Mercurial > repos > cpt > cpt_search_file

annotate searchFile.py @ 2:21ae0e340d80 draft default tip

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:57:22 +0000
parents 6e3a843b6304
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
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1 ##### User input File(s), that are BLAST XML, gff3, and/or Genbank and then searched for containing user designated terms
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2
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3 import argparse
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4 import explodeJSON as ej
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5 import gffutils # THIS IS REQUIREMENT
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6 from Bio.Blast import NCBIXML
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7 from Bio import SeqIO
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8 import re
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9 import os
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10
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11 SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
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12
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13 ####### TERM FUNCTIONS
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14 def dbaseTerms(terms, galaxy=True):
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15 """Index into dictionary object and retrieve all desired terms"""
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16 db_path = os.path.join(SCRIPT_DIR, "data/lysis-family-v1.0.3.json")
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17 db = ej.explodeJSON(db_path)
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18 db = db.readJSON()
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19 dbase_terms = []
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20 if terms:
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21 for term in terms:
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22 index_list = term.split(",")
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23 for t in index_list:
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24 if t != "None":
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25 dbase_terms.extend(db[t])
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26 else:
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27 dbase_terms = []
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28 return dbase_terms
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29 else:
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30 pass
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31
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32
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33 def userTerms(file, text):
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34 """Select terms input by user"""
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35 user_terms = []
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36 if file:
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37 terms = open(file.name).read().splitlines()
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38 user_terms.extend(terms)
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39 else:
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40 pass
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41 if text:
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42 if re.search(("__cn__"), str(text[0])):
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43 # s = text[0].split("__cn__")
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44 # print(s)
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45 # print(text[0])
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46 s = text[0]
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47 # print(type(s))
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48 split = s.split("__cn__")
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49 # print(split)
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50 user_terms.extend(split)
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51 else:
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52 user_terms.extend(text)
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53 else:
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54 pass
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55
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56 return user_terms
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57
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58
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59 def glueTerms(dbase_terms, user_terms):
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60 """glue dbaseTerms and userTerms together for eventual query item"""
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61 glued = []
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62 if dbase_terms:
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63 glued.extend(dbase_terms)
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64 else:
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65 pass
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66 if user_terms:
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67 glued.extend(user_terms)
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68 else:
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69 pass
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70
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71 return glued
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72
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73
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74 ####### FILE FUNCTIONS
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75 def glueFiles(gff, gbk, fa, blast):
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76 """glue files into one list...I think this is a decent way to go about this...#CHECK LATER#..."""
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77 files = []
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78 gffs = []
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79 gbks = []
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80 blasts = []
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81 if gff:
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82 for gff_file in gff:
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83 gffs.extend(gff_file)
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84 else:
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85 pass
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86 if gbk:
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87 for gbk_file in gbk:
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88 gbks.extend(gbk_file)
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89 # print(gbks)
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90 else:
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91 pass
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92 fas = []
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93 if fa:
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94 for fa_file in fa:
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95 fas.extend(fa_file)
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96 else:
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97 pass
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98 if blast:
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99 for blast_file in blast:
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100 blasts.extend(blast_file)
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101 else:
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102 pass
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103 files = [gffs, gbks, fas, blasts]
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104
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105 return files
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106
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107
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108 ######## PARSE FILE FUNCTIONS
