(sequence)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	237 self.readDict = defaultdict(list) # with a {+/-offset:[size1, size2, ...], ...}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	238 self.matchedreadsUp = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	239 self.matchedreadsDown = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	240 self.norm=norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	241
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	242 def addread (self, polarity, offset, size):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	243 '''ATTENTION ATTENTION ATTENTION'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	244 ''' We removed the conversion from 0 to 1 based offset, as we do this now during readparsing.'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	245 if polarity == "+":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	246 self.readDict[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	247 self.matchedreadsUp += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	248 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	249 self.readDict[-(offset + size -1)].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	250 self.matchedreadsDown += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	251 return
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	252
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	253 def barycenter (self, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	254 '''refactored 24-12-2013 to save memory and introduce offset filtering see readcount method for further discussion on that
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	255 In this version, attempt to replace the dictionary structure by a list of tupple to save memory too'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	256 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	257 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	258 window_size = downstream_coord - upstream_coord +1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	259 def weigthAverage (TuppleList):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	260 weightSum = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	261 PonderWeightSum = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	262 for tuple in TuppleList:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	263 PonderWeightSum += tuple[0] * tuple[1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	264 weightSum += tuple[1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	265 if weightSum > 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	266 return PonderWeightSum / float(weightSum)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	267 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	268 return 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	269 forwardTuppleList = [(k, len(self.readDict[k])) for k in self.readDict.keys() if (k > 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both forward and in the proper offset window
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	270 reverseTuppleList = [(-k, len(self.readDict[k])) for k in self.readDict.keys() if (k < 0 and abs(k) >= upstream_coord and abs(k) <= downstream_coord)] # both reverse and in the proper offset window
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	271 Fbarycenter = (weigthAverage (forwardTuppleList) - upstream_coord) / window_size
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	272 Rbarycenter = (weigthAverage (reverseTuppleList) - upstream_coord) / window_size
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	273 return Fbarycenter, Rbarycenter
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	274
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	275 def correlation_mapper (self, reference, window_size):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	276 '''to map correlation with a sliding window 26-2-2013'''
1 ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09 drosofff parents: 0 diff changeset	277 from scipy import stats
ca3845fb0b31 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09 drosofff parents: 0 diff changeset	278
0 b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	279 if window_size > self.size:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	280 return []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	281 F=open(reference, "r")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	282 reference_forward = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	283 reference_reverse = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	284 for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	285 fields=line.split()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	286 reference_forward.append(int(float(fields[1])))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	287 reference_reverse.append(int(float(fields[2])))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	288 F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	289 local_object_forward=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	290 local_object_reverse=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	291 ## Dict to list for the local object
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	292 for i in range(1, self.size+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	293 local_object_forward.append(len(self.readDict[i]))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	294 local_object_reverse.append(len(self.readDict[-i]))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	295 ## start compiling results by slides
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	296 results=[]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	297 for coordinate in range(self.size - window_size):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	298 local_forward=local_object_forward[coordinate:coordinate + window_size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	299 local_reverse=local_object_reverse[coordinate:coordinate + window_size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	300 if sum(local_forward) == 0 or sum(local_reverse) == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	301 continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	302 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	303 reference_to_local_cor_forward = stats.spearmanr(local_forward, reference_forward)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	304 reference_to_local_cor_reverse = stats.spearmanr(local_reverse, reference_reverse)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	305 if (reference_to_local_cor_forward[0] > 0.2 or reference_to_local_cor_reverse[0]>0.2):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	306 results.append([coordinate+1, reference_to_local_cor_forward[0], reference_to_local_cor_reverse[0]])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	307 except:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	308 pass
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	309 return results
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	310
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	311 def readcount (self, size_inf=0, size_sup=1000, upstream_coord=None, downstream_coord=None, polarity="both", method="conservative"):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	312 '''refactored 24-12-2013 to save memory and introduce offset filtering
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	313 take a look at the defaut parameters that cannot be defined relatively to the instance are they are defined before instanciation
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	314 the trick is to pass None and then test
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	315 polarity parameter can take "both", "forward" or "reverse" as value'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	316 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	317 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	318 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "both":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	319 return self.matchedreadsUp + self.matchedreadsDown
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	320 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "forward":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	321 return self.matchedreadsUp
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	322 if upstream_coord == 1 and downstream_coord == self.windowoffset+self.size-1 and polarity == "reverse":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	323 return self.matchedreadsDown
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	324 n=0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	325 if polarity == "both":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	326 for offset in xrange(upstream_coord, downstream_coord+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	327 if self.readDict.has_key(offset):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	328 for read in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	329 if (read>=size_inf and read<= size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	330 n += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	331 if method != "conservative":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	332 del self.readDict[offset] ## Carefull ! precludes re-use on the self.readDict dictionary !!!!!! TEST
