Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate bin/edger_dge_table_to_bedgraph @ 115:f06dceb5b966 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty
author yhoogstrate
date Tue, 01 Sep 2015 08:01:02 -0400
parents 049d8bc2214e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
107
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
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1 #!/usr/bin/env python
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yhoogstrate
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2
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yhoogstrate
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3 import re,sys,os,os.path,argparse,textwrap,datetime
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4
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yhoogstrate
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5 class GTF:
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yhoogstrate
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6 def __init__(self,filename,features=["exon"],symbol="gene_id"):
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yhoogstrate
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7 self.features = features
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yhoogstrate
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8 if(re.match("^[a-zA-Z0-9_\-]+$",symbol)):
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yhoogstrate
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9 self.symbol = symbol
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yhoogstrate
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10 else:
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yhoogstrate
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11 raise ValueError('False symbol matching symbol: '+str(symbol))
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yhoogstrate
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12 self.index = {}
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yhoogstrate
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13 self.parse(filename)
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14
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15 def parse(self,filename):
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yhoogstrate
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16 with open(filename) as infile:
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yhoogstrate
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17 for line in infile:
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yhoogstrate
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18 self.parse_line(line)
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19
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yhoogstrate
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20 def parse_line(self,line):
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yhoogstrate
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21 line = line.strip().split("\t")
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yhoogstrate
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22 if(len(line) == 9):
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yhoogstrate
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23 if(line[2] in self.features):
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yhoogstrate
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24 gene_id = self.parse_column_9(line[8])
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yhoogstrate
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25 if(gene_id):
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yhoogstrate
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26 if(not self.index.has_key(gene_id)):
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yhoogstrate
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27 self.index[gene_id] = []
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yhoogstrate
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28 self.index[gene_id].append([line[0],line[3],line[4]])
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29
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yhoogstrate
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30 def parse_column_9(self,line):
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31 query = self.symbol+'[ =]+([^ ;]+)'
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yhoogstrate
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32 m = re.search(query, line)
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33
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34 if(m):
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35 return m.group(1).strip("'").strip('"')
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36 else:
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37 return None
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38
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39 def get(self,key):
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40 try:
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41 return self.index[key]
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42 except:
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43 return False
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44
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45
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yhoogstrate
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46 class EdgeR_table:
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47 def __init__(self,table,gtf,columns=[3,7]):
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48 self.index = {}
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49 self.gtf = gtf
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50 self.columns = columns
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51 self.parse(table)
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52
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53 def parse(self,filename):
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54 i = 0
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55 with open(filename) as infile:
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56 for line in infile:
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57 if(i == 0):
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yhoogstrate
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58 self.parse_header(line)
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59 else:
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60 self.parse_line(line)
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61 i += 1
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62
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63 def parse_header(self,line):
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64 params = line.strip().split("\t")
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65 if(params[1].lower().find("genes") == -1):
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66 raise ValueError('False header in file - no "genes" in 2nd colum: '+line)
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67 if(params[2].lower().find("logfc") == -1):
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68 raise ValueError('False header in file - no "logfc" in 3rd colum: '+line)
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69 if(params[3].lower().find("logcpm") == -1):
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70 raise ValueError('False header in file - no "logcpm" in 4th colum: '+line)
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71 if(params[4].lower().find("lr") == -1):
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72 raise ValueError('False header in file - no "lr" in 5th colum: '+line)
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73 if(params[5].lower().find("pvalue") == -1):
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74 raise ValueError('False header in file - no "pvalue" in 6th colum: '+line)
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75 if(params[6].lower().find("fdr") == -1):
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76 raise ValueError('False header in file - no "fdr" in 7th colum: '+line)
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77
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parents:
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78 def parse_line(self,line):
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yhoogstrate
parents:
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79 line = line.strip().split("\t")
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yhoogstrate
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80
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yhoogstrate
parents:
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81 if(len(line) == 7):
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yhoogstrate
parents:
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82 gene_id = line[1].strip('"').strip("'")
