Mercurial > repos > chrisb > gap_all_glycan_tools
changeset 1:0a5e0df17054 draft default tip
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/.idea/kegg_glycan.iml Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<module type="PYTHON_MODULE" version="4"> + <component name="NewModuleRootManager"> + <content url="file://$MODULE_DIR$" /> + <orderEntry type="inheritedJdk" /> + <orderEntry type="sourceFolder" forTests="false" /> + </component> + <component name="TestRunnerService"> + <option name="projectConfiguration" value="Nosetests" /> + <option name="PROJECT_TEST_RUNNER" value="Nosetests" /> + </component> +</module> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/.idea/misc.xml Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project version="4"> + <component name="ProjectLevelVcsManager" settingsEditedManually="false"> + <OptionsSetting value="true" id="Add" /> + <OptionsSetting value="true" id="Remove" /> + <OptionsSetting value="true" id="Checkout" /> + <OptionsSetting value="true" id="Update" /> + <OptionsSetting value="true" id="Status" /> + <OptionsSetting value="true" id="Edit" /> + <ConfirmationsSetting value="0" id="Add" /> + <ConfirmationsSetting value="0" id="Remove" /> + </component> + <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.5 (/usr/bin/python2.7)" project-jdk-type="Python SDK" /> +</project> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/.idea/modules.xml Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0" encoding="UTF-8"?> +<project version="4"> + <component name="ProjectModuleManager"> + <modules> + <module fileurl="file://$PROJECT_DIR$/.idea/kegg_glycan.iml" filepath="$PROJECT_DIR$/.idea/kegg_glycan.iml" /> + </modules> + </component> +</project> \ No newline at end of file
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show_stripe_button="true" weight="0.25" sideWeight="0.5" order="4" side_tool="false" content_ui="tabs" /> + <window_info id="Hierarchy" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="2" side_tool="false" content_ui="combo" /> + <window_info id="Message" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" /> + <window_info id="Commander" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="0" side_tool="false" content_ui="tabs" /> + <window_info id="Find" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.33" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" /> + <window_info id="Inspection" active="false" anchor="bottom" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.4" sideWeight="0.5" order="5" side_tool="false" content_ui="tabs" /> + <window_info id="Ant Build" active="false" anchor="right" auto_hide="false" internal_type="DOCKED" type="DOCKED" visible="false" show_stripe_button="true" weight="0.25" sideWeight="0.5" order="1" side_tool="false" content_ui="tabs" /> + </layout> + </component> + <component name="Vcs.Log.UiProperties"> + <option name="RECENTLY_FILTERED_USER_GROUPS"> + <collection /> + </option> + <option name="RECENTLY_FILTERED_BRANCH_GROUPS"> + <collection /> + </option> + </component> + <component name="VcsContentAnnotationSettings"> + <option name="myLimit" value="2678400000" /> + </component> + <component name="XDebuggerManager"> + <breakpoint-manager /> + <watches-manager /> + </component> + <component name="editorHistoryManager"> + <entry file="file://$PROJECT_DIR$/test_findKEGG.py"> + <provider selected="true" editor-type-id="text-editor"> + <state relative-caret-position="255"> + <caret line="45" column="22" selection-start-line="45" selection-start-column="22" selection-end-line="45" selection-end-column="22" /> + <folding /> + </state> + </provider> + </entry> + </component> +</project> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/2 Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,54 @@ + +from KEGG searches as follows should work + + +/find/genes/shiga+toxin for keywords "shiga" and "toxin" +/find/genes/"shiga toxin" for keywords "shiga toxin" + +these do not function on all databases esp. enzyme + +http://rest.kegg.jp/find/enzyme/deoxy+1.1.1 AND works +http://rest.kegg.jp/find/enzyme/"deoxy%201.1.1" OR does not work +http://rest.kegg.jp/find/enzyme/"deoxy 1.1.1" OR does not work + +0 +http://rest.kegg.jp/find/enzyme/ec:2.4.99.1+ec:2.4.99.6 AND works but return nothing as no overlap +http://rest.kegg.jp/find/enzyme/"ec:2.4.99.1 ec:2.4.99.6" OR doesn't work +http://rest.kegg.jp/find/enzyme/ec:2.4.99. works + + ../../../virtualpy/bin/python findKEGG.py -d enzyme -q 2.4.99.1+2.4.99.6 . works but return None in python. which breaks file writing. rather fix this. + + + + + +# updated notes on KEGG behaviour + +True for release Release 78.0+/05-05, May 16 (see http://rest.kegg.jp/info/genes) + +multiple complex queries are not recommended. + +Using the shiga toxin example from http://www.genome.jp/kegg/rest/keggapi.html +/find/genes/shiga+toxin for keywords "shiga" and "toxin" +/find/genes/"shiga toxin" for keywords "shiga toxin" + +## AND example +/find/genes/shiga+toxin for keywords "shiga" and "toxin" +http://rest.kegg.jp/find/genes/shiga+toxin + +## OR example +/find/genes/"shiga toxin" for keywords "shiga toxin" +http://rest.kegg.jp/find/genes/"shiga%20toxin" + +## BROKEN AND +http://rest.kegg.jp/find/genes/"shiga+toxin" +If query is in put in quotes. + this result is the same as OR. + +## BROKEN OR +http://rest.kegg.jp/find/genes/shiga%20toxin +If query is not placed in quotations. + this result is the same as AND. + +# Recommendation +Do not combine AND with OR queries
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/KEGGnotes.md Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,51 @@ + +# notes on KEGG behaviour + +Tested with Release 78.0+/05-05, May 16 (see http://rest.kegg.jp/info/genes) + +*Recommendation 1 - Do not combine AND with OR queries* +multiple complex queries are not recommended. + +*OR's on certain db's e.g. glycan, enzyme do not always return correctly* + +## Shiga toxin behaviour test +Using the shiga toxin example from http://www.genome.jp/kegg/rest/keggapi.html +/find/genes/shiga+toxin for keywords "shiga" and "toxin" +/find/genes/"shiga toxin" for keywords "shiga toxin" + +results in test-data + - test-data/shiga-toxin-example-AND + - test-data/shiga-toxin-example-AND-broken + - test-data/shiga-toxin-example-OR + - test-data/shiga-toxin-example-OR-broken + + +### AND example +/find/genes/shiga+toxin for keywords "shiga" and "toxin" +http://rest.kegg.jp/find/genes/shiga+toxin + +### OR example +/find/genes/"shiga toxin" for keywords "shiga toxin" +http://rest.kegg.jp/find/genes/"shiga%20toxin" + +### BROKEN AND +http://rest.kegg.jp/find/genes/"shiga+toxin" +If query is in put in quotes. + this result is the same as OR. + +### BROKEN OR +http://rest.kegg.jp/find/genes/shiga%20toxin +If query is not placed in quotations. + this result is the same as AND. + +## Enzyme tests + +http://rest.kegg.jp/find/enzyme/deoxy+1.1.1 AND works +http://rest.kegg.jp/find/enzyme/"deoxy%201.1.1" OR does not work +http://rest.kegg.jp/find/enzyme/"deoxy 1.1.1" OR does not work + +0 +http://rest.kegg.jp/find/enzyme/ec:2.4.99.1+ec:2.4.99.6 AND works but return nothing as no overlap +http://rest.kegg.jp/find/enzyme/"ec:2.4.99.1 ec:2.4.99.6" OR doesn't work +http://rest.kegg.jp/find/enzyme/ec:2.4.99. works +
