Mercurial > repos > galaxyp > mqppep_preproc

annotate search_ppep.py @ 5:b889e05ce77d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
author galaxyp
date Fri, 17 Feb 2023 22:38:40 +0000
parents b76c75521d91
children
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1 #!/usr/bin/env python
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2 # Search and memoize phosphopeptides in Swiss-Prot SQLite table UniProtKB
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3
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4 import argparse
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5 import os.path
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6 import re
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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7 import sqlite3
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8 import sys # import the sys module for exc_info
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9 import time
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10 import traceback # import the traceback module for format_exception
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11 from codecs import getreader as cx_getreader
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12
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13 # For Aho-Corasick search for fixed set of substrings
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14 # - add_word
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15 # - make_automaton
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16 # - iter
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17 import ahocorasick
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19
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20 # ref: https://stackoverflow.com/a/8915613/15509512
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21 # answers: "How to handle exceptions in a list comprehensions"
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22 # usage:
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23 # from math import log
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24 # eggs = [1,3,0,3,2]
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25 # print([x for x in [catch(log, egg) for egg in eggs] if x is not None])
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26 # producing:
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27 # for <built-in function log>
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28 # with args (0,)
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29 # exception: math domain error
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30 # [0.0, 1.0986122886681098, 1.0986122886681098, 0.6931471805599453]
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31 def catch(func, *args, handle=lambda e: e, **kwargs):
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32
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33 try:
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34 return func(*args, **kwargs)
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35 except Exception as e:
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36 print("For %s" % str(func))
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37 print(" with args %s" % str(args))
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38 print(" caught exception: %s" % str(e))
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39 (ty, va, tb) = sys.exc_info()
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40 print(" stack trace: " + str(traceback.format_exception(ty, va, tb)))
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41 # exit(-1)
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42 return None # was handle(e)
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43
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44
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45 def __main__():
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46
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47 DROP_TABLES_SQL = """
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48 DROP VIEW IF EXISTS ppep_gene_site_view;
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49 DROP VIEW IF EXISTS uniprot_view;
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50 DROP VIEW IF EXISTS uniprotkb_pep_ppep_view;
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51 DROP VIEW IF EXISTS ppep_intensity_view;
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52 DROP VIEW IF EXISTS ppep_metadata_view;
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53
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54 DROP TABLE IF EXISTS sample;
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55 DROP TABLE IF EXISTS ppep;
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56 DROP TABLE IF EXISTS site_type;
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57 DROP TABLE IF EXISTS deppep_UniProtKB;
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58 DROP TABLE IF EXISTS deppep;
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59 DROP TABLE IF EXISTS ppep_gene_site;
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60 DROP TABLE IF EXISTS ppep_metadata;
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61 DROP TABLE IF EXISTS ppep_intensity;
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62 """
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63
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64 CREATE_TABLES_SQL = """
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65 CREATE TABLE deppep
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66 ( id INTEGER PRIMARY KEY
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67 , seq TEXT UNIQUE ON CONFLICT IGNORE
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68 )
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69 ;
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70 CREATE TABLE deppep_UniProtKB
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71 ( deppep_id INTEGER REFERENCES deppep(id) ON DELETE CASCADE
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72 , UniProtKB_id TEXT REFERENCES UniProtKB(id) ON DELETE CASCADE
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73 , pos_start INTEGER
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74 , pos_end INTEGER
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75 , PRIMARY KEY (deppep_id, UniProtKB_id, pos_start, pos_end)
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76 ON CONFLICT IGNORE
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77 )
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78 ;
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79 CREATE TABLE ppep
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80 ( id INTEGER PRIMARY KEY
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81 , deppep_id INTEGER REFERENCES deppep(id) ON DELETE CASCADE
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82 , seq TEXT UNIQUE ON CONFLICT IGNORE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
83 , scrubbed TEXT
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
84 );
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
85 CREATE TABLE site_type
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
86 ( id INTEGER PRIMARY KEY
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
87 , type_name TEXT UNIQUE ON CONFLICT IGNORE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
88 );
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
89 CREATE INDEX idx_ppep_scrubbed on ppep(scrubbed)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
90 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
91 CREATE TABLE sample
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
92 ( id INTEGER PRIMARY KEY
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
93 , name TEXT UNIQUE ON CONFLICT IGNORE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
94 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
95 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
96 CREATE VIEW uniprot_view AS
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
97 SELECT DISTINCT
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
98 Uniprot_ID
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
99 , Description
