Mercurial > repos > melissacline > ucsc_xena_platform
annotate xena_query.py @ 51:47926759295a
fix GALAXY_URL parameter
| author | jingchunzhu |
|---|---|
| date | Thu, 13 Aug 2015 10:24:12 -0700 |
| parents | 02b0824c7d60 |
| children |
| rev | line source |
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| 0 | 1 """ |
| 2 Utilities for xena queries. | |
| 3 | |
| 4 A basic query example. | |
| 5 Queries are scheme expressions. | |
| 6 | |
| 7 >>> import xena_query as xena | |
| 8 >>> xena.post("https://genome-cancer.ucsc.edu/proj/public/xena", "(+ 1 2)") | |
| 9 '3.0' | |
| 10 | |
| 11 >>> xena.post("https://genome-cancer.ucsc.edu/proj/public/xena", "(let [x 2 y (+ x 3)] (* x y))") | |
| 12 '10.0' | |
| 13 | |
| 14 Looking up sample ids for the TCGA LGG cohort. | |
| 15 | |
| 16 >>> r = xena.post("https://genome-cancer.ucsc.edu/proj/public/xena", | |
| 17 xena.patient_to_sample_query("TCGA.LGG.sampleMap", | |
| 18 ["TCGA-CS-4938", | |
| 19 "TCGA-HT-7693", | |
| 20 "TCGA-CS-6665", | |
| 21 "TCGA-S9-A7J2", | |
| 22 "TCGA-FG-A6J3"])) | |
| 23 '{"TCGA.LGG.sampleMap":["TCGA-CS-4938-01","TCGA-CS-6665-01","TCGA-FG-A6J3-01","TCGA-HT-7693-01","TCGA-S9-A7J2-01"]}' | |
| 24 | |
| 25 >>> r = xena.post("https://genome-cancer.ucsc.edu/proj/public/xena", | |
| 26 xena.find_sample_by_field_query("TCGA.LGG.sampleMap", | |
| 27 "_PATIENT", | |
| 28 ["TCGA-CS-4938", | |
| 29 "TCGA-HT-7693", | |
| 30 "TCGA-CS-6665", | |
| 31 "TCGA-S9-A7J2", | |
| 32 "TCGA-FG-A6J3"])) | |
| 33 '{"TCGA.LGG.sampleMap":["TCGA-CS-4938-01","TCGA-CS-6665-01","TCGA-FG-A6J3-01","TCGA-HT-7693-01","TCGA-S9-A7J2-01"]}' | |
| 34 >>> import json | |
| 35 >>> json.loads(r) | |
| 36 {u'TCGA.LGG.sampleMap': [u'TCGA-CS-4938-01', u'TCGA-CS-6665-01', u'TCGA-FG-A6J3-01', u'TCGA-HT-7693-01', u'TCGA-S9-A7J2-01']} | |
| 37 """ | |
| 38 | |
|
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39 import urllib2, json |
| 0 | 40 import re |
| 41 | |
| 42 def compose1(f, g): | |
| 43 def composed(*args, **kwargs): | |
| 44 return f(g(*args, **kwargs)) | |
| 45 return composed | |
| 46 | |
| 47 # funcitonal composition, e.g. | |
| 48 # compose(f, g)(a, ...) == f(g(a, ...)) | |
| 49 compose = lambda *funcs: reduce(compose1, funcs) | |
| 50 | |
| 51 def quote(s): | |
| 52 return '"' + s + '"' | |
| 53 | |
| 54 def array_fmt(l): | |
| 55 return '[' + ', '.join((quote(s) for s in l)) + ']' | |
| 56 | |
| 57 # The strategy here is | |
| 58 # o Do table scan on code to find codes matching field values | |
| 59 # o Do IN query on unpack(field, x) to find rows matching codes | |
| 60 # o Project to unpack(sample, x) to get sampleID code | |
| 61 # o Join with code to get sampleID values | |
| 62 # | |
| 63 # Note the :limit on the table scan. This makes the table scan exit after we've | |
| 64 # found enough values, rather than continuing to the end. We can do this because | |
| 65 # enumerated values are unique. An alternative would be to index all the enumerated | |
| 66 # values in the db. | |
| 67 | |
| 68 cohort_query_str = """ | |
| 69 (map :cohort (query {:select [:%distinct.cohort] | |
| 70 :from [:dataset] | |
| 71 :where [:not [:is nil :cohort]]})) | |
| 72 """ | |
| 73 | |
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74 datasets_list_in_cohort_str =""" |
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75 (map :name (query {:select [:name :type :datasubtype :probemap :text :status] |
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76 :from [:dataset] |
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77 :where [:= :cohort %s]})) |
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78 """ |
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79 |
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80 dataset_type_str = """ |
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81 (map :type (query {:select [:type] |
| 0 | 82 :from [:dataset] |
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83 :where [:= :name %s]})) |
| 0 | 84 """ |
| 85 | |
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86 dataset_field_str = """ |
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87 (map :name (query {:select [:field.name] |
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88 :from [:dataset] |
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89 :join [:field [:= :dataset.id :dataset_id]] |