--- a/get_data/kegg_glycan/README_KEGG.md Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/README_KEGG.md Fri May 06 08:05:48 2016 -0400 @@ -20,6 +20,9 @@ findKEGG.py -d $dbname -q $searchpattern -o $output ``` +## Known Issues +Yes, the and/or functionality of the KEGG rest API (Release 78.0+/05-05, May 16 ) does not always function as expected. This has been resolved in the code. More details, [KEGGnotes.md ](KEGGnotes.md) + ## Help ``` ../../virtualpy/bin/activate @@ -31,7 +34,7 @@ ``` ../../virtualpy/bin/activate -python test_findKEGG.py +nosetests test_findKEGG.py ``` # 2. getkcfKEGG,py @@ -67,7 +70,7 @@ ``` ../../virtualpy/bin/activate -python test_getkcfKEGG.py +nosetests test_getkcfKEGG.py ``` # 3. linkKEGG.py @@ -101,6 +104,6 @@ ``` ../../virtualpy/bin/activate -python test_linkKEGG.py +nosetests test_linkKEGG.py ```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/db.output Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,83 @@ +ENTRY G10495 Glycan +NAME 1,4-alpha-D-Glucan; + 1,4-alpha-Glucan; + Amylose; + Maltodextrin +COMPOSITION (Glc)1 (*)2 +CLASS Polysaccharide +REMARK Same as: C00718 C01935 D02329 +REACTION R06049 R06050 R06051 R06052 R06069 R06158 R06159 R06160 + R06184 R06185 R06186 R06243 +ENZYME 2.4.1.1 2.4.1.2 2.4.1.4 2.4.1.11 + 2.4.1.18 2.4.1.21 2.4.1.25 3.2.1.2 + 3.2.1.33 3.2.1.54 5.4.99.15 +DBLINKS GlycomeDB: 12100 +NODE 3 + 1 * 8 0 + 2 Glc 0 0 + 3 * -8 0 +EDGE 2 + 1 2:a1 1 + 2 3 2:4 +BRACKET 1 -4.0 2.0 -4.0 -2.0 + 1 5.0 -2.0 5.0 2.0 + 1 n +/// +ENTRY G10608 Glycan +NAME UDP-D-glucose; + UDP-glucose; + Uridine diphosphate glucose +COMPOSITION (UDP-Glc)1 +REMARK Same as: C00029 +REACTION R06020 R06023 R06036 R06043 R06045 R06051 R06062 R06073 + R06181 R06226 R06275 R09315 R09316 +ENZYME 2.4.1.11 2.4.1.12 2.4.1.13 2.4.1.14 + 2.4.1.15 2.4.1.34 2.4.1.53 2.4.1.80 + 2.4.1.183 2.4.1.188 2.4.1.- +NODE 1 + 1 UDP-Glc -0.3 0 +EDGE 0 +/// +ENTRY G10619 Glycan +NAME UDP; + Uridine 5'-diphosphate +COMPOSITION (UDP)1 +REMARK Same as: C00015 +REACTION R05901 R05902 R05903 R05907 R05908 R05909 R05910 R05912 + R05915 R05916 R05925 R05926 R05927 R05928 R05929 R05930 + R05931 R05932 R05933 R05934 R05935 R05936 R05938 R05939 + R05941 R05946 R05948 R05952 R05953 R05956 R05960 R05962 + R05964 R05965 R05970 R05971 R05974 R05975 R05977 R05978 + R05983 R05985 R05986 R05987 R05989 R05991 R05992 R06006 + R06011 R06013 R06014 R06016 R06020 R06021 R06023 R06028 + R06029 R06033 R06036 R06043 R06045 R06051 R06055 R06062 + R06067 R06068 R06072 R06073 R06083 R06097 R06129 R06130 + R06145 R06167 R06168 R06169 R06172 R06173 R06174 R06181 + R06182 R06187 R06189 R06190 R06191 R06192 R06193 R06197 + R06198 R06210 R06214 R06226 R06234 R06275 R06276 R06277 + R06278 R07131 R07609 R07610 R07611 R07614 R07615 R07616 + R07617 R07619 R07621 R07622 R07623 R07624 R07625 R07628 + R09290 R09296 R09299 R09304 R09315 R09316 R09320 R10138 + R10139 +ENZYME 2.4.1.11 2.4.1.12 2.4.1.13 2.4.1.14 + 2.4.1.15 2.4.1.16 2.4.1.22 2.4.1.34 + 2.4.1.37 2.4.1.38 2.4.1.40 2.4.1.41 + 2.4.1.43 2.4.1.45 2.4.1.47 2.4.1.53 + 2.4.1.62 2.4.1.70 2.4.1.79 2.4.1.80 + 2.4.1.86 2.4.1.87 2.4.1.88 2.4.1.90 + 2.4.1.92 2.4.1.101 2.4.1.102 2.4.1.122 + 2.4.1.123 2.4.1.133 2.4.1.134 2.4.1.135 + 2.4.1.138 2.4.1.141 2.4.1.143 2.4.1.144 + 2.4.1.145 2.4.1.146 2.4.1.147 2.4.1.148 + 2.4.1.149 2.4.1.150 2.4.1.155 2.4.1.163 + 2.4.1.164 2.4.1.165 2.4.1.167 2.4.1.174 + 2.4.1.175 2.4.1.183 2.4.1.187 2.4.1.188 + 2.4.1.198 2.4.1.201 2.4.1.206 2.4.1.212 + 2.4.1.222 2.4.1.223 2.4.1.224 2.4.1.225 + 2.4.1.226 2.4.1.227 2.4.1.228 2.4.1.244 + 2.4.1.255 2.4.1.274 2.4.1.275 2.4.1.- + 2.4.2.24 2.4.2.26 2.4.2.38 2.4.2.- +NODE 1 + 1 UDP -0.4 0.3 +EDGE 0 +///