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
100 , Organism_Name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
101 , Organism_ID
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
102 , Gene_Name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
103 , PE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
104 , SV
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
105 , Sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
106 , Description ||
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
107 CASE WHEN Organism_Name = 'N/A'
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
108 THEN ''
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
109 ELSE ' OS='|| Organism_Name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
110 END ||
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
111 CASE WHEN Organism_ID = -1
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
112 THEN ''
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
113 ELSE ' OX='|| Organism_ID
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
114 END ||
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
115 CASE WHEN Gene_Name = 'N/A'
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
116 THEN ''
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
117 ELSE ' GN='|| Gene_Name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
118 END ||
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
119 CASE WHEN PE = 'N/A'
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
120 THEN ''
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
121 ELSE ' PE='|| PE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
122 END ||
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
123 CASE WHEN SV = 'N/A'
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
124 THEN ''
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
125 ELSE ' SV='|| SV
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
126 END AS long_description
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
127 , Database
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
128 FROM UniProtKB
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
129 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
130 CREATE VIEW uniprotkb_pep_ppep_view AS
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
131 SELECT deppep_UniProtKB.UniprotKB_ID AS accession
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
132 , deppep_UniProtKB.pos_start AS pos_start
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
133 , deppep_UniProtKB.pos_end AS pos_end
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
134 , deppep.seq AS peptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
135 , ppep.seq AS phosphopeptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
136 , ppep.scrubbed AS scrubbed
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
137 , uniprot_view.Sequence AS sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
138 , uniprot_view.Description AS description
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
139 , uniprot_view.long_description AS long_description
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
140 , ppep.id AS ppep_id
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
141 FROM ppep, deppep, deppep_UniProtKB, uniprot_view
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
142 WHERE deppep.id = ppep.deppep_id
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
143 AND deppep.id = deppep_UniProtKB.deppep_id
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
144 AND deppep_UniProtKB.UniprotKB_ID = uniprot_view.Uniprot_ID
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
145 ORDER BY UniprotKB_ID, deppep.seq, ppep.seq
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
146 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
147 CREATE TABLE ppep_gene_site
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
148 ( ppep_id INTEGER REFERENCES ppep(id)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
149 , gene_names TEXT
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
150 , site_type_id INTEGER REFERENCES site_type(id)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
151 , kinase_map TEXT
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
152 , PRIMARY KEY (ppep_id, kinase_map) ON CONFLICT IGNORE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
153 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
154 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
155 CREATE VIEW ppep_gene_site_view AS
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
156 SELECT DISTINCT
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
157 ppep.seq AS phospho_peptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
158 , ppep_id
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
159 , gene_names
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
160 , type_name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
161 , kinase_map
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
162 FROM
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
163 ppep, ppep_gene_site, site_type
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
164 WHERE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
165 ppep_gene_site.ppep_id = ppep.id
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
166 AND
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
167 ppep_gene_site.site_type_id = site_type.id
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168 ORDER BY
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169 ppep.seq
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170 ;
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171 CREATE TABLE ppep_metadata
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172 ( ppep_id INTEGER REFERENCES ppep(id)
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galaxyp
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173 , protein_description TEXT
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174 , gene_name TEXT
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galaxyp
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175 , FASTA_name TEXT
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176 , phospho_sites TEXT
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galaxyp
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177 , motifs_unique TEXT
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galaxyp
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178 , accessions TEXT
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galaxyp
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179 , motifs_all_members TEXT
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180 , domain TEXT
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181 , ON_FUNCTION TEXT
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182 , ON_PROCESS TEXT
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183 , ON_PROT_INTERACT TEXT
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galaxyp
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184 , ON_OTHER_INTERACT TEXT
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185 , notes TEXT
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186 , PRIMARY KEY (ppep_id) ON CONFLICT IGNORE
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parents:
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187 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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188 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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189 CREATE VIEW ppep_metadata_view AS
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parents:
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190 SELECT DISTINCT
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galaxyp
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191 ppep.seq AS phospho_peptide
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192 , protein_description
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parents:
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193 , gene_name
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galaxyp
parents:
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194 , FASTA_name
