Mercurial > repos > bornea > saint_preprocessing

comparison mzID_process2.py @ 65:a551998e1068 draft

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author bornea
date Sat, 27 Aug 2016 22:13:31 -0400
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64:e382e24af909 65:a551998e1068
1 # -*- coding: utf-8 -*-
2 """
3 Python-code: Preprocess mzIdentML
4 @author = Brent Kuenzi
5 @email = Brent.Kuenzi@moffitt.org
6 """
7 #######################################################################################
8 ## Description: ##
9 # This program will create inter, prey, and bait files from mzIdentML files
10 ## Required input: ##
11 # 1) mzIdentML file to be reformatted
12 # 2) minimum PSM for quantification
13
14
15 import sys
16 import os
17
18 ins_path = sys.argv[5]
19
20 class ReturnValue1(object):
21 def __init__(self, sequence, gene):
22 self.seqlength = sequence
23 self.genename = gene
24 class ReturnValue2(object):
25 def __init__(self, inter, accessions):
26 self.inter = inter
27 self.accessions = accessions
28 def read_tab(infile):
29 with open(infile,'r') as x:
30 output = []
31 for line in x:
32 line = line.strip()
33 temp = line.split('\t')
34 output.append(temp)
35 return output
36 def printProgress (iteration, total, prefix = '', suffix = '', decimals = 1, barLength = 100):
37 """
38 Call in a loop to create terminal progress bar
39 @params:
40 iteration - Required : current iteration (Int)
41 total - Required : total iterations (Int)
42 prefix - Optional : prefix string (Str)
43 suffix - Optional : suffix string (Str)
44 decimals - Optional : positive number of decimals in percent complete (Int)
45 barLength - Optional : character length of bar (Int)
46 """
47 formatStr = "{0:." + str(decimals) + "f}"
48 percents = formatStr.format(100 * (iteration / float(total)))
49 filledLength = int(round(barLength * iteration / float(total)))
50 bar = '=' * filledLength + '-' * (barLength - filledLength)
51 sys.stdout.write('\r%s |%s| %s%s %s' % (prefix, bar, percents, '%', suffix)),
52 sys.stdout.flush()
53 if iteration == total:
54 sys.stdout.write('\n')
55 sys.stdout.flush()
56 def get_info(uniprot_accession_in,fasta_db):
57 # Get aminoacid lengths and gene name.
58 error = open('error proteins.txt', 'a+')
59 data = open(fasta_db, 'r')
60 data_lines = data.readlines()
61 db_len = len(data_lines)
62 seqlength = 0
63 count = 0
64 last_line = data_lines[-1]
65 for data_line in data_lines:
66 if ">sp" in data_line:
67 namer = data_line.split("|")[2]
68 if uniprot_accession_in == data_line.split("|")[1]:
69 match = count + 1
70 if 'GN=' in data_line:
71 lst = data_line.split('GN=')
72 lst2 = lst[1].split(' ')
73 genename = lst2[0]
74 if 'GN=' not in data_line:
75 genename = 'NA'
76 while ">sp" not in data_lines[match]:
77 if match <= db_len:
78 seqlength = seqlength + len(data_lines[match].strip())
79 if data_lines[match] == last_line:
80 break
81 match = match + 1
82 else:
83 break
84 return ReturnValue1(seqlength, genename)
85 if uniprot_accession_in == namer.split(" ")[0]:
86 match = count + 1
87 # Ensures consistent spacing throughout.