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109 def readGFF3(files, search_list):
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110 "Searches through gff3 file(s) and appends"
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111 if files:
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112 for idx, file in enumerate(files):
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113 if idx == 0:
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114 print("Parsing - " + file.name)
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115 db = gffutils.create_db(
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116 file.name, dbfn="file.db", force=True, keep_order=False
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117 )
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118 db = gffutils.FeatureDB("file.db")
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119 features = db.all_features()
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120 gff3_matches = []
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121 for feature in features:
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122 gff3_matches.extend(
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diff changeset
123 searchInput(str(feature), search_list=search_list)
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cpt
parents:
diff changeset
124 )
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parents:
diff changeset
125 gff3_matches = list(
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cpt
parents:
diff changeset
126 set(gff3_matches)
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cpt
parents:
diff changeset
127 ) # make sure we don't fluff the list
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cpt
parents:
diff changeset
128 else:
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parents:
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129 print("Parsing - " + file.name)
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cpt
parents:
diff changeset
130 db = gffutils.create_db(
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cpt
parents:
diff changeset
131 file.name, dbfn=str(idx) + "_file.db", force=True, keep_order=False
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cpt
parents:
diff changeset
132 )
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parents:
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133 db = gffutils.FeatureDB(str(idx) + "_file.db")
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cpt
parents:
diff changeset
134 features = db.all_features()
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cpt
parents:
diff changeset
135 for feature in features:
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parents:
diff changeset
136 gff3_matches.extend(
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cpt
parents:
diff changeset
137 searchInput(str(feature), search_list=search_list)
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cpt
parents:
diff changeset
138 )
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parents:
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139 gff3_matches = list(
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cpt
parents:
diff changeset
140 set(gff3_matches)
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cpt
parents:
diff changeset
141 ) # make sure we don't fluff the list
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cpt
parents:
diff changeset
142 gff3_matches.sort()
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cpt
parents:
diff changeset
143 return gff3_matches
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parents:
diff changeset
144 else:
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parents:
diff changeset
145 pass
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cpt
parents:
diff changeset
146
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cpt
parents:
diff changeset
147
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parents:
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148 def readGBK(files, search_list):
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cpt
parents:
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149 if files:
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parents:
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150 for idx, file in enumerate(files):
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parents:
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151 if idx == 0:
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parents:
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152 print("Parsing - " + file.name)
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cpt
parents:
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153 record = SeqIO.read(file.name, "genbank")
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parents:
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154 gbk_matches = []
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cpt
parents:
diff changeset
155 for feature in record.features:
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cpt
parents:
diff changeset
156 try:
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cpt
parents:
diff changeset
157 if (
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cpt
parents:
diff changeset
158 searchInput(
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parents:
diff changeset
159 str(feature.qualifiers["product"]),
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cpt
parents:
diff changeset
160 search_list=search_list,
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cpt
parents:
diff changeset
161 )
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cpt
parents:
diff changeset
162 or searchInput(
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parents:
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163 str(feature.qualifiers["note"]), search_list=search_list
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cpt
parents:
diff changeset
164 )
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cpt
parents:
diff changeset
165 or searchInput(
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parents:
diff changeset
166 str(feature.qualifiers["dbxref"]),
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cpt
parents:
diff changeset
167 search_list=search_list,
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cpt
parents:
diff changeset
168 )
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cpt
parents:
diff changeset
169 ):
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parents:
diff changeset
170 gbk_matches.extend([str(feature)])
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cpt
parents:
diff changeset
171 else:
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cpt
parents:
diff changeset
172 continue
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parents:
diff changeset
173 except KeyError:
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cpt
parents:
diff changeset
174 continue
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parents:
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175 gbk_matches = list(set(gbk_matches))
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cpt
parents:
diff changeset
176 else:
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parents:
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177 print("Parsing - " + file.name)
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cpt
parents:
diff changeset
178 record = SeqIO.read(file.name, "genbank")
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cpt
parents:
diff changeset
179 for feature in record.features:
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cpt
parents:
diff changeset
180 try:
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cpt
parents:
diff changeset
181 if (
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cpt
parents:
diff changeset
182 searchInput(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 str(feature.qualifiers["product"]),
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cpt
parents:
diff changeset
184 search_list=search_list,
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cpt
parents:
diff changeset
185 )
