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comparison config.py @ 0:f6ebec6e235e draft

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author petrn
date Thu, 19 Dec 2019 13:46:43 +0000
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1 '''
2 All configuration for clustering
3 '''
4 import os
5 import tempfile
6 from math import exp
7 from collections import namedtuple
8 MAIN_DIR = os.path.dirname(os.path.realpath(__file__))
9 def add_base_path(base):
10 '''automates generating absolute path in config'''
11 def joined_path(p):
12 '''create absolute path function '''
13 return os.path.join(base, p)
14 return joined_path
15
16 PATH = add_base_path(MAIN_DIR)
17
18 # clustering general settings
19 DIRECTORY_TREE = {'libdir': 'libdir',
20 'seqclust': 'seqclust',
21 'assembly': 'seqclust/small_clusters_assembly',
22 'blastx': 'seqclust/blastx',
23 'clustering': 'seqclust/clustering',
24 'clusters': 'seqclust/clustering/clusters',
25 'superclusters': 'seqclust/clustering/superclusters',
26 'mgblast': 'seqclust/mgblast',
27 'blastn': 'seqclust/blastn',
28 'prerun': 'seqclust/prerun',
29 'prerun_clusters': 'seqclust/prerun/clusters',
30 'sequences': 'seqclust/reads',
31 'custom_databases': 'seqclust/custom_databases'}
32
33 if "TEMP" in os.environ:
34 DIRECTORY_TREE['TEMP'] = os.environ["TEMP"]
35 else:
36 DIRECTORY_TREE['TEMP'] = tempfile.TemporaryDirectory().name
37
38 FILES = {'sample_db': DIRECTORY_TREE['TEMP'] + "/sample.db",
39 'sample_fasta': DIRECTORY_TREE['prerun'] + "/sample.fasta",
40 'prerun_cls_file' : DIRECTORY_TREE['prerun'] + "/sample_hitsort.cls",
41 'filter_sequences_file' : DIRECTORY_TREE['prerun'] + "/filter_sequences.fasta",
42 'sequences_db': DIRECTORY_TREE['TEMP'] + "/sequences.db",
43 'sequences_fasta': DIRECTORY_TREE['sequences'] + "/reads.fasta",
44 'hitsort': DIRECTORY_TREE['clustering'] + "/hitsort",
45 'hitsort_db': DIRECTORY_TREE['TEMP'] + "/hitsort.db",
46 'cls_file': DIRECTORY_TREE['clustering'] + "/hitsort.cls",
47 'clusters_summary_csv': "CLUSTER_TABLE.csv",
48 'profrep_classification_csv': "PROFREP_CLASSIFICATION_TEMPLATE.csv",
49 'superclusters_csv_summary': "SUPERCLUSTER_TABLE.csv",
50 'comparative_analysis_counts_csv': "COMPARATIVE_ANALYSIS_COUNTS.csv",
51 'clusters_info': ".clusters_info.csv",
52 'tarean_report_html': "tarean_report.html",
53 'cluster_report_html' : "cluster_report.html",
54 'supercluster_report_html' : 'supercluster_report.html',
55 'repeat_annotation_summary_rds' : 'repeat_annotation_summary.rds',
56 'summarized_annotation_html' :'summarized_annotation.html',
57 'main_report_html' : 'index.html',
58 'TR_consensus_fasta': "TAREAN_consensus_rank_{}.fasta",
59 'summary_histogram' : 'summary_histogram.png',
60 'comparative_summary_map': 'comparative_summary.png',
61 "how_to_cite" : "HOW_TO_CITE.html",
62 'logfile' : "logfile.txt",
63 'contigs' : "contigs.fasta",
64 'filter_omitted' : DIRECTORY_TREE['sequences'] + "/removed_filtering_positive_reads.fasta",
65 'filter_kept' : DIRECTORY_TREE['sequences'] + "/kept_filtering_positive_reads.fasta"
66 }
67
68
69 # include in output- [source, destination]
70 INCLUDE = [
71 [PATH("HOW_TO_CITE.html"), FILES["how_to_cite"]]
72 ]
73
74 # this is attribute of path - not a file name!