--- a/get_data/kegg_glycan/findKEGG.py Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/findKEGG.py Fri May 06 08:05:48 2016 -0400 @@ -1,6 +1,6 @@ __author__ = 'cbarnett' __license__ = "MIT" -__version__ = "0.3" +__version__ = "0.4" # http://www.kegg.jp/kegg/rest/keggapi.html @@ -16,8 +16,18 @@ raise IOError("no db given") if query == [] or query == "" or query is None: raise IOError("no query given") - query = query.replace('\n', ' ') # in case of new lines - query = query.replace('\r', ' ') # in case of new lines + query = query.replace('\n', '+') # in case of new lines, assume this means the user want to "AND" + query = query.replace('\r', '+') # in case of new lines, assume this means the user want to "AND" + query = query.replace('ec: ', 'ec:') # in case of ec: spaces - e.g. issue "ec: 2.4.99.1" spaces are ok usually as allows for combination searching "2.4.99.1 2.4.99.6" + + import re + p = re.compile(' *\+ *') # ensure no unneccesary space in an AND query, otherwise incorrect behaviour from KEGG + queryfix = p.subn('+', query) + query=queryfix[0] + + if ' ' in query: + query='"'+query+'"' # if spaces, query must be placed in quotes, otherwise incorrect behaviour from KEGG + query = query.replace(' ', '%20') # previous behaviour was ignoring text after a space, rather convert to '%20' and pass on to KEGG REST service uri = 'http://rest.kegg.jp/find/' fulluri = uri + db + "/" + query try: @@ -25,7 +35,7 @@ except Exception as e: raise urllib2.HTTPError(e.url, e.code, e.msg, e.hdrs, e.fp) if str(response.strip()) == "": - return None + return "" # change return from None to "" for easily writing to file return response
--- a/get_data/kegg_glycan/findKEGG.xml Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/findKEGG.xml Fri May 06 08:05:48 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="glytools_kegg_find" name="GAP Find KEGG glycans " version="0.3.1"> +<tool id="glytools_kegg_find" name="GAP Find KEGG glycans " version="0.4.0"> <description> using the KEGG database</description> <requirements> <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/found_entries.txt Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,19 @@ +ec:1.1.1.133 dTDP-4-dehydrorhamnose reductase; dTDP-4-keto-L-rhamnose reductase; dTDP-4-ketorhamnose reductase; TDP-4-keto-rhamnose reductase; thymidine diphospho-4-ketorhamnose reductase; dTDP-6-deoxy-L-mannose:NADP+ 4-oxidoreductase; dTDP-6-deoxy-beta-L-mannose:NADP+ 4-oxidoreductase +ec:1.1.1.340 1-deoxy-11beta-hydroxypentalenate dehydrogenase; 1-deoxy-11beta-hydroxypentalenic acid dehydrogenase; ptlF (gene name); penF (gene name) +ec:1.14.11.35 1-deoxypentalenic acid 11beta-hydroxylase; ptlH (gene name); sav2991 (gene name); pntH (gene name) +ec:2.3.1.202 UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase; PseH +ec:2.4.1.27 DNA beta-glucosyltransferase; T4-HMC-beta-glucosyl transferase; T4-beta-glucosyl transferase; T4 phage beta-glucosyltransferase; UDP glucose-DNA beta-glucosyltransferase; uridine diphosphoglucose-deoxyribonucleate beta-glucosyltransferase +ec:2.4.1.28 glucosyl-DNA beta-glucosyltransferase; T6-glucosyl-HMC-beta-glucosyl transferase; T6-beta-glucosyl transferase; uridine diphosphoglucose-glucosyldeoxyribonucleate beta-glucosyltransferase +ec:2.4.1.335 dolichyl N-acetyl-alpha-D-glucosaminyl phosphate 3-beta-D-2,3-diacetamido-2,3-dideoxy-beta-D-glucuronosyltransferase; AglC; UDP-Glc-2,3-diNAcA glycosyltransferase +ec:2.6.1.87 UDP-4-amino-4-deoxy-L-arabinose aminotransferase; UDP-(beta-L-threo-pentapyranosyl-4''-ulose diphosphate) aminotransferase; UDP-4-amino-4-deoxy-L-arabinose---oxoglutarate aminotransferase; UDP-Ara4O