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cpt
parents:
diff changeset
186 or searchInput(
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cpt
parents:
diff changeset
187 str(feature.qualifiers["note"]), search_list=search_list
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cpt
parents:
diff changeset
188 )
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cpt
parents:
diff changeset
189 or searchInput(
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cpt
parents:
diff changeset
190 str(feature.qualifiers["dbxref"]),
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cpt
parents:
diff changeset
191 search_list=search_list,
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cpt
parents:
diff changeset
192 )
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cpt
parents:
diff changeset
193 ):
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cpt
parents:
diff changeset
194 gbk_matches.extend([str(feature)])
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cpt
parents:
diff changeset
195 else:
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cpt
parents:
diff changeset
196 continue
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197 except KeyError:
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cpt
parents:
diff changeset
198 continue
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cpt
parents:
diff changeset
199 gbk_matches = list(set(gbk_matches))
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cpt
parents:
diff changeset
200 gbk_matches.sort()
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201 return gbk_matches
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cpt
parents:
diff changeset
202 else:
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 pass
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206 def readFASTA(files, search_list):
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cpt
parents:
diff changeset
207 if files:
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cpt
parents:
diff changeset
208 for idx, file in enumerate(files):
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cpt
parents:
diff changeset
209 if idx == 0:
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cpt
parents:
diff changeset
210 print("Parsing - " + file.name)
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211 record = SeqIO.parse(file.name, "fasta")
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 fa_matches = []
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cpt
parents:
diff changeset
213 for feature in record:
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cpt
parents:
diff changeset
214 fa_matches.extend(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 searchInput(feature.description, search_list=search_list)
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cpt
parents:
diff changeset
216 )
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cpt
parents:
diff changeset
217 fa_matches = list(set(fa_matches))
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cpt
parents:
diff changeset
218 else:
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cpt
parents:
diff changeset
219 print("Parsing - " + file.name)
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220 record = SeqIO.parse(file.name, "fasta")
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221 for feature in record:
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cpt
parents:
diff changeset
222 fa_matches.extend(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 searchInput(feature.description, search_list=search_list)
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cpt
parents:
diff changeset
224 )
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cpt
parents:
diff changeset
225 fa_matches = list(set(fa_matches))
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 fa_matches.sort()
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 return fa_matches
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cpt
parents:
diff changeset
228 else:
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cpt
parents:
diff changeset
229 pass
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231
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cpt
parents:
diff changeset
232 def readBLAST(files, search_list):
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cpt
parents:
diff changeset
233 if files:
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cpt
parents:
diff changeset
234 for idx, file in enumerate(files):
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235 if idx == 0:
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 print("Parsing - " + file.name)
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237 blast_records = NCBIXML.parse(open(file.name))
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cpt
parents:
diff changeset
238 blast_matches = []
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cpt
parents:
diff changeset
239 for blast_record in blast_records:
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 for desc in blast_record.descriptions:
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cpt
parents:
diff changeset
241 pretty = prettifyXML(str(desc))
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cpt
parents:
diff changeset
242 for each_ret in pretty:
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cpt
parents:
diff changeset
243 blast_matches.extend(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 searchInput(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245 each_ret,
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
246 search_list=search_list,
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
247 blast=True,
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248 q_id=blast_record.query,
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249 )
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250 )
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251 blast_matches = list(set(blast_matches))
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252 else:
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253 print("Parsing - " + file.name)
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254 blast_records = NCBIXML.parse(open(file.name))
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255 for blast_record in blast_records:
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parents:
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256 for desc in blast_record.descriptions:
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257 pretty = prettifyXML(str(desc))
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parents:
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258 blast_matches.extend(
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parents:
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259 searchInput(
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260 each_ret,
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261 search_list=search_list,
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262 blast=True,
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263 q_id=blast_record.query,
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parents:
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264 )
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parents:
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265 )
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266 blast_matches = list(set(blast_matches))
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267 blast_matches.sort()
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268 return blast_matches
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269 else:
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270 pass
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parents:
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271
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parents:
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272
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273 ######## SEARCH FILE FUNCTIONS
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274 def searchInput(input, search_list, blast=False, q_id=None):
