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1 """
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2 Python-code: Merge Scaffold Samples Report files
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3 @author = Brent Kuenzi
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4 @email = Brent.Kuenzi@moffitt.org
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5 """
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6 #######################################################################################
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7 import sys
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8 import urllib2
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9 import os.path
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6
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10 import pandas
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11 #######################################################################################
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12 ## Description: ##
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13 # This program will merge either 2 or 3 scaffold
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14 # sample report files together
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15 ## Required input: ##
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16 infile1 = sys.argv[1] # scaffold report #1 -- filename
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17 infile2 = sys.argv[2] # scaffold report #2 -- filename
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18 infile3 = sys.argv[3] # scaffold report #3 -- filename or "False"
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19 baitfile = sys.argv[4] # Bait file -- filename
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20 outfile = sys.argv[5] # output filename
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21 class ScaffoldReturn(object):
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22 def __init__(self, getdata, getproteins, getheader):
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23 self.data = getdata
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24 self.proteins = getproteins
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25 self.header = getheader
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26 class ProteinInfo(object):
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27 def __init__(self, getMW, getDescr):
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28 self.mw = getMW
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29 self.descr = getDescr
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30 def readtab(infile):
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31 with open(infile,'r') as x: # read in tab-delim text
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32 output = []
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33 for line in x:
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34 line = line.strip()
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35 temp = line.split('\t')
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36 output.append(temp)
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37 return output
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38 def read_scaffold(scaffold_input): # Get data, proteins and header from scaffold output
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39 dupes = readtab(scaffold_input)
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40 cnt = 0
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41 for i in dupes:
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42 if "Accession Number" in i: # finds the start of header
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43 header_start = cnt
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44 break
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45 cnt += 1
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46 header = dupes[header_start]
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47 prot_start = header.index("Accession Number")
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48 data = dupes[header_start+1:len(dupes)-2] # cut off blank line and END OF FILE
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49 proteins = []
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50 for i in data:
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51 i[prot_start] = i[prot_start].split()[0] # removes the (+##) that sometimes is attached
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52 for protein in data:
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53 proteins.append(protein[prot_start])
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54 return ScaffoldReturn(data, proteins, header)
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55 def MakeDF(scaffold_input,bait_input):
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56 bait = readtab(bait_input)
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57 data = read_scaffold(scaffold_input).data
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58 header = read_scaffold(scaffold_input).header
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59 proteins = read_scaffold(scaffold_input).proteins
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60 prot_start = header.index("Accession Number")
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61 bait_index = []
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62 ind = []
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63 for i in bait:
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64 if i[0] in header:
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65 bait_index.append(header.index(i[0])) # Find just the baits defined in bait file
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66 ind.append(i[0])
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67 frames = {}
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68 for i in proteins:
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69 protein = i.split()[0]
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70 if protein not in frames:
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71 frames[protein] = [] # create dictionary of proteins for each bait value
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72 for i in data:
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73 temp = i[prot_start]
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74 protein = temp.split()[0]
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75 for j in bait_index: # create dataframe
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76 frames[protein].append(i[j])
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77 df = pd.DataFrame(frames,index=ind)
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78 return df
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79 def get_info(input1,input2,input3):
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80 files = [input1,input2]
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81 molwt = {}
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82 protdesc = {}
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83 if input3 != "False":
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84 files.append(input3)
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85 for i in files:
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86 data = read_scaffold(i).data
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87 header = read_scaffold(i).header
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88 prot_start = header.index("Accession Number") # find header
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89 prot = 0
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90 mw = 0
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91 cnt=0
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92 for j in header: # find info
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93 if "Identified" in j:
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94 prot=cnt
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95 if "Molecular Weight" in j:
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96 mw=cnt
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97 cnt+=1
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98 for k in data: # append info
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99 temp = k[prot_start]
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100 protein = temp.split()[0]
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101 if protein not in protdesc:
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102 protdesc[protein] = k[prot]
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103 molwt[protein] = k[mw]
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104 mw = pd.DataFrame(molwt,index=["Molecular Weight"])
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105 descr = pd.DataFrame(protdesc,index=["Identified Proteins"])
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106 return ProteinInfo(mw,descr) # return info as dataframe
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107 def MakeFile(input1,input2,input3,bait_input):
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108 files = [input1,input2]
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109 if input3 != "False":
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110 files.append(input3)
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111 DFs = []
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112 DFs.append(get_info(input1,input2,input3).descr)
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113 DFs.append(get_info(input1,input2,input3).mw)
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114 for i in files:
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115 DFs.append(MakeDF(i,bait_input))
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116 final_df = pd.concat(DFs)
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117 temp = final_df.T
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118 temp.index.name = "Accession Number"
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119 output = temp.fillna(0)
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120 output["Accession Number"] = output.index.get_values()
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121 output.index = range(1, len(output.index) + 1)
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122 output.index.name = "#"
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123 output.to_csv(outfile,sep="\t")
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124
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125 #######################################################################################
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126 MakeFile(input1 = infile1,input2= infile2,input3 = infile3,bait_input=baitfile, outfile="merged.txt")
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127 #######################################################################################
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