aminotransferase; UDP-L-Ara4N transaminase +ec:2.6.1.92 UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase; PseC +ec:2.7.7.7 DNA-directed DNA polymerase; DNA polymerase I; DNA polymerase II; DNA polymerase III; DNA polymerase alpha; DNA polymerase beta; DNA polymerase gamma; DNA nucleotidyltransferase (DNA-directed); DNA nucleotidyltransferase (DNA-directed); deoxyribonucleate nucleotidyltransferase; deoxynucleate polymerase; deoxyribonucleic acid duplicase; deoxyribonucleic acid polymerase; deoxyribonucleic duplicase; deoxyribonucleic polymerase; deoxyribonucleic polymerase I; DNA duplicase; DNA nucleotidyltransferase; DNA polymerase; DNA replicase; DNA-dependent DNA polymerase; duplicase; Klenow fragment; sequenase; Taq DNA polymerase; Taq Pol I; Tca DNA polymerase +ec:3.1.6.9 chondro-4-sulfatase; chondroitin-4-sulfatase; 4-deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine-4-sulfate 4-sulfohydrolase +ec:3.1.6.10 chondro-6-sulfatase; 4-deoxy-beta-D-gluc-4-enuronosyl-(1,3)-N-acetyl-D-galactosamine-6-sulfate 6-sulfohydrolase +ec:3.2.1.52 beta-N-acetylhexosaminidase; hexosaminidase; beta-acetylaminodeoxyhexosidase; N-acetyl-beta-D-hexosaminidase; N-acetyl-beta-hexosaminidase; beta-hexosaminidase; beta-acetylhexosaminidinase; beta-D-N-acetylhexosaminidase; beta-N-acetyl-D-hexosaminidase; beta-N-acetylglucosaminidase; hexosaminidase A; N-acetylhexosaminidase; beta-D-hexosaminidase +ec:3.2.1.92 peptidoglycan beta-N-acetylmuramidase; exo-beta-N-acetylmuramidase; exo-beta-acetylmuramidase; beta-2-acetamido-3-O-(D-1-carboxyethyl)-2-deoxy-D-glucoside acetamidodeoxyglucohydrolase +ec:3.2.1.96 mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase; N,N'-diacetylchitobiosyl beta-N-acetylglucosaminidase; endo-beta-N-acetylglucosaminidase; mannosyl-glycoprotein endo-beta-N-acetylglucosamidase; di-N-acetylchitobiosyl beta-N-acetylglucosaminidase; endo-beta-acetylglucosaminidase; endo-beta-(1->4)-N-acetylglucosaminidase; mannosyl-glycoprotein 1,4-N-acetamidodeoxy-beta-D-glycohydrolase; endoglycosidase S; endo-N-acetyl-beta-D-glucosaminidase; endo-N-acetyl-beta-glucosaminidase; endo-beta-N-acetylglucosaminidase D; endo-beta-N-acetylglucosaminidase F; endo-beta-N-acetylglucosaminidase H; endo-beta-N-acetylglucosaminidase L; glycopeptide-D-mannosyl-4-N-(N-acetyl-D-glucosaminyl)2-asparagine 1,4-N-acetyl-beta-glucosaminohydrolase; endoglycosidase H +ec:3.5.1.105 chitin disaccharide deacetylase; chitobiose amidohydolase; COD; chitin oligosaccharide deacetylase; chitin oligosaccharide amidohydolase; 2-(acetylamino)-4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-2-deoxy-D-glucopyranose acetylhydrolase +ec:3.6.1.57 UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase; PseG; UDP-6-deoxy-AltdiNAc hydrolase; Cj1312; UDP-2,4-bis(acetamido)-2,4,6-trideoxy-beta-L-altropyranose hydrolase +ec:4.1.2.20 2-dehydro-3-deoxyglucarate aldolase; 2-keto-3-deoxyglucarate aldolase; alpha-keto-beta-deoxy-D-glucarate aldolase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming) +ec:4.2.1.115 UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting); FlaA1; UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase; PseB; UDP-N-acetylglucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-beta-L-arabino-hex-4-ulose-forming)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/kcf.output Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,22 @@ +ENTRY G10495 Glycan +NODE 3 + 1 * 8 0 + 2 Glc 0 0 + 3 * -8 0 +EDGE 2 + 1 2:a1 1 + 2 3 2:4 +BRACKET 1 -4.0 2.0 -4.0 -2.0 + 1 5.0 -2.0 5.0 2.0 + 1 n +/// +ENTRY G10608 Glycan +NODE 1 + 1 UDP-Glc -0.3 0 +EDGE 0 +/// +ENTRY G10619 Glycan +NODE 1 + 1 UDP -0.4 0.3 +EDGE 0 +///