049d8bc2214e planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty
yhoogstrate
parents:
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83 column_data = {}
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yhoogstrate
parents:
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84 for column in self.columns:
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yhoogstrate
parents:
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85 if(column in [6,7]):
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yhoogstrate
parents:
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86 column_data[column] = str(1.0 - float(line[column-1]))
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87 else:
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yhoogstrate
parents:
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88 column_data[column] = line[column-1]
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yhoogstrate
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89
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yhoogstrate
parents:
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90 locations = self.gtf.get(gene_id)
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yhoogstrate
parents:
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91 if(not locations):
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yhoogstrate
parents:
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92 print "Warning: no location found for gene "+gene_id
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yhoogstrate
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93 else:
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yhoogstrate
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94 for location in locations:
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yhoogstrate
parents:
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95 self.insert(location,column_data)
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96
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yhoogstrate
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97 def insert(self,location,data):
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98 chrom = location[0]
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yhoogstrate
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99 start = location[1]
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yhoogstrate
parents:
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100 end = location[2]
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101
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yhoogstrate
parents:
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102 if(not self.index.has_key(chrom)):
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yhoogstrate
parents:
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103 self.index[chrom] = {}
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104
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yhoogstrate
parents:
diff changeset
105 if(not self.index[chrom].has_key(start)):
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yhoogstrate
parents:
diff changeset
106 self.index[chrom][start] = {}
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107
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yhoogstrate
parents:
diff changeset
108 if(not self.index[chrom][start].has_key(end)):
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yhoogstrate
parents:
diff changeset
109 self.index[chrom][start][end] = []
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110
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yhoogstrate
parents:
diff changeset
111 self.index[chrom][start][end].append(data)
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112
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113 def export(self,filenames={3:"log_cpm.txt",7:"fdr.txt"}):
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114 for column in self.columns:
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115 fh = open(filenames[column],"w")
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116
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117 buf = False
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118
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119 for chrom in sorted(self.index.keys()):
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120 for start in sorted(self.index[chrom].keys()):
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121 for end in sorted(self.index[chrom][start].keys()):
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122 fh.write(chrom+"\t"+start+"\t"+end+"\t"+self.index[chrom][start][end][0][column]+"\n")
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123
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124 fh.close()
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125
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126 os.system("sort -k1,1V -k2,2g -k3,3g '"+filenames[column]+"' > '"+filenames[column]+".sorted'")
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127
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128
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129 def remove_overlap_in_bedgraph(bedgraph_file_dirty,bedgraph_file_clean):
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130 fh = open(bedgraph_file_clean,"w")
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131 buf = False
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132
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133 with open(bedgraph_file_dirty,"r") as f:
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parents:
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134 for line in f:
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diff changeset
135 cur = line.strip().split("\t")
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yhoogstrate
parents:
diff changeset
136 cur[1] = int(cur[1])
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parents:
diff changeset
137 cur[2] = int(cur[2])
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138
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139 if(not buf):
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yhoogstrate
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diff changeset
140 buf = cur
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141 else:
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142 if(cur[0] == buf[0] and cur[1] <= buf[2] ):
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yhoogstrate
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diff changeset
143 if(buf[1] == cur[1]): #is subset
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diff changeset
144 newscore = (float(buf[3])+float(cur[3]))/2
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145 buf[2] = cur[2]
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yhoogstrate
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146 buf[3] = newscore
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147 else:
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148 c1 = buf[1]
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149 c2 = cur[1]
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150 c3 = min(buf[2],cur[2])
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151 c4 = max(buf[2],cur[2])
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152
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153 fh.write(buf[0]+"\t"+str(c1)+"\t"+str(c2-1)+"\t"+str(buf[3])+"\n")
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154
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155 newscore = (float(buf[3])+float(cur[3]))/2
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156 #fh.write(buf[0]+"\t"+str(c2+1)+"\t"+str(c3)+"\t"+str(newscore)+"\tp2\n")
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yhoogstrate
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157 #buf = [buf[0], c3+1 , c4 , cur[3]]
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yhoogstrate
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158
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yhoogstrate
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159 buf = [buf[0], c2 , c4 , cur[3]]
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yhoogstrate
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160
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yhoogstrate
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161 # find if buf is a subset -> if so, merge and send to buffer
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yhoogstrate
parents:
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162 # or find the overlapping region
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yhoogstrate
parents:
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163
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yhoogstrate
parents:
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164 # if current is overlapping with buffer; merge:
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yhoogstrate
