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1 import requests
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2 import json
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3 import sys
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4 from __builtin__ import False
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5 #Gets the input and output from galaxy
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6 input_filename = sys.argv[1]
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7 output_filename = sys.argv[2]
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8
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9 #opens each file, in to read, out to write
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10 in_file = open(input_filename, "r")
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11 out_file = open(output_filename, "w")
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12
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13
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14 #sets replacements to replace each space in genomic coordinates with an underscore to run with the query
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15 replacements = {' ':'_'}
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16 #so we only print out the Keys once
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17 write_header = True
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18
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19 #loops through the input file line by line
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20 for line in in_file:
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21 #strips the input line of \n (new line) and replaces every space with an underscore
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22 line = "_".join( line.split() )
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23 #gets request from CRAVAT server with the inputed mutation line
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24 call = requests.get('http://staging.cravat.us/CRAVAT/rest/service/query', params={'mutation': line} )
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25 #puts the string of data into a json dictionary
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26 json_data = json.loads(call.text)
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27 #manually sets the order of the Keys to the same as CRAVAT Server
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28 keys = ["Chromosome","Position","Strand","Reference base(s)","Alternate base(s)","HUGO symbol",
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29 "Sequence ontology transcript","Sequence ontology protein change","Sequence ontology",
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30 "Sequence ontology all transcripts","ExAC total allele frequency",
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31 "ExAC allele frequency (African/African American)","ExAC allele frequency (Latino)",
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32 "ExAC allele frequency (East Asian)","ExAC allele frequency (Finnish)",
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33 "ExAC allele frequency (Non-Finnish European)","ExAC allele frequency (Other)",
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34 "ExAC allele frequency (South Asian)", "1000 Genomes allele frequency",
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35 "ESP6500 allele frequency (European American)","ESP6500 allele frequency (African American)",
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36 "Transcript in COSMIC","Protein sequence change in COSMIC",
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37 "Occurrences in COSMIC [exact nucleotide change]","Mappability Warning","Driver Genes",
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38 "TARGET","dbSNP","MuPIT Link"]
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39 print json_data
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40
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41 #Spit out first 8 or 9, then loop through rest and print out
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42 for key in json_data:
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43 if key not in keys:
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44 keys.append(key)
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45
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46 #used so we only print out the Keys once
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47 if write_header == True:
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48 #writes out the keys of the dictionary
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49 out_file.write('\t'.join(keys) + '\n')
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50 write_header = False
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51
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52 #sets value to the first value in the first key
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53 value = json_data[keys[0]]
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54 #actually writes out the value
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55 out_file.write(value)
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56 #print "key[" + key[0] + "] value[" + str(value) + "]"
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57 #sets value to the second key
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58 value = json_data[keys[1]]
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59 out_file.write('\t' + value)
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60 #print "key[" + key[1] + "] value[" + str(value) + "]"
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61
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62
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63 #loops through all other values for each key
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64 for key in keys[2:]:
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65 #strips the value
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66 value = json_data[key].strip()
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67 #another try, except statement to convert the rest of the values to floats, and then round them to four decimals
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68 try:
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69 value = float(value)
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70 value = '%.4f'%value
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71 except:
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72 pass
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73 #writes out the value with a tab after for galaxy formatting
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74 out_file.write("\t" + str(value))
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75 #print for debugging
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76 print "key[" + key + "] value[" + str(value) + "]"
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77 #creates a new line for the next set of values
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78 out_file.write('\n')
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79
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80
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81 #closes both files
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82 in_file.close()
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83 out_file.close()
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