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annotate scripts/functions.py @ 8:471ed956ff13 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
author abims-sbr
date Wed, 28 Feb 2018 10:37:14 -0500
parents 6709645eff5d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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471ed956ff13 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
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1 import string, itertools
4
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3 # Used in S05 and
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4 def split_file(path_in, keyword):
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6 file_in = open(path_in, "r")
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7 RUN = ''
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8 BASH1={}
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10 with open(path_in, "r") as file_in:
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11 for nextline in file_in.readlines():
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13 ##################################
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14 ### [A] FORMATTING QUERY NAME ###
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16 # Get query name
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17 if nextline[0:6]=='Query=':
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18 L1 = string.split(nextline, "||")
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19 L2 = string.split(L1[0], " ")
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20 query = L2[1]
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21 if query[-1] == "\n":
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22 query = query[:-1]
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24 ### [A] END FORMATTING QUERY NAME ###
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25 ######################################
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28 ### split the file with keyword ###
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29 if keyword in nextline:
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30 # Two cases here:
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31 #1# If it is the first "RUN" in the block (i.e. the first occurence of "BLASTN" in the file), we have just to add the new lines in the "RUN" list ... 2nd , we have also to detect the 'key' of bash1, which is the "query" name ... and third we will have to save this "RUN" in the bash1, once we will have detected a new "RUN" (i.e. a new line beginning with "BLASTN".
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32 #2# If it isn't the first run, we have the save the previous "RUN" in the "bash1", before to re-initialize the RUN list (RUN =[]), before to append lines to the new "RUN"
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34 if RUN == '': # case #1#
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35 RUN = RUN + nextline # we just added the first line of the file
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37 else: # case #2# (there was a run before)
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38 BASH1[query] = RUN # add the previous run to the bash
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39 RUN = '' # re-initialize the "RUN"
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40 RUN = RUN + nextline # add the line starting with the keyword ("BLASTN") (except the first line of the file (the first "RUN")
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42 else: # Treatment of the subsequent lines of the one starting with the keyword ("BLASTN") (which is not treated here but previously)
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43 RUN = RUN + nextline
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46 if RUN:
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47 BASH1[query] = RUN # add the last "RUN"
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50 return(BASH1)
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52 def detect_Matches(query, MATCH, WORK_DIR, bash1):
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53 F5 = open("%s/blastRun2.tmp" %WORK_DIR, 'w')
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54 F5.write(bash1[query])
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55 F5.close()
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57 F6 = open("%s/blastRun2.tmp" %WORK_DIR, 'r')
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58 list1 =[]
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59 list2 =[]
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61 while 1:
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62 nexteu = F6.readline()
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64 if not nexteu : break
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66 if "***** No hits found ******" in nexteu :
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67 hit = 0
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68 break
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70 if 'Sequences producing significant alignments:' in nexteu:
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71 hit = 1
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72 F6.readline() # jump a line
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74 while 1:
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75 nexteu2 = F6.readline()
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77 if nexteu2[0]==">": break
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79 ######################################
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80 ### [B] FORMAT MATCH NAME 1st STEP ###
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82 if nexteu2 != '\n':
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83 LL1 = string.split(nexteu2, " ") # specific NORTH database names !!!!!!!
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84 match = LL1[0] #### SOUTH databank // NORTH will have "|" separators
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85 list1.append(match)
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87 match2 = ">" + LL1[0] # more complete name // still specific NORTH database names !!!!!!!