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195 , phospho_sites
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galaxyp
parents:
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196 , motifs_unique
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197 , accessions
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198 , motifs_all_members
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galaxyp
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199 , domain
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200 , ON_FUNCTION
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galaxyp
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201 , ON_PROCESS
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galaxyp
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202 , ON_PROT_INTERACT
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galaxyp
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203 , ON_OTHER_INTERACT
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204 , notes
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galaxyp
parents:
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205 FROM
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206 ppep, ppep_metadata
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207 WHERE
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208 ppep_metadata.ppep_id = ppep.id
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209 ORDER BY
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210 ppep.seq
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211 ;
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212 CREATE TABLE ppep_intensity
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213 ( ppep_id INTEGER REFERENCES ppep(id)
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214 , sample_id INTEGER
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215 , intensity INTEGER
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216 , PRIMARY KEY (ppep_id, sample_id) ON CONFLICT IGNORE
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217 )
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218 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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219 CREATE VIEW ppep_intensity_view AS
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220 SELECT DISTINCT
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221 ppep.seq AS phospho_peptide
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galaxyp
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222 , sample.name AS sample
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223 , intensity
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
224 FROM
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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225 ppep, sample, ppep_intensity
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parents:
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226 WHERE
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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227 ppep_intensity.sample_id = sample.id
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228 AND
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229 ppep_intensity.ppep_id = ppep.id
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230 ;
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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231 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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232
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parents:
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233 UNIPROT_SEQ_AND_ID_SQL = """
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galaxyp
parents:
diff changeset
234 select Sequence, Uniprot_ID
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parents:
diff changeset
235 from UniProtKB
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
236 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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237
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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238 # Parse Command Line
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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239 parser = argparse.ArgumentParser(
1
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galaxyp
parents: 0
diff changeset
240 description=" ".join([
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parents: 0
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241 "Phopsphoproteomic Enrichment",
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242 "phosphopeptide SwissProt search (in place in SQLite DB)."
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galaxyp
parents: 0
diff changeset
243 ])
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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244 )
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galaxyp
parents:
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245
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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246 # inputs:
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parents:
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247 # Phosphopeptide data for experimental results, including the intensities
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galaxyp
parents:
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248 # and the mapping to kinase domains, in tabular format.
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parents:
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249 parser.add_argument(
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parents:
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250 "--phosphopeptides",
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galaxyp
parents:
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251 "-p",
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parents:
diff changeset
252 nargs=1,
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253 required=True,
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diff changeset
254 dest="phosphopeptides",
1
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255 help=" ".join([
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256 "Phosphopeptide data for experimental results,",
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257 "generated by the Phopsphoproteomic Enrichment Localization",
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258 "Filter tool"
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259 ]),
0
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260 )
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261 parser.add_argument(
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262 "--uniprotkb",
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263 "-u",
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264 nargs=1,
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265 required=True,
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266 dest="uniprotkb",
1
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267 help=" ".join([
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268 "UniProtKB/Swiss-Prot data, converted from FASTA format by the",
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269 "Phopsphoproteomic Enrichment Kinase Mapping tool"
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270 ]),
0
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271 )
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272 parser.add_argument(
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273 "--schema",
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274 action="store_true",
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275 dest="db_schema",
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276 help="show updated database schema",
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277 )
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278 parser.add_argument(
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279 "--warn-duplicates",
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280 action="store_true",
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281 dest="warn_duplicates",