--- a/get_data/kegg_glycan/linkKEGG.py Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/linkKEGG.py Fri May 06 08:05:48 2016 -0400 @@ -1,6 +1,6 @@ __author__ = 'cbarnett' __license__ = "MIT" -__version = "0.3" +__version = "0.3.1" # http://www.kegg.jp/kegg/rest/keggapi.html @@ -13,6 +13,15 @@ import urllib2 uri = 'http://rest.kegg.jp/link/' + + import re + p = re.compile(' *\+ *') # ensure no unneccessary space in an AND query + sdbfix = p.subn('+', sourcedb) + sourcedb=sdbfix[0] + + if ' ' in sourcedb: + sourcedb = sourcedb.replace(' ', '%20') # previous behaviour was ignoring text after a space, rather convert to '%20' and pass on to KEGG REST service + fulluri = uri + targetdb + "/" + sourcedb try: response = urllib2.urlopen(fulluri).read()
--- a/get_data/kegg_glycan/linkKEGG.xml Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/linkKEGG.xml Fri May 06 08:05:48 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="glytools_kegg_link" name="GAP Cross-reference with KEGG databases " version="0.3.1"> +<tool id="glytools_kegg_link" name="GAP Cross-reference with KEGG databases " version="0.3.2"> <description> searches KEGG for related database entries</description> <requirements> <requirement type="package" version="1.0">python_for_glycan_tools</requirement> @@ -34,7 +34,7 @@ <tests> <test> <param name="targetdb" value="glycan" /> - <param name="source" value="ec:2.4.1.11"" /> + <param name="source" value="ec:2.4.1.11" /> <output name="output" file="link_test1.txt" /> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/plus Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,21 @@ +ec:1.1.1.125 2-deoxy-D-gluconate 3-dehydrogenase; 2-deoxygluconate dehydrogenase +ec:1.1.1.126 2-dehydro-3-deoxy-D-gluconate 6-dehydrogenase; 2-keto-3-deoxy-D-gluconate dehydrogenase; 2-keto-3-deoxygluconate dehydrogenase +ec:1.1.1.127 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase; 2-keto-3-deoxygluconate 5-dehydrogenase; 2-keto-3-deoxy-D-gluconate dehydrogenase; 2-keto-3-deoxygluconate (nicotinamide adenine dinucleotide (phosphate)) dehydrogenase; 2-keto-3-deoxy-D-gluconate (3-deoxy-D-glycero-2,5-hexodiulosonic acid) dehydrogenase +ec:1.1.1.133 dTDP-4-dehydrorhamnose reductase; dTDP-4-keto-L-rhamnose reductase; dTDP-4-ketorhamnose reductase; TDP-4-keto-rhamnose reductase; thymidine diphospho-4-ketorhamnose reductase; dTDP-6-deoxy-L-mannose:NADP+ 4-oxidoreductase; dTDP-6-deoxy-beta-L-mannose:NADP+ 4-oxidoreductase +ec:1.1.1.134 dTDP-6-deoxy-L-talose 4-dehydrogenase (NADP+); thymidine diphospho-6-deoxy-L-talose dehydrogenase; TDP-6-deoxy-L-talose dehydrogenase; dTDP-6-deoxy-L-talose dehydrogenase (4-reductase); dTDP-6-deoxy-L-talose:NADP+ 4-oxidoreductase +ec:1.1.1.135 GDP-6-deoxy-D-talose 4-dehydrogenase; guanosine diphospho-6-deoxy-D-talose dehydrogenase; GDP-6-deoxy-D-talose:NAD(P)+ 4-oxidoreductase +ec:1.1.1.136 UDP-N-acetylglucosamine 6-dehydrogenase; uridine diphosphoacetylglucosamine dehydrogenase; UDP-acetylglucosamine dehydrogenase; UDP-2-acetamido-2-deoxy-D-glucose:NAD oxidoreductase; UDP-GlcNAc dehydrogenase; WbpA; WbpO +ec:1.1.1.187 GDP-4-dehydro-D-rhamnose reductase; GDP-4-keto-6-deoxy-D-mannose reductase; GDP-4-keto-D-rhamnose reductase; guanosine diphosphate-4-keto-D-rhamnose reductase; GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase; GDP-6-deoxy-alpha-D-mannose:NAD(P)+ 4-oxidoreductase +ec:1.1.1.235 8-oxocoformycin reductase; 8-ketodeoxycoformycin reductase +ec:1.1.1.266 dTDP-4-dehydro-6-deoxyglucose reductase; dTDP-4-keto-6-deoxyglucose reductase; dTDP-D-fucose:NADP+ oxidoreductase; Fcf1; dTDP-6-deoxy-D-xylo-hex-4-ulopyranose