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90 :where [:= :dataset.name %s]})) |
| 0 | 91 """ |
| 92 | |
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93 dataset_samples_str = """ |
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94 (map :value (query {:select [:value] |
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95 :from [:dataset] |
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96 :join [:field [:= :dataset.id :dataset_id] |
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97 :code [:= :field.id :field_id]] |
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98 :where [:and |
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99 [:= :dataset.name %s] |
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100 [:= :field.name "sampleID"]]})) |
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101 """ |
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102 |
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103 dataset_probe_str = """ |
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104 (fetch [{:table %s |
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105 :columns %s |
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106 :samples %s}]) |
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107 """ |
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108 |
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109 |
| 0 | 110 def find_sample_by_field_query(cohort, field, values): |
| 111 """Return a xena query which looks up sample ids for the given field=values.""" | |
| 112 return sample_query_str % (quote(cohort), quote(field), array_fmt(values)) | |
| 113 | |
| 114 def patient_to_sample_query(cohort, patients): | |
| 115 """Return a xena query which looks up sample ids for the given patients.""" | |
| 116 return find_sample_by_field_query(cohort, "_PATIENT", patients) | |
| 117 | |
| 118 headers = { 'Content-Type' : "text/plain" } | |
| 119 | |
| 120 def post(url, query): | |
| 121 """POST a xena data query to the given url.""" | |
| 122 req = urllib2.Request(url + '/data/', query, headers) | |
| 123 response = urllib2.urlopen(req) | |
| 124 result = response.read() | |
| 125 return result | |
| 126 | |
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127 def find_cohorts(url): |
| 0 | 128 """ Return a list of cohorts on a host at a specific url """ |
| 129 """ return example: ["chinSF2007_public","TCGA.BRCA.sampleMap","cohort3"] """ | |
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130 return json.loads(post(url,cohort_query_str)) |
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131 |
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132 def dataset_field(host, dataset): |
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133 """return probes or features of a dataset""" |
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134 return json.loads(post(host, dataset_field_str % (quote(dataset)))) |
| 0 | 135 |
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136 def datasets_list_in_cohort (host, cohort): |
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137 """return datasets in a cohort""" |
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138 return json.loads(post(host, datasets_list_in_cohort_str % (quote(cohort)))) |
| 0 | 139 |
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140 def dataset_samples (host, dataset): |
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141 return json.loads(post(host, dataset_samples_str % (quote(dataset)))) |
| 0 | 142 |
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143 def dataset_probe_values (host, dataset, samples, probes): |
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144 return json.loads(post(host, dataset_probe_str % (quote(dataset), array_fmt(probes), array_fmt(samples)))) |
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145 |
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146 def dataset_type (host, dataset): |
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147 return json.loads(post(host, dataset_type_str % (quote(dataset)))) |
| 0 | 148 |
| 149 def strip_first_url_dir(path): | |
| 150 return re.sub(r'^[^/]*', '', path) | |
| 151 | |
| 152 # proj/<proj>/xena/<proj>/<path> | |
| 153 # download/<proj>/xena/<path> | |
| 154 def name_to_url(base_url, name): | |
| 155 return base_url.replace('/proj/', '/download/') + strip_first_url_dir(name) |