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282 help="show warnings for duplicated sequences",
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283 )
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284 parser.add_argument(
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285 "--verbose",
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286 action="store_true",
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287 dest="verbose",
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288 help="show somewhat verbose program tracing",
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289 )
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290 # "Make it so!" (parse the arguments)
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291 options = parser.parse_args()
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292 if options.verbose:
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293 print("options: " + str(options) + "\n")
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294
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295 # path to phosphopeptide (e.g., "outputfile_STEP2.txt") input tabular file
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296 if options.phosphopeptides is None:
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297 exit('Argument "phosphopeptides" is required but not supplied')
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298 try:
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299 f_name = os.path.abspath(options.phosphopeptides[0])
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300 except Exception as e:
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301 exit("Error parsing phosphopeptides argument: %s" % (e))
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302
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303 # path to SQLite input/output tabular file
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304 if options.uniprotkb is None:
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305 exit('Argument "uniprotkb" is required but not supplied')
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306 try:
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307 db_name = os.path.abspath(options.uniprotkb[0])
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308 except Exception as e:
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309 exit("Error parsing uniprotkb argument: %s" % (e))
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310
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311 # print("options.schema is %d" % options.db_schema)
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312
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313 # db_name = "demo/test.sqlite"
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314 # f_name = "demo/test_input.txt"
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315
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316 con = sqlite3.connect(db_name)
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317 cur = con.cursor()
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318 ker = con.cursor()
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319
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320 cur.executescript(DROP_TABLES_SQL)
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321
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322 # if options.db_schema:
1
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323 # print("\nAfter dropping tables/views that are to be created,"
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324 # + schema is:")
0
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325 # cur.execute("SELECT * FROM sqlite_schema")
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326 # for row in cur.fetchall():
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327 # if row[4] is not None:
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328 # print("%s;" % row[4])
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329
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330 cur.executescript(CREATE_TABLES_SQL)
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331
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332 if options.db_schema:
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333 print(
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334 "\nAfter creating tables/views that are to be created, schema is:"
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335 )
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336 cur.execute("SELECT * FROM sqlite_schema")
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337 for row in cur.fetchall():
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338 if row[4] is not None:
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339 print("%s;" % row[4])
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340
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
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341 def generate_ppep(f):
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parents:
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342 # get keys from upstream tabular file using readline()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
343 # ref: https://stackoverflow.com/a/16713581/15509512
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
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344 # answer to "Use codecs to read file with correct encoding"
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parents:
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345 file1_encoded = open(f, "rb")
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galaxyp
parents:
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346 file1 = cx_getreader("latin-1")(file1_encoded)
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parents:
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347
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galaxyp
parents:
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348 count = 0
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parents:
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349 re_tab = re.compile("^[^\t]*")
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galaxyp
parents:
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350 re_quote = re.compile('"')
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galaxyp
parents:
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351 while True:
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galaxyp
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352 count += 1
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galaxyp
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353 # Get next line from file
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354 line = file1.readline()
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galaxyp
parents:
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355 # if line is empty
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356 # end of file is reached
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357 if not line:
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galaxyp
parents:
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358 break
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galaxyp
parents:
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359 if count > 1:
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galaxyp
parents:
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360 m = re_tab.match(line)
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galaxyp
parents:
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361 m = re_quote.sub("", m[0])
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galaxyp
parents:
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362 yield m
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galaxyp
parents:
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363 file1.close()
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galaxyp
parents:
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364 file1_encoded.close()
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galaxyp