75 FILES_TO_DISCARD_AT_CLEANUP = [
76 'prerun', 'mgblast', 'blastn', "blastx",
77 'hitsort', "repeat_annotation_summary_rds"
78 ]
79
80 # relative links for html files
81 HTML_LINKS = {
82 "CLUSTER_TO_SUPERCLUSTER" : "../../superclusters/dir_SC%04d/index.html",
83 "SUPERCLUSTER_TO_CLUSTER" : "../../clusters/dir_CL%04d/index.html",
84 "CLUSTER_TO_CLUSTER" : "../dir_CL%04d/index.html",
85 "SUPERCLUSTER_TO_SUPERCLUSTER" : "../dir_SC%04d/index.html",
86 "CLUSTER_TO_CLUSTER_TABLE" : "../../../../cluster_report.html",
87 "SEPERCLUSTER_TO_CLUSTER_TABLE" : "../../../../cluster_report.html",
88 "ROOT_TO_CLUSTER" : "seqclust/clustering/clusters/dir_CL%04d/index.html",
89 "ROOT_TO_SUPERCLUSTER" : "seqclust/clustering/superclusters/dir_SC%04d/index.html",
90 "ROOT_TO_TAREAN" : "seqclust/clustering/clusters/dir_CL%04d/tarean/report.html",
91 "CLUSTER_TO_KMER_REPORT" : "tarean/report.html",
92 "INDEX_TO_TAREAN": "tarean_report.html",
93 "INDEX_TO_CLUSTER_REPORT": "cluster_report.html",
94 "INDEX_TO_SUPERCLUSTER_REPORT" : "supercluster_report.html",
95 "INDEX_TO_SUMMARIZED_ANNOTATION" : "summarized_annotation.html"
96 }
97
98
99 EMAX = 42.6 # define how many graph edges can be processed in 1Kb RAM
100 # MINIMUM_NUMBER_OF_INPUT_SEQUENCES = 5000
101 # FOR TESTING:
102 MINIMUM_NUMBER_OF_INPUT_SEQUENCES = 1000
103 MINIMUM_NUMBER_OF_READS_IN_CLUSTER = 20 # smaller clusters are not analyzed
104 MINIMUM_NUMBER_OF_READS_FOR_MERGING = 20 # smaller clusters will not be merged
105 MINIMUM_NUMBER_OF_SHARED_PAIRS_FOR_MERGING = 20 # min size of W param
106
107
108 NUMBER_OF_SEQUENCES_FOR_PRERUN_WITH_FILTERING = 50000
109 NUMBER_OF_SEQUENCES_FOR_PRERUN_WITHOUT_FILTERING = 20000
110 NUMBER_OF_SEQUENCES_FOR_PRERUN = NUMBER_OF_SEQUENCES_FOR_PRERUN_WITHOUT_FILTERING
111 CHUNK_SIZE = 20000
112
113
114 CLUSTER_EMAX = 2E7 # this parameter higle affect memory usage!
115
116 CLUSTER_VMAX = 40000
117 SUPERCLUSTER_THRESHOLD = 0.1
118 # Number of processors to use - it will be set at runtime
119 PROC = None
120 RSERVE_PORT = 6311
121
122 #some settings related to repeats annotation
123 ORF_THRESHOLD = 1200
124 PBS_THRESHOLD = 2
125 # threshold for rDNA detection - percentage of similarity hits
126 RDNA_THRESHOLD = 20
127 # threshold for contamination detection
128 CONTAMINATION_THRESHOLD = 10
129 # tandem ranks codes:
130 # 1 : putative tandem repeats - high confidence
131 # 2 : putative tandem repeats - low confidence
132 # 3 : potential LTR element
133 # 4 : rDNA
134 TANDEM_RANKS = [1, 2, 3, 4]
135 SKIP_CAP3_ASSEMBLY_TANDEM_RANKS = [1]
136 FILTER_MIN_PROP_THRESHOLD = 0.03 # this is minimal proportion of graph edges!
137 FILTER_MIN_SIZE_THRESHOLD = 1000 # minimal size of the cluster to be consider for filtering
138 FILTER_PROPORTION_OF_KEPT = 0.1
139
140 R = 'lib'
141 # external scripts
142 RSOURCE_tarean = PATH('lib/tarean/tarean.R')
143 RSOURCE_reporting = PATH('lib/reporting.R')
144 RSOURCE_create_annotation = PATH('lib/create_annotation.R')
145 LTR_DETECTION = PATH("lib/detect_LTR_insertion_sites.pl")
146
147 #PATH to DATABASES:
148 DNA_DATABASE = PATH("databases/dna_database_masked.fasta")
149 TRNA_DATABASE = PATH("databases/tRNA_database.fasta")
150 SATELLITE_MODEL = PATH("databases/satellite_model.rds")
151 LASTAL_PARAMS = PATH("databases/lastal_params")
152 # for testing
153 PROTEIN_DATABASE = None
154 CLASSIFICATION_HIERARCHY = None
155 CUSTOM_DNA_DATABASE = None
156
157 # when modifying this section check if makefile has most recent target for protein database
158 PROTEIN_DATABASE_DEFAULT = "VIRIDIPLANTAE3.0"
159 PROTEIN_DATABASE_OPTIONS = {'VIRIDIPLANTAE3.0' :
160 (PATH("databases/protein_database_viridiplantae_v3.0.fasta"), # change according if you use custom protein database
161 PATH("databases/classification_tree_viridiplantae_v3.0.rds")), # classification schem - data.tree object
162 'VIRIDIPLANTAE2.2' :
163 (PATH("databases/protein_database_viridiplantae_v2.2.fasta"), # change according if you use custom protein database
164 PATH("databases/classification_viridiplantae_tree.rds")), # classification schem - data.tree object
165 'METAZOA2.0' :
166 (PATH("databases/protein_database_metazoa_v3.fasta"), # change according if you use custom protein database
167 PATH("databases/classification_tree_metazoa_v3.rds")), # classification schem - data.tree object
168 'METAZOA3.0' :
169 (PATH("databases/protein_database_metazoa_v3.fasta"), # change according if you use custom protein database
170 PATH("databases/classification_tree_metazoa_v3.rds")) # classification schem - data.tree object
171 }
172 # if you change PROTEIN_DATABASE_OPTIONS, do not forget to use 'makeblastdb' build blast database
173 # and 'diamond makedb' to build diamond database
174
175 # PATH to binaries
176 LOUVAIN = PATH("louvain")
177 BINARIES = PATH("bin")
178
179 CAP3_PATTERNS_REPLACE = {"{}.{}.contigs" : [">Contig", ">{}Contig"],
180 "{}.{}.aln" : ["* Contig", "* {}Contig"],
181 "{}.{}.contigs.qual" : [">Contig", ">{}Contig"],
182 "{}.{}.ace" : ["CO Contig", "CO {}Contig"],
183 "{}.{}.singlets" : None,
184 "{}.{}.info" : None,
185 "{}.{}.contigs.links" : None}
186
187 CAP3_FILES_MAPPING = {"{}.{}.contigs" : "small_clusters.fasta",
188 "{}.{}.contigs.qual" : "small_clusters.contigs.qual",
189 "{}.{}.aln" : "small_clusters.aln",
190 "{}.{}.ace" : "small_clusters.ace",
191 "{}.{}.singlets" : None,
192 "{}.{}.info" : None,
193 "{}.{}.contigs.links" : None}
194
195 CAP3_FILENAMES = list(CAP3_PATTERNS_REPLACE.keys())
196
197 CAP3_FILES_GOODNAMES = {"{}.{}.contigs" : "contigs.fasta",
198 "{}.{}.contigs.qual" : "contigs.qual",
199 "{}.{}.aln" : "contigs.aln",
200 "{}.{}.ace" : "contigs.ace",
201 "{}.{}.singlets" : "singlets.fasta",
202 "{}.{}.info" : "assembly.info",
203 "{}.{}.contigs.links" : "contigs.links"}
204
205
206
207
208 CAP3_PARAMS = " -p 80 -o 40 " ## not implemented yet
209
210 LTR_DETECTION_FILES = {'ADJ': 'LTR_info.ADJ',
211 'LTR': 'LTR_info.LTR',
212 'PBS_BLAST': 'LTR_info.with_PBS_blast.csv',
213 'BASE' : 'LTR_info'}
214
215 # options for all-2-all search and annotations
216 FilteringThreshod = namedtuple("FilteringThreshold",
217 "min_lcov min_pid min_ovl min_scov evalue")
218 AnnotationParams = namedtuple("AnnotationParams", "blastn blastx blastn_trna")