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	333 if self.readDict.has_key(-offset):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	334 for read in self.readDict[-offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	335 if (read>=size_inf and read<= size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	336 n += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	337 if method != "conservative":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	338 del self.readDict[-offset]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	339 return n
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	340 elif polarity == "forward":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	341 for offset in xrange(upstream_coord, downstream_coord+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	342 if self.readDict.has_key(offset):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	343 for read in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	344 if (read>=size_inf and read<= size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	345 n += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	346 return n
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	347 elif polarity == "reverse":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	348 for offset in xrange(upstream_coord, downstream_coord+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	349 if self.readDict.has_key(-offset):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	350 for read in self.readDict[-offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	351 if (read>=size_inf and read<= size_sup):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	352 n += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	353 return n
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	354
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	355 def readsizes (self):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	356 '''return a dictionary of number of reads by size (the keys)'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	357 dicsize = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	358 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	359 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	360 dicsize[size] = dicsize.get(size, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	361 for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	362 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	363 return dicsize
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	364
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	365 # def size_histogram(self):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	366 # norm=self.norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	367 # hist_dict={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	368 # hist_dict['F']={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	369 # hist_dict['R']={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	370 # for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	371 # for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	372 # if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	373 # hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	374 # else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	375 # hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	376 # ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	377 # if not (hist_dict['F']) and (not hist_dict['R']):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	378 # hist_dict['F'][21] = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	379 # hist_dict['R'][21] = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	380 # ##
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	381 # return hist_dict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	382
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	383 def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	384 '''refactored on 7-9-2014 to debug size_histogram tool'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	385 norm=self.norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	386 size_dict={}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	387 size_dict['F']= defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	388 size_dict['R']= defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	389 size_dict['both']= defaultdict (float)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	390 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	391 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	392 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	393 size_dict['R'][size] = size_dict['R'][size] - 1*norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	394 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	395 size_dict['F'][size] = size_dict['F'][size] + 1*norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	396 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	397 if not (size_dict['F']) and (not size_dict['R']):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	398 size_dict['F'][21] = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	399 size_dict['R'][21] = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	400 ##
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	401 allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	402 for size in allSizeKeys:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	403 size_dict['both'][size] = size_dict['F'][size] - size_dict['R'][size]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	404 if minquery:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	405 for polarity in size_dict.keys():
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	406 for size in xrange(minquery, maxquery+1):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	407 if not size in size_dict[polarity].keys():
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	408 size_dict[polarity][size]=0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	409 return size_dict
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	410
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	411 def statsizes (self, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	412 ''' migration to memory saving by specifying possible subcoordinates
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	413 see the readcount method for further discussion'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	414 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	415 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	416 L = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	417 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	418 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	419 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	420 L.append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	421 meansize = mean(L)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	422 stdv = std(L)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	423 mediansize = median(L)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	424 return meansize, mediansize, stdv
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	425
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	426 def foldEnergy (self, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	427 ''' migration to memory saving by specifying possible subcoordinates
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	428 see the readcount method for further discussion'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	429 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	430 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	431 Energy = RNAfold ([self.sequence[upstream_coord-1:downstream_coord] ])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	432 return float(Energy[self.sequence[upstream_coord-1:downstream_coord]])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	433
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	434 def Ufreq (self, size_scope, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	435 ''' migration to memory saving by specifying possible subcoordinates
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	436 see the readcount method for further discussion. size_scope must be an interable'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	437 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	438 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	439 freqDic = {"A":0,"T":0,"G":0,"C":0, "N":0}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	440 convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	441 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	442 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	443 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	444 if size in size_scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	445 startbase = self.sequence[abs(offset)-self.windowoffset]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	446 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	447 startbase = convertDic[startbase]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	448 freqDic[startbase] += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	449 base_sum = float ( sum( freqDic.values()) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	450 if base_sum == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	451 return "."