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88 list2.append(match2) #### SOUTH databank // NORTH will have "|" separators
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90 if MATCH == 0: ## Only read the 1rst line (i.e. the First Match)
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91 break
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92 else: ## Read the other lines (i.e. All the Matches)
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93 continue
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95 ### [B] END FORMAT MATCH NAME 1st STEP ###
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96 ##########################################
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98 break
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100 F6.close()
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101 return(list1, list2, hit) # list1 = short name // list2 = more complete name
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102
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103 def get_information_on_matches(list_of_line):
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104
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105 for line in list_of_line:
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106
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107 ## Score and Expect
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108 if "Score" in line:
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109 line = line[:-1] # remove "\n"
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110 S_line = string.split(line, " = ")
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111 Expect = S_line[-1] ## ***** Expect
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112 S_line2 = string.split(S_line[1], " bits ")
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113 Score = string.atof(S_line2[0])
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114
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115 ## Identities/gaps/percent/divergence/length_matched
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116 elif "Identities" in line:
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117 line = line[:-1] # remove "\n"
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118 g = 0
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119
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120 if "Gaps" in line:
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121 pre_S_line = string.split(line, ",")
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122 identity_line = pre_S_line[0]
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123 gaps_line = pre_S_line[1]
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124 g = 1
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125 else:
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126 identity_line = line
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127 g = 0
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128
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129 ## treat identity line
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130 S_line = string.split(identity_line, " ")
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131
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132 identities = S_line[-2] ## ***** identities
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133
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134 S_line2 = string.split(identities, "/")
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135 hits = string.atof(S_line2[0]) ## ***** hits
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136 length_matched = string.atof(S_line2[1]) ## ***** length_matched
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137 abs_nb_differences = length_matched - hits ## ***** abs_nb_differences
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138
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139 identity_percent = hits/length_matched * 100 ## ***** identity_percent
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140
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141 divergence_percent = abs_nb_differences/length_matched*100 ## ***** divergence_percent
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142
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143 ## treat gap line if any
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144 if g ==1: # means there are gaps
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145 S_line3 = string.split(gaps_line, " ")
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146 gaps_part = S_line3[-2]
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147 S_line4 = string.split(gaps_part, "/")
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148 gaps_number = string.atoi(S_line4[0]) ## ***** gaps_number
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149
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150 real_differences = abs_nb_differences - gaps_number ## ***** real_differences
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151 real_divergence_percent = (real_differences/length_matched)*100 ## ***** real_divergence_percent
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152 else:
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153 gaps_number = 0
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154 real_differences = 0
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155 real_divergence_percent = divergence_percent
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156
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157 ## Frame
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158 elif "Frame" in line:
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159 line = line[:-1] # remove "\n"
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160 S_line = string.split(line, " = ")
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161 frame = S_line[1]
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162
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163 list_informations=[length_matched, Expect, Score, identities, hits, identity_percent, divergence_percent,gaps_number, real_divergence_percent, frame, length_matched]
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164
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165 return(list_informations)
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166
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167 # Used in S06, S09, S11
8
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168 def get_pairs(fasta_file_path):
4
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169 list_pairwises = []
8
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170 with open(fasta_file_path, "r") as F2:
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171 for name, sequence, name2, sequence2 in itertools.izip_longest(*[F2]*4):
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172 if name[0] == ">":
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173 fasta_name_query = name[:-1]
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174 fasta_seq_query = sequence[:-1]
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175 fasta_name_match = name2[:-1]
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176 fasta_seq_match = sequence2[:-1]
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177 pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
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178
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179 ## ADD pairwise with condition
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180 list_pairwises.append(pairwise)
4
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181 return(list_pairwises)
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182
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183 def extract_length(length_string): # format length string = 57...902
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184 l3 = string.split(length_string, "...")
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185 n1 = string.atoi(l3[0])
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186 n2 = string.atoi(l3[1])
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187 length = n2-n1
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188 return(length)
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189
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190 def filter_redondancy(list_paireu, MIN_LENGTH):
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191
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192 bash1 = {}
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193 list_pairout = []
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194
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195 for pair in list_paireu:
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196 query_name = pair[0]
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197 query_seq = pair[1]
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198 match_name = pair[2]
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199 match_seq = pair[3]
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200
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201 l1 = string.split(query_name, "||")
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202 short_query_name = l1[0][1:]
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203 length_matched = extract_length(l1[1])
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204 l2 = string.split(match_name, "||")
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205 short_match_name = l2[0][1:]
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206 binom = "%s_%s" %(short_query_name, short_match_name)
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207
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208 if binom not in bash1.keys():
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209 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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210 else:
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211 old_length = bash1[binom][-1]
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212 if length_matched > old_length:
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213 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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214
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215
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216 for bino in bash1.keys():
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217 length = bash1[bino][-1]
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218 if length > MIN_LENGTH:
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219 list_pairout.append(bash1[bino])
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220
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221 return(list_pairout)