219 Option = namedtuple('Options',
220 ('name database all2all_search_params filtering_threshold '
221 'filter_self_hits legacy_database lastdb annotation_search_params'))
222
223 # protein domain search options:
224 DIAMOND = {
225 'args': ' -p {max_proc} --max-target-seqs 1 --min-score 30 --freq-sd 1000 --more-sensitive',
226 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
227 'column_types' : [str, str, float, float, float, float, float],
228 'program': 'diamond blastx',
229 'filter_function' : lambda x: x.bitscore >= 30,
230 'parallelize' : False
231 }
232 BLASTX_W3 = {
233 'args': ' -num_alignments 1 -word_size 2 -evalue 0.01 ',
234 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
235 'column_types' : [str, str, float, float, float, float, float],
236 'program': 'blastx',
237 'filter_function' : lambda x: x.bitscore >= 33
238 }
239 BLASTX_W2 = BLASTX_W3
240 BLASTX_W2['args'] = ' -num_alignments 1 -word_size 3 -evalue 0.01 '
241
242
243 ARGS = None
244
245 ILLUMINA = Option(
246 name="illumina",
247 database='blastdb_legacy',
248 all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF -F '
249 '"m D" -v100000000 -b100000000'
250 ' -D4 -C 30 -H 30 -i {query} -d {blastdb}'),
251 filtering_threshold=FilteringThreshod(55, 90, 0, 0, 1),
252 filter_self_hits=False,
253 legacy_database=True,
254 lastdb=False,
255 annotation_search_params=AnnotationParams(
256 blastn={
257 'args': ' -task blastn -num_alignments 1 -evalue 0.01 ',
258 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
259 'column_types' : [str, str, float, float, float, float, float],
260 'program': 'blastn',
261 'filter_function' : lambda x: x.length > 30 and x.bitscore > 60
262
263 },
264 blastx=BLASTX_W3,
265 blastn_trna={
266 'args': ' -task blastn -num_alignments 1 -word_size 7',
267 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
268 'column_types' : [str, str, float, float, float, float, float],
269 'program': 'blastn',
270 'filter_function' : lambda x: x.length > 18 and x.bitscore > 60
271 }
272 )
273 )
274
275 ILLUMINA_DUST_OFF = ILLUMINA._replace(
276 all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF -F '
277 'F -v100000000 -b100000000'
278 ' -D4 -C 30 -H 30 -i {query} -d {blastdb}'),
279 )
280
281 ILLUMINA_SHORT = ILLUMINA._replace(
282 name="illumina_short",
283 all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF -F '
284 '"m D" -v100000000 -b100000000'
285 ' -D4 -C 20 -H 30 -i {query} -d {blastdb}'),
286 filtering_threshold=FilteringThreshod(40, 90, 0, 0, 0.1)
287 )
288
289
290 OXFORD_NANOPORE = Option(
291 name="oxford_nanopore",
292 database='lastdb',
293 all2all_search_params=('last_wrapper.py -f blasttab+ -P1 '
294 ' -m 700 -p {} '
295 ' {{blastdb}} {{query}} ').format(LASTAL_PARAMS),
296 filtering_threshold=FilteringThreshod(40, 50, 0, 0, 0.01),
297 filter_self_hits=True,
298 legacy_database=False,
299 lastdb=True,
300 annotation_search_params=AnnotationParams(
301 blastn={
302 'args': ' -task blastn -num_alignments 1 -evalue 0.01 -word_size 11',
303 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
304 'column_types' : [str, str, float, float, float, float, float],
305 'program': 'blastn',
306 'filter_function' : lambda x: x.length > 30 and x.bitscore > 50
307 },
308 blastx={
309 'args': ' -num_alignments 1 -word_size 2 -evalue 0.1',
310 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
311 'column_types' : [str, str, float, float, float, float, float],
312 'program': 'blastx',
313 'filter_function' : lambda x: x.bitscore >= 30
314 },
315 blastn_trna={
316 'args': ' -task blastn -num_alignments 1 -word_size 7',
317 'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
318 'column_types' : [str, str, float, float, float, float, float],
319 'program': 'blastn',
320 'filter_function' : lambda x: x.length > 18 and x.length > 60
321 }
322 )
323 )