parents:
diff changeset
365
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parents:
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366 # Build an Aho-Corasick automaton from a trie
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galaxyp
parents:
diff changeset
367 # - ref:
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galaxyp
parents:
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368 # - https://pypi.org/project/pyahocorasick/
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galaxyp
parents:
diff changeset
369 # - https://en.wikipedia.org/wiki/Aho%E2%80%93Corasick_algorithm
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galaxyp
parents:
diff changeset
370 # - https://en.wikipedia.org/wiki/Trie
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galaxyp
parents:
diff changeset
371 auto = ahocorasick.Automaton()
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galaxyp
parents:
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372 re_phos = re.compile("p")
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galaxyp
parents:
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373 # scrub out unsearchable characters per section
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parents:
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374 # "Match the p_peptides to the @sequences array:"
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galaxyp
parents:
diff changeset
375 # of the original
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galaxyp
parents:
diff changeset
376 # PhosphoPeptide Upstream Kinase Mapping.pl
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galaxyp
parents:
diff changeset
377 # which originally read
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parents:
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378 # $tmp_p_peptide =~ s/#//g;
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parents:
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379 # $tmp_p_peptide =~ s/\d//g;
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galaxyp
parents:
diff changeset
380 # $tmp_p_peptide =~ s/\_//g;
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parents:
diff changeset
381 # $tmp_p_peptide =~ s/\.//g;
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galaxyp
parents:
diff changeset
382 #
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galaxyp
parents:
diff changeset
383 re_scrub = re.compile("0-9_.#")
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
384 ppep_count = 0
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galaxyp
parents:
diff changeset
385 for ppep in generate_ppep(f_name):
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
386 ppep_count += 1
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galaxyp
parents:
diff changeset
387 add_to_trie = False
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
388 # print(ppep)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
389 scrubbed = re_scrub.sub("", ppep)
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galaxyp
parents:
diff changeset
390 deppep = re_phos.sub("", scrubbed)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
391 if options.verbose:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
392 print("deppep: %s; scrubbed: %s" % (deppep, scrubbed))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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parents:
diff changeset
393 # print(deppep)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
394 cur.execute("SELECT id FROM deppep WHERE seq = (?)", (deppep,))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
395 if cur.fetchone() is None:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
396 add_to_trie = True
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
397 cur.execute("INSERT INTO deppep(seq) VALUES (?)", (deppep,))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
398 cur.execute("SELECT id FROM deppep WHERE seq = (?)", (deppep,))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
399 deppep_id = cur.fetchone()[0]
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
400 if add_to_trie:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
401 # print((deppep_id, deppep))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
402 # Build the trie
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
403 auto.add_word(deppep, (deppep_id, deppep))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
404 cur.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
405 "INSERT INTO ppep(seq, scrubbed, deppep_id) VALUES (?,?,?)",
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
406 (ppep, scrubbed, deppep_id),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
407 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
408 # def generate_deppep():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
409 # cur.execute("SELECT seq FROM deppep")
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
410 # for row in cur.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
411 # yield row[0]
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
412 cur.execute("SELECT count(*) FROM (SELECT seq FROM deppep GROUP BY seq)")
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
413 for row in cur.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
414 deppep_count = row[0]
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
415
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
416 cur.execute(
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
417 """
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
418 SELECT count(*) FROM (
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
419 SELECT Sequence FROM UniProtKB GROUP BY Sequence
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
420 )
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
421 """
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
422 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
423 for row in cur.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
424 sequence_count = row[0]
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
425
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
426 print("%d phosphopeptides were read from input" % ppep_count)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
427 print(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
428 "%d corresponding dephosphopeptides are represented in input"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
429 % deppep_count
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
430 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
431 # Look for cases where both Gene_Name and Sequence are identical
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
432 cur.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
433 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
434 SELECT Uniprot_ID, Gene_Name, Sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
435 FROM UniProtKB
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
436 WHERE Sequence IN (
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
437 SELECT Sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
438 FROM UniProtKB
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
439 GROUP BY Sequence, Gene_Name
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
440 HAVING count(*) > 1
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
441 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
442 ORDER BY Sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
443 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
444 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
445 duplicate_count = 0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
446 old_seq = ""
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
447 for row in cur.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
448 if duplicate_count == 0:
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
449 print(" ".join([
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
450 "\nEach of the following sequences is associated with several",
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
451 "accession IDs (which are listed in the first column) but",
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
452 "the same gene ID (which is listed in the second column)."