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275 """Takes an input search string, and returns uniques of passing"""
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276 output = []
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277 for search_term in search_list:
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278 if blast:
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279 if re.search(re.escape(search_term), input):
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280 add_query = (
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281 "QueryID: "
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282 + str(q_id)
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283 + "\nSearchQuery: "
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284 + search_term
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285 + "\nMatch: "
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286 + input
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287 + "\n"
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parents:
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288 )
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289 output.extend([add_query])
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290 else:
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291 continue
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292 # print(search_term)
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293 # st = r"\b"+search_term+r"\b"
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294 else:
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295 if re.search(re.escape(search_term), input):
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296 # print(search_term+" -> was found")
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297 output.extend([input])
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298 else:
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299 continue
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300 return list(set(output))
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parents:
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301
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parents:
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302
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303 ######## prettify-XML function
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parents:
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304 def prettifyXML(input):
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parents:
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305 """prettifies a string input from a BLAST-xml"""
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306 s = input
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parents:
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307 split = s.split(">")
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parents:
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308
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309 return split
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parents:
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310
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parents:
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311
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312 ########## Output File Writer
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parents:
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313 def writeResults(gffs, gbks, fas, blasts, outName="termHits.txt"):
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parents:
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314 """Takes an input list for each parameter, and writes each result to the output file"""
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parents:
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315
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parents:
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316 with open(outName.name, "w+") as out_file:
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parents:
diff changeset
317 if gffs:
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parents:
diff changeset
318
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parents:
diff changeset
319 out_file.writelines(
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parents:
diff changeset
320 "\n==================== GFF3 Term Hits ====================\n\n"
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cpt
parents:
diff changeset
321 )
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parents:
diff changeset
322 for gff_hits in gffs:
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cpt
parents:
diff changeset
323 out_file.writelines(gff_hits + "\n")
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cpt
parents:
diff changeset
324 else:
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parents:
diff changeset
325 gffs = []
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parents:
diff changeset
326 if gbks:
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parents:
diff changeset
327 out_file.writelines(
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cpt
parents:
diff changeset
328 "\n==================== GBK Term Hits ====================\n\n"
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cpt
parents:
diff changeset
329 )
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cpt
parents:
diff changeset
330 for gbk_hits in gbks:
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cpt
parents:
diff changeset
331 out_file.writelines(gbk_hits + "\n")
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cpt
parents:
diff changeset
332 else:
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parents:
diff changeset
333 gbks = []
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cpt
parents:
diff changeset
334 if fas:
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cpt
parents:
diff changeset
335
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cpt
parents:
diff changeset
336 out_file.writelines(
6e3a843b6304 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
337 "\n==================== FASTA Term Hits ====================\n\n"
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cpt
parents:
diff changeset
338 )
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parents:
diff changeset
339 for fa_hits in fas:
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cpt
parents:
diff changeset
340 out_file.writelines(fa_hits + "\n")
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cpt
parents:
diff changeset
341 else:
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parents:
diff changeset
342 fas = []
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cpt
parents:
diff changeset
343 if blasts:
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cpt
parents:
diff changeset
344
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cpt
parents:
diff changeset
345 out_file.writelines(
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cpt
parents:
diff changeset
346 "\n==================== BLAST Term Hits ====================\n\n"
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cpt
parents:
diff changeset
347 )
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parents:
diff changeset
348 for blast_hits in blasts:
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cpt
parents:
diff changeset
349 out_file.writelines(blast_hits + "\n")
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cpt
parents:
diff changeset
350 else:
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parents:
diff changeset
351 blasts = []
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parents:
diff changeset
352 if len(gffs) or len(gbks) or len(fas) or len(blasts):
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parents:
diff changeset
353 print("Terms Found")
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parents:
diff changeset
354 else:
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parents:
diff changeset
355 out_file.writelines("No query matches, try again with new terms!")
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cpt
parents:
diff changeset
356 print("No query matches, try again with new terms!")