reductase +ec:1.1.1.267 1-deoxy-D-xylulose-5-phosphate reductoisomerase; DXP-reductoisomerase; 1-deoxy-D-xylulose-5-phosphate isomeroreductase; 2-C-methyl-D-erythritol 4-phosphate (MEP) synthase +ec:1.1.1.271 GDP-L-fucose synthase; GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase; GDP-L-fucose:NADP+ 4-oxidoreductase (3,5-epimerizing) +ec:1.1.1.281 GDP-4-dehydro-6-deoxy-D-mannose reductase; GDP-4-keto-6-deoxy-D-mannose reductase [ambiguous]; GDP-6-deoxy-D-lyxo-4-hexulose reductase; Rmd; GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase (D-rhamnose-forming); GDP-6-deoxy-alpha-D-mannose:NAD(P)+ 4-oxidoreductase (D-rhamnose-forming) +ec:1.1.1.329 2-deoxy-scyllo-inosamine dehydrogenase; neoA (gene name); kanK (gene name, ambiguous); kanE (gene name, ambiguous) +ec:1.1.1.335 UDP-N-acetyl-2-amino-2-deoxyglucuronate dehydrogenase; WlbA; WbpB +ec:1.1.1.339 dTDP-6-deoxy-L-talose 4-dehydrogenase (NAD+); tll (gene name) +ec:1.1.1.340 1-deoxy-11beta-hydroxypentalenate dehydrogenase; 1-deoxy-11beta-hydroxypentalenic acid dehydrogenase; ptlF (gene name); penF (gene name) +ec:1.1.1.344 dTDP-6-deoxy-L-talose 4-dehydrogenase [NAD(P)+]; tal (gene name) +ec:1.1.1.364 dTDP-4-dehydro-6-deoxy-alpha-D-gulose 4-ketoreductase; dTDP-4-dehydro-6-deoxygulose reductase; tylD (gene name); gerKI (gene name); chmD (gene name); mydI (gene name) +ec:1.1.1.384 dTDP-3,4-didehydro-2,6-dideoxy-alpha-D-glucose 3-reductase; KijD10; dTDP-4-keto-2,6-dideoxy-D-glucose 3-oxidoreductase; dTDP-4-dehydro-2,6-dideoxy-alpha-D-glucose 3-oxidoreductase +ec:1.1.1.389 2-dehydro-3-deoxy-L-galactonate 5-dehydrogenase
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/test-data/shiga-toxin-example-AND Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,103 @@ +ece:Z1464 stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W; K11006 shiga toxin subunit A +ece:Z1465 stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W; K11007 shiga toxin subunit B +ece:Z3343 stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V; K11007 shiga toxin subunit B +ece:Z3344 stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V; K11006 shiga toxin subunit A +ecs:ECs1205 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecs:ECs1206 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +ecs:ECs2973 Shiga toxin I subunit B; K11007 shiga toxin subunit B +ecs:ECs2974 Shiga toxin I subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_2905 shigatoxin 2, subunit B; K11007 shiga toxin subunit B +ecf:ECH74115_2906 shiga toxin subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_3532 shiga toxin 2 B subunit; K11007 shiga toxin subunit B +ecf:ECH74115_3533 shiga toxin subunit A; K11006 shiga toxin subunit A +etw:ECSP_2722 stx2cB; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +etw:ECSP_2723 stx2A1; Shiga-like toxin II subunit A precursor; K11006 shiga toxin subunit A +etw:ECSP_3252 stx2B; shiga toxin II subunit B; K11007 shiga toxin subunit B +etw:ECSP_3253 stx2A2; shiga toxin II subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1154 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1155 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +elx:CDCO157_2738 Shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +elx:CDCO157_2739 Shiga toxin I subunit A precursor; K11006 shiga toxin subunit A +eoj:ECO26_1599 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoj:ECO26_1600 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2429 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2430 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3361 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3362 