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	452 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	453 return freqDic["T"] / base_sum * 100
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	454
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	455 def Ufreq_stranded (self, size_scope, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	456 ''' migration to memory saving by specifying possible subcoordinates
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	457 see the readcount method for further discussion. size_scope must be an interable
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	458 This method is similar to the Ufreq method but take strandness into account'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	459 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	460 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	461 freqDic = {"Afor":0,"Tfor":0,"Gfor":0,"Cfor":0, "Nfor":0,"Arev":0,"Trev":0,"Grev":0,"Crev":0, "Nrev":0}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	462 convertDic = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	463 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	464 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	465 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	466 if size in size_scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	467 startbase = self.sequence[abs(offset)-self.windowoffset]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	468 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	469 startbase = convertDic[startbase]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	470 freqDic[startbase+"rev"] += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	471 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	472 freqDic[startbase+"for"] += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	473 forward_sum = float ( freqDic["Afor"]+freqDic["Tfor"]+freqDic["Gfor"]+freqDic["Cfor"]+freqDic["Nfor"])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	474 reverse_sum = float ( freqDic["Arev"]+freqDic["Trev"]+freqDic["Grev"]+freqDic["Crev"]+freqDic["Nrev"])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	475 if forward_sum == 0 and reverse_sum == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	476 return ". \| ."
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	477 elif reverse_sum == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	478 return "%s \| ." % (freqDic["Tfor"] / forward_sum * 100)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	479 elif forward_sum == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	480 return ". \| %s" % (freqDic["Trev"] / reverse_sum * 100)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	481 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	482 return "%s \| %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	483
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	484
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	485 def readplot (self):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	486 norm=self.norm
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	487 readmap = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	488 for offset in self.readDict.keys():
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	489 readmap[abs(offset)] = ( len(self.readDict.get(-abs(offset),[]))norm , len(self.readDict.get(abs(offset),[]))norm )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	490 mylist = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	491 for offset in sorted(readmap):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	492 if readmap[offset][1] != 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	493 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, readmap[offset][1], "F") )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	494 if readmap[offset][0] != 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	495 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "R") )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	496 ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	497 if not mylist:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	498 mylist.append("%s\t%s\t%s\t%s" % (self.gene, 1, 0, "F") )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	499 ###
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	500 return mylist
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	501
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	502 def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	503 '''Use by MirParser tool'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	504 upstream_coord = upstream_coord or 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	505 downstream_coord = downstream_coord or self.size
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	506 windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	507 forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+1)])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	508 totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	509 totalreverse = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="reverse")
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	510 if totalforward > totalreverse:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	511 majorcoverage = "forward"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	512 for offset in self.readDict.keys():
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	513 if (offset > 0) and ((offset-upstream_coord+1) in forORrev_coverage.keys() ):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	514 for read in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	515 for i in xrange(read):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	516 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	517 forORrev_coverage[offset-upstream_coord+1+i] += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	518 except KeyError:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	519 continue # a sense read may span over the downstream limit
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	520 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	521 majorcoverage = "reverse"
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	522 for offset in self.readDict.keys():
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	523 if (offset < 0) and (-offset-upstream_coord+1 in forORrev_coverage.keys() ):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	524 for read in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	525 for i in xrange(read):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	526 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	527 forORrev_coverage[-offset-upstream_coord-i] += 1 ## positive coordinates in the instance, with + for forward coverage and - for reverse coverage
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	528 except KeyError:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	529 continue # an antisense read may span over the upstream limit
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	530 output_list = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	531 maximum = max (forORrev_coverage.values()) or 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	532 for n in sorted (forORrev_coverage):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	533 output_list.append("%s\t%s\t%s\t%s\t%s\t%s\t%s" % (self.biosample, windowName, n, float(n)/(downstream_coord-upstream_coord+1), forORrev_coverage[n], float(forORrev_coverage[n])/maximum, majorcoverage))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	534 return "\n".join(output_list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	535
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	536
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	537 def signature (self, minquery, maxquery, mintarget, maxtarget, scope, zscore="no", upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	538 ''' migration to memory saving by specifying possible subcoordinates
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	539 see the readcount method for further discussion
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	540 scope must be a python iterable; scope define the relative offset range to be computed'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	541 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	542 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	543 query_range = range (minquery, maxquery+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	544 target_range = range (mintarget, maxtarget+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	545 Query_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	546 Target_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	547 frequency_table = dict ([(i, 0) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	548 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	549 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	550 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	551 if size in query_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	552 Query_table[offset] = Query_table.get(offset, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	553 if size in target_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	554 Target_table[offset] = Target_table.get(offset, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	555 for offset in Query_table:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	556 for i in scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	557 frequency_table[i] += min(Query_table[offset], Target_table.get(-offset -i +1, 0))