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
453 ]))
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
454 if row[2] != old_seq:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
455 old_seq = row[2]
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
456 duplicate_count += 1
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
457 if options.warn_duplicates:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
458 print("\n%s\t%s\t%s" % row)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
459 else:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
460 if options.warn_duplicates:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
461 print("%s\t%s" % (row[0], row[1]))
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
462 if duplicate_count > 0:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
463 print(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
464 "\n%d sequences have duplicated accession IDs\n" % duplicate_count
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
465 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
466
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
467 print("%s accession sequences will be searched\n" % sequence_count)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
468
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
469 # print(auto.dump())
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
470
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
471 # Convert the trie to an automaton (a finite-state machine)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
472 auto.make_automaton()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
473
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
474 # Execute query for seqs and metadata without fetching the results yet
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
475 uniprot_seq_and_id = cur.execute(UNIPROT_SEQ_AND_ID_SQL)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
476 while 1:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
477 batch = uniprot_seq_and_id.fetchmany(size=50)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
478 if not batch:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
479 break
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
480 for Sequence, UniProtKB_id in batch:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
481 if Sequence is not None:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
482 for end_index, (insert_order, original_value) in auto.iter(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
483 Sequence
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
484 ):
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
485 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
486 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
487 INSERT INTO deppep_UniProtKB
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
488 (deppep_id,UniProtKB_id,pos_start,pos_end)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
489 VALUES (?,?,?,?)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
490 """,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
491 (
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
492 insert_order,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
493 UniProtKB_id,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
494 1 + end_index - len(original_value),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
495 end_index,
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
496 ),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
497 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
498 else:
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
499 raise ValueError(
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
500 "UniProtKB_id %s, but Sequence is None: %s %s"
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
501 % (
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
502 UniProtKB_id,
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
503 "Check whether SwissProt file is missing",
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
504 "the sequence for this ID")
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
505 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
506 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
507 """
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
508 SELECT
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
509 count(*) ||
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
510 ' accession-peptide-phosphopeptide combinations were found'
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
511 FROM
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
512 uniprotkb_pep_ppep_view
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
513 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
514 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
515 for row in ker.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
516 print(row[0])
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
517
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
518 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
519 """
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
520 SELECT
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
521 count(*) || ' accession matches were found',
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
522 count(*) AS accession_count
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
523 FROM (
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
524 SELECT accession
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
525 FROM uniprotkb_pep_ppep_view
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
526 GROUP BY accession
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
527 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
528 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
529 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
530 for row in ker.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
531 print(row[0])
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
532
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
533 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
534 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
535 SELECT count(*) || ' peptide matches were found'
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
536 FROM (
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
537 SELECT peptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
538 FROM uniprotkb_pep_ppep_view
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
539 GROUP BY peptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
540 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
541 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
542 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
543 for row in ker.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
544 print(row[0])
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
545
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
546 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
547 """
1
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
548 SELECT
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
549 count(*) || ' phosphopeptide matches were found',
b76c75521d91 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents: 0
diff changeset
550 count(*) AS phosphopeptide_count
0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
551 FROM (
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
552 SELECT phosphopeptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
553 FROM uniprotkb_pep_ppep_view
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
554 GROUP BY phosphopeptide
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
555 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
556 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
557 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
558 for row in ker.fetchall():
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
559 print(row[0])
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
560
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
561 # link peptides not found in sequence database to a dummy sequence-record
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
562 ker.execute(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
563 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
564 INSERT INTO deppep_UniProtKB(deppep_id,UniProtKB_id,pos_start,pos_end)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
565 SELECT id, 'No Uniprot_ID', 0, 0
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
566 FROM deppep
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
567 WHERE id NOT IN (SELECT deppep_id FROM deppep_UniProtKB)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
568 """
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
569 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
570
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
571 con.commit()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
572 ker.execute("vacuum")
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
573 con.close()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
574
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
575
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
576 if __name__ == "__main__":
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
577 wrap_start_time = time.perf_counter()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
578 __main__()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
579 wrap_stop_time = time.perf_counter()
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
580 # print(wrap_start_time)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
581 # print(wrap_stop_time)
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
582 print(
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
583 "\nThe matching process took %d milliseconds to run.\n"
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
584 % ((wrap_stop_time - wrap_start_time) * 1000),
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
585 )
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
586
8dfd5d2b5903 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff changeset
587 # vim: sw=4 ts=4 et ai :