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cpt
parents:
diff changeset
357
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cpt
parents:
diff changeset
358
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parents:
diff changeset
359 def write_gff3(gffs, outName="proxHits.gff3"):
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parents:
diff changeset
360 """writes output to gff3 file for prox2lysis pipeline"""
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cpt
parents:
diff changeset
361
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parents:
diff changeset
362 with open(outName.name, "w+") as out_file:
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cpt
parents:
diff changeset
363 out_file.writelines("##gff-version 3\n")
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parents:
diff changeset
364 if gffs:
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parents:
diff changeset
365 for gff_hits in gffs:
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cpt
parents:
diff changeset
366 out_file.writelines(gff_hits + "\n")
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cpt
parents:
diff changeset
367 else:
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parents:
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368 # raise Exception("No terms were found from query set")
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cpt
parents:
diff changeset
369 out_file.writelines("##No terms were found from query set\n")
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parents:
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370
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371
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372 if __name__ == "__main__":
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373 print(os.getcwd())
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374 parser = argparse.ArgumentParser(
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375 description="Uses a selection of terms to query an input file for matching cases"
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376 )
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377 parser.add_argument(
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378 "--dbaseTerms", nargs="*", help="dbase terms to search"
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379 ) # will be a select option, based on KEY within the JSON dbase
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380 parser.add_argument(
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381 "--custom_txt",
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382 nargs="*",
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383 help="custom user input terms, if using Galaxy, terms will be __cn__ sep, otherwise by space",
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384 )
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385 parser.add_argument(
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386 "--custom_file",
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387 type=argparse.FileType("r"),
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388 help="custom new line separated search term file",
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389 )
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390 parser.add_argument(
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391 "--gff3_files",
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392 type=argparse.FileType("r"),
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393 nargs="*",
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394 action="append",
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395 help="GFF3 File(s), if multiple files, use another flag",
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396 )
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397 parser.add_argument(
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398 "--gbk_files",
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399 type=argparse.FileType("r"),
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400 nargs="*",
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401 action="append",
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402 help="GBK File(s), if multiple files, use another flag",
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403 )
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404 parser.add_argument(
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405 "--fa_files",
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406 type=argparse.FileType("r"),
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407 nargs="*",
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408 action="append",
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409 help="FASTA File(s), if multiple files, use another flag",
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410 )
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411 parser.add_argument(
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412 "--blast_files",
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413 type=argparse.FileType("r"),
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414 nargs="*",
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415 action="append",
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416 help="BLAST.xml File(s), if multiple files, use another flag",
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417 )
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418 parser.add_argument(
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419 "--output", type=argparse.FileType("w+"), default="termHits.txt"
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420 )
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421 parser.add_argument(
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422 "--prox", action="store_true", help="Use when running the prox2lysis pipeline"
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423 )
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424 args = parser.parse_args()
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425
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426 ############ STEP I
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427 ##### Determine user's terms to query
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428 dbase_terms = dbaseTerms(terms=args.dbaseTerms, galaxy=True)
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429 user_terms = userTerms(file=args.custom_file, text=args.custom_txt)
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430 glued_terms = glueTerms(dbase_terms=dbase_terms, user_terms=user_terms)
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431
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432 ############ STEP II
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433 ##### Create list with matches
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434 files = glueFiles(
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435 gff=args.gff3_files,
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436 gbk=args.gbk_files,
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437 fa=args.fa_files,
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438 blast=args.blast_files,
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439 )
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440 gffs = readGFF3(files=files[0], search_list=glued_terms)
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441 gbks = readGBK(files=files[1], search_list=glued_terms)
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442 fas = readFASTA(files=files[2], search_list=glued_terms)
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443 blasts = readBLAST(files=files[3], search_list=glued_terms)
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444
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445 ############ STEP III
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446 ##### Output results to a text file or gff3
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447 if args.prox:
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448 write_gff3(gffs, outName=args.output)
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449 else:
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450 writeResults(gffs, gbks, fas, blasts, outName=args.output)