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	558 if minquery==mintarget and maxquery==maxtarget: ## added to incorporate the division by 2 in the method (26/11/2013), see signature_options.py and lattice_signature.py
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	559 frequency_table = dict([(i,frequency_table[i]/2) for i in frequency_table])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	560 if zscore == "yes":
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	561 z_mean = mean(frequency_table.values() )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	562 z_std = std(frequency_table.values() )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	563 if z_std == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	564 frequency_table = dict([(i,0) for i in frequency_table] )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	565 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	566 frequency_table = dict([(i, (frequency_table[i]- z_mean)/z_std) for i in frequency_table] )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	567 return frequency_table
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	568
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	569 def hannon_signature (self, minquery, maxquery, mintarget, maxtarget, scope, upstream_coord=None, downstream_coord=None):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	570 ''' migration to memory saving by specifying possible subcoordinates see the readcount method for further discussion
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	571 note that scope must be an iterable (a list or a tuple), which specifies the relative offsets that will be computed'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	572 upstream_coord = upstream_coord or self.windowoffset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	573 downstream_coord = downstream_coord or self.windowoffset+self.size-1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	574 query_range = range (minquery, maxquery+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	575 target_range = range (mintarget, maxtarget+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	576 Query_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	577 Target_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	578 Total_Query_Numb = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	579 general_frequency_table = dict ([(i,0) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	580 ## filtering the appropriate reads for the study
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	581 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	582 if (abs(offset) < upstream_coord or abs(offset) > downstream_coord): continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	583 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	584 if size in query_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	585 Query_table[offset] = Query_table.get(offset, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	586 Total_Query_Numb += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	587 if size in target_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	588 Target_table[offset] = Target_table.get(offset, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	589 for offset in Query_table:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	590 frequency_table = dict ([(i,0) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	591 number_of_targets = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	592 for i in scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	593 frequency_table[i] += Query_table[offset] * Target_table.get(-offset -i +1, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	594 number_of_targets += Target_table.get(-offset -i +1, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	595 for i in scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	596 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	597 general_frequency_table[i] += (1. / number_of_targets / Total_Query_Numb) * frequency_table[i]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	598 except ZeroDivisionError :
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	599 continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	600 return general_frequency_table
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	601
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	602 def phasing (self, size_range, scope):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	603 ''' to calculate autocorelation like signal - scope must be an python iterable'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	604 read_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	605 total_read_number = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	606 general_frequency_table = dict ([(i, 0) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	607 ## read input filtering
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	608 for offset in self.readDict:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	609 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	610 if size in size_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	611 read_table[offset] = read_table.get(offset, 0) + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	612 total_read_number += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	613 ## per offset read phasing computing
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	614 for offset in read_table:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	615 frequency_table = dict ([(i, 0) for i in scope]) # local frequency table
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	616 number_of_targets = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	617 for i in scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	618 if offset > 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	619 frequency_table[i] += read_table[offset] * read_table.get(offset + i, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	620 number_of_targets += read_table.get(offset + i, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	621 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	622 frequency_table[i] += read_table[offset] * read_table.get(offset - i, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	623 number_of_targets += read_table.get(offset - i, 0)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	624 ## inclusion of local frequency table in the general frequency table (all offsets average)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	625 for i in scope:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	626 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	627 general_frequency_table[i] += (1. / number_of_targets / total_read_number) * frequency_table[i]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	628 except ZeroDivisionError :
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	629 continue
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	630 return general_frequency_table
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	631
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	632
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	633
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	634 def z_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	635 '''Must do: from numpy import mean, std, to use this method; scope must be a python iterable and defines the relative offsets to compute'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	636 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	637 z_table = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	638 frequency_list = [frequency_table[i] for i in sorted (frequency_table)]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	639 if std(frequency_list):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	640 meanlist = mean(frequency_list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	641 stdlist = std(frequency_list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	642 z_list = [(i-meanlist)/stdlist for i in frequency_list]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	643 return dict (zip (sorted(frequency_table), z_list) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	644 else:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	645 return dict (zip (sorted(frequency_table), [0 for i in frequency_table]) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	646
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	647 def percent_signature (self, minquery, maxquery, mintarget, maxtarget, scope):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	648 frequency_table = self.signature (minquery, maxquery, mintarget, maxtarget, scope)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	649 total = float(sum ([self.readsizes().get(i,0) for i in set(range(minquery,maxquery)+range(mintarget,maxtarget))]) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	650 if total == 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	651 return dict( [(i,0) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	652 return dict( [(i, frequency_table[i]/total*100) for i in scope])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	653