88 if 'GN=' in data_line:
89 lst = data_line.split('GN=')
90 lst2 = lst[1].split(' ')
91 genename = lst2[0]
92 if 'GN=' not in data_line:
93 genename = 'NA'
94 while ">sp" not in data_lines[match]:
95 if match <= db_len:
96 seqlength = seqlength + len(data_lines[match].strip())
97 if data_lines[match] == last_line:
98 break
99 match = match + 1
100 else:
101 break
102 return ReturnValue1(seqlength, genename)
103 count = count + 1
104 if seqlength == 0:
105 error.write(uniprot_accession_in + '\t' + "Uniprot not in Fasta" + '\n')
106 error.close
107 seqlength = 'NA'
108 genename = 'NA'
109 return ReturnValue1(seqlength, genename)
110 def make_inter(mzIdentML,replicate,grouping):
111 accession_index = mzIdentML[0].index("accession")
112 PSMs = {}
113 accessions = []
114 cnt = 0
115 unique_lines = [mzIdentML[1:]]
116 for i in mzIdentML[1:]:
117 PSMs[i[accession_index]] = 0
118 if i[accession_index] not in accessions:
119 accessions.append(i[accession_index])
120 if i not in unique_lines:
121 unique_lines.append(i)
122 for i in accessions:
123 for j in unique_lines[1:]:
124 if j[accession_index] == i:
125 PSMs[j[accession_index]] +=1
126 inter = ""
127 for i in accessions:
128 inter = inter + replicate + "\t" + grouping + "\t" + i + "\t" + str(PSMs[i]) + "\n"
129 return ReturnValue2(inter,accessions)
130
131
132 files = sys.argv[1]
133 file_list = files.split(",")
134 bait = read_tab(sys.argv[2])
135 make_prey = sys.argv[3]
136 db = sys.argv[4]
137 if db == "None":
138 db = str(ins_path) + "/SwissProt_HUMAN_2015_12.fasta"
139 make_bait = sys.argv[6]
140 bait_bool = sys.argv[7]
141 prey_file = sys.argv[8]
142 bait_out = sys.argv[9]
143 inter_out = sys.argv[10]
144
145 def bait_create(baits, infile):
146 # Verifies the Baits are valid in the Scaffold file and writes the Bait.txt.
147 baits = make_bait.split()
148 i = 0
149 bait_file_tmp = open("bait.txt", "w")
150 order = []
151 bait_cache = []
152 while i < len(baits):
153 if baits[i+2] == "true":
154 T_C = "C"
155 else:
156 T_C = "T"
157 bait_line = baits[i] + "\t" + baits[i+1] + "\t" + T_C + "\n"
158 bait_cache.append(str(bait_line))
159 i = i + 3
160
161 for cache_line in bait_cache:
162 bait_file_tmp.write(cache_line)
163
164 bait_file_tmp.close()
165
166 if bait_bool == 'false':
167 bait_create(make_bait, infile)
168 bait = "bait.txt"
169 else:
170 bait_temp_file = open(sys.argv[9], 'r')
171 bait_cache = bait_temp_file.readlines()
172 bait_file_tmp = open("bait.txt", "wr")
173 for cache_line in bait_cache:
174 bait_file_tmp.write(cache_line)
175 bait_file_tmp.close()
176 bait = "bait.txt"
177
178 inter = ""
179 cnt = 0
180 accessions = []
181 for i in file_list:
182 cmd = (r"Rscript "+ str(ins_path) +"flatten_mzIdentML.R " + i)
183 os.system(cmd)
184 mzIdentML = read_tab("flat_mzIdentML.txt")
185 inter = inter + make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).inter
186 accessions.append(make_inter(mzIdentML,bait[cnt][0],bait[cnt][1]).accessions)
187 cnt+=1
188
189 with open("inter.txt","w") as x:
190 x.write(inter)
191 if make_prey == "Y":
192 unique_accessions = []
193 prey = ""
194 for i in accessions:
195 for j in i:
196 if j not in unique_accessions:
197 unique_accessions.append(j)
198 start = 0
199 end = len(unique_accessions)
200 printProgress(start,end,prefix = "Making Prey File:",suffix = "Complete",barLength=50)
201
202 for i in unique_accessions:
203 prey = prey + i + "\t" + str(get_info(i,db).seqlength) + "\t" + get_info(i,db).genename + "\n"
204 start+=1
205 printProgress(start, end)
206 with open("prey.txt","w") as x:
207 x.write(prey)
208
209 os.rename("bait.txt", sys.argv[2])
210 os.rename("inter.txt", sys.argv[10])
211 if str(prey) != "None":
212 os.rename("prey.txt", sys.argv[11])