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2844 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2845 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5197 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5198 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eso:O3O_09170 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eso:O3O_09165 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esm:O3M_16105 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esm:O3M_16110 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esl:O3K_16130 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esl:O3K_16135 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecoo:ECRM13514_3144 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoo:ECRM13514_3145 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +ecoh:ECRM13516_2315 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoh:ECRM13516_2316 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +stm:STM0284 shiga-like toxin A subunit +seo:STM14_0332 putative Shiga-like toxin A subunit +sev:STMMW_02891 putative shiga-like toxin A subunit +sem:STMDT12_C02790 putative Shiga-like toxin A subunit +sej:STMUK_0287 putative Shiga-like toxin A subunit +setu:STU288_13325 putative shiga-like toxin A subunit +setc:CFSAN001921_15985 Shiga toxin A subunit +send:DT104_02831 sciR; shiga-like toxin a subunit, type VI secretion system SciR protein flags: precursor +seni:CY43_01420 Shiga toxin A subunit +seen:SE451236_07435 Shiga toxin A subunit +spt:SPA2480 putative shiga-like toxin A subunit +sek:SSPA2315 shiga-like toxin A subunit +sei:SPC_0292 putative shiga-like toxin A subunit +sec:SCH_0277 putative shiga-like toxin A subunit +shb:SU5_0926 SciR Shiga-like toxin A subunit +senh:CFSAN002069_07720 Shiga toxin A subunit +seeh:SEEH1578_10515 putative shiga-like toxin A subunit +seec:CFSAN002050_07960 Shiga toxin A subunit +sene:IA1_01505 Shiga toxin A subunit +senc:SEET0819_08350 Shiga toxin A subunit +sdy:SDY_1389 stxA; Shiga toxin subunit A; K11006 shiga toxin subunit A +sdy:SDY_1390 stxB; Shiga toxin subunit B; K11007 shiga toxin subunit B +sdz:Asd1617_01826 Shiga toxin subunit A (EC:3.2.2.22); K11006 shiga toxin subunit A +ebi:EbC_13780 Putative shiga-like toxin A subunit +psos:POS17_2009 P9; putative Shiga-like toxin alpha subunit +ssab:SSABA_v1c03870 hypothetical protein; K11006 shiga toxin subunit A +ssab:SSABA_v1c09020 hypothetical protein; K11006 shiga toxin subunit A +calt:Cal6303_2132 ribosome-inactivating protein; K11006 shiga toxin subunit A +vg:22277199 PI30_gp34; Shigella phage POCJ13; shiga toxin A-chain precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:22277200 PI30_gp35; Shigella phage POCJ13; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +vg:1262301 APSE-1_07; Endosymbiont phage APSE-1; P7; K11007 shiga toxin subunit B +vg:1481747 stx1A, Stx1_p142; Escherichia Stx1 converting phage; Shiga toxin1 subunit A; K11006 shiga toxin subunit A +vg:1481748 stx1B, Stx1_p143; Escherichia Stx1 converting phage; Shiga toxin1 subunit B; K11007 shiga toxin subunit B +vg:1481767 stx2A, Stx2II_p143; Stx2 converting phage II; Shiga toxin2 subunit A; K11006 shiga toxin subunit A +vg:1481768 stx2B, Stx2II_p144; Stx2 converting phage II; Shiga toxin2 subunit B; K11007 shiga toxin subunit B +vg:26228052 AS349_gp84; Escherichia phage PA2; shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26228100 AS349_gp83; Escherichia phage PA2; shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +vg:26516496 stx2A, AU085_gp42; Enterobacteria phage VT2phi_272; Shiga toxin 2 A subunit; K11006 shiga toxin subunit A +vg:26516448 stx