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	654 def pairer (self, overlap, minquery, maxquery, mintarget, maxtarget):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	655 queryhash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	656 targethash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	657 query_range = range (int(minquery), int(maxquery)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	658 target_range = range (int(mintarget), int(maxtarget)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	659 paired_sequences = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	660 for offset in self.readDict: # selection of data
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	661 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	662 if size in query_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	663 queryhash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	664 if size in target_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	665 targethash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	666 for offset in queryhash:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	667 if offset >= 0: matched_offset = -offset - overlap + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	668 else: matched_offset = -offset - overlap + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	669 if targethash[matched_offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	670 paired = min ( len(queryhash[offset]), len(targethash[matched_offset]) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	671 if offset >= 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	672 for i in range (paired):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	673 paired_sequences.append("+%s" % RNAtranslate ( self.sequence[offset:offset+queryhash[offset][i]]) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	674 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-targethash[matched_offset][i]+1:-matched_offset+1]) ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	675 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	676 for i in range (paired):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	677 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-queryhash[offset][i]+1:-offset+1]) ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	678 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+targethash[matched_offset][i]] ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	679 return paired_sequences
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	680
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	681 def pairable (self, overlap, minquery, maxquery, mintarget, maxtarget):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	682 queryhash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	683 targethash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	684 query_range = range (int(minquery), int(maxquery)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	685 target_range = range (int(mintarget), int(maxtarget)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	686 paired_sequences = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	687
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	688 for offset in self.readDict: # selection of data
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	689 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	690 if size in query_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	691 queryhash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	692 if size in target_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	693 targethash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	694
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	695 for offset in queryhash:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	696 matched_offset = -offset - overlap + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	697 if targethash[matched_offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	698 if offset >= 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	699 for i in queryhash[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	700 paired_sequences.append("+%s" % RNAtranslate (self.sequence[offset:offset+i]) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	701 for i in targethash[matched_offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	702 paired_sequences.append( "-%s" % RNAtranslate (antipara (self.sequence[-matched_offset-i+1:-matched_offset+1]) ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	703 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	704 for i in queryhash[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	705 paired_sequences.append("-%s" % RNAtranslate (antipara (self.sequence[-offset-i+1:-offset+1]) ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	706 for i in targethash[matched_offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	707 paired_sequences.append("+%s" % RNAtranslate (self.sequence[matched_offset:matched_offset+i] ) )
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	708 return paired_sequences
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	709
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	710 def newpairable_bowtie (self, overlap, minquery, maxquery, mintarget, maxtarget):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	711 ''' revision of pairable on 3-12-2012, with focus on the offset shift problem (bowtie is 1-based cooordinates whereas python strings are 0-based coordinates'''
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	712 queryhash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	713 targethash = defaultdict(list)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	714 query_range = range (int(minquery), int(maxquery)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	715 target_range = range (int(mintarget), int(maxtarget)+1)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	716 bowtie_output = []
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	717
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	718 for offset in self.readDict: # selection of data
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	719 for size in self.readDict[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	720 if size in query_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	721 queryhash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	722 if size in target_range:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	723 targethash[offset].append(size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	724 counter = 0
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	725 for offset in queryhash:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	726 matched_offset = -offset - overlap + 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	727 if targethash[matched_offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	728 if offset >= 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	729 for i in queryhash[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	730 counter += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	731 bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "+", self.gene, offset-1, self.sequence[offset-1:offset-1+i]) ) # attention a la base 1-0 de l'offset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	732 if offset < 0:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	733 for i in queryhash[offset]:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	734 counter += 1
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	735 bowtie_output.append("%s\t%s\t%s\t%s\t%s" % (counter, "-", self.gene, -offset-i, self.sequence[-offset-i:-offset])) # attention a la base 1-0 de l'offset
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	736 return bowtie_output
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	737
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	738
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	739 def __main__(bowtie_index_path, bowtie_output_path):
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	740 sequenceDic = get_fasta (bowtie_index_path)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	741 objDic = {}
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	742 F = open (bowtie_output_path, "r") # F is the bowtie output taken as input
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	743 for line in F:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	744 fields = line.split()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	745 polarity = fields[1]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	746 gene = fields[2]
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	747 offset = int(fields[3])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	748 size = len (fields[4])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	749 try:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	750 objDic[gene].addread (polarity, offset, size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	751 except KeyError:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	752 objDic[gene] = SmRNAwindow(gene, sequenceDic[gene])
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	753 objDic[gene].addread (polarity, offset, size)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	754 F.close()
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	755 for gene in objDic:
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	756 print gene, objDic[gene].pairer(19,19,23,19,23)
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	757
b996480cd604 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	758 if __name__ == "__main__" : __main__(sys.argv[1], sys.argv[2])

Mercurial > repos > drosofff > msp_sr_bowtie_parser

annotate smRtools.py @ 1:ca3845fb0b31 draft default tip