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165 ## [ ] < buf
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yhoogstrate
parents:
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166 ## [ ] < cur
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yhoogstrate
parents:
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167 ##
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yhoogstrate
parents:
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168 ## [ ] < buf
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yhoogstrate
parents:
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169 ## [ ] < cur
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yhoogstrate
parents:
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170 ## 111112222333333 << write 1 and 2 and keep 3 in buf
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yhoogstrate
parents:
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171 else:
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yhoogstrate
parents:
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172 fh.write(buf[0]+"\t"+str(buf[1])+"\t"+str(buf[2])+"\t"+str(buf[3])+"\n")
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yhoogstrate
parents:
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173 buf=cur
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yhoogstrate
parents:
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174
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yhoogstrate
parents:
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175 fh.write(buf[0]+"\t"+str(buf[1])+"\t"+str(buf[2])+"\t"+str(buf[3])+"\n")
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yhoogstrate
parents:
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176 fh.close()
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yhoogstrate
parents:
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177
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yhoogstrate
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178
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yhoogstrate
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179
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yhoogstrate
parents:
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180 if __name__ == "__main__":
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yhoogstrate
parents:
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181 parser = argparse.ArgumentParser()
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yhoogstrate
parents:
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182
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yhoogstrate
parents:
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183 parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,epilog="For more info please visit:\n<https://github.com/yhoogstrate/fuma>")
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yhoogstrate
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184
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yhoogstrate
parents:
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185 parser.add_argument("-t",help="CPM table to extract columns from",nargs=1,required=True)
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yhoogstrate
parents:
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186 parser.add_argument("-g",help="GTF file used to extract genomic location",nargs=1,required=True)
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yhoogstrate
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187
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yhoogstrate
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188 parser.add_argument("-c3",help="Output (bedgraph) for column 3 (logFC)",nargs="?",required=False)
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yhoogstrate
parents:
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189 parser.add_argument("-c4",help="Output (bedgraph) for column 4 (logCPM)",nargs="?",required=False)
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yhoogstrate
parents:
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190 parser.add_argument("-c5",help="Output (bedgraph) for column 5 (LR)",nargs="?",required=False)
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yhoogstrate
parents:
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191 parser.add_argument("-c6",help="Output (bedgraph) for column 6 (PValue)",nargs="?",required=False)
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yhoogstrate
parents:
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192 parser.add_argument("-c7",help="Output (bedgraph) for column 7 (FDR)",nargs="?",required=False)
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yhoogstrate
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193
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yhoogstrate
parents:
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194 args = parser.parse_args()
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yhoogstrate
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195
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yhoogstrate
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196 #files = {3:"VCAP_logFC.hg19.bedgraph",7:"VCAP_fdr.hg19.bedgraph"}
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yhoogstrate
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197 files = {}
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yhoogstrate
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198
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yhoogstrate
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199 if(args.c3):
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yhoogstrate
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200 files[3] = args.c3
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yhoogstrate
parents:
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201 if(args.c4):
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yhoogstrate
parents:
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202 files[4] = args.c4
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yhoogstrate
parents:
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203 if(args.c5):
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yhoogstrate
parents:
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204 files[5] = args.c5
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yhoogstrate
parents:
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205 if(args.c6):
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yhoogstrate
parents:
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206 files[6] = args.c6
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yhoogstrate
parents:
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207 if(args.c7):
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yhoogstrate
parents:
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208 files[7] = args.c7
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yhoogstrate
parents:
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209
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yhoogstrate
parents:
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210 print "Parsing GTF file"
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yhoogstrate
parents:
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211 g = GTF(args.g[0])
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yhoogstrate
parents:
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212
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yhoogstrate
parents:
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213 print "Parsing EdgeR table"
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yhoogstrate
parents:
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214 e = EdgeR_table(args.t[0],g,files.keys())
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yhoogstrate
parents:
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215
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yhoogstrate
parents:
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216 print "Exporting raw bedgraph(s)"
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yhoogstrate
parents:
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217 e.export(files)
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yhoogstrate
parents:
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218
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yhoogstrate
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219 print "Removing overlapping entries in bedgraph(s)"
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yhoogstrate
parents:
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220 for key in files.keys():
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yhoogstrate
parents:
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221 remove_overlap_in_bedgraph(files[key]+".sorted",files[key])
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yhoogstrate
parents:
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222 os.system("rm '"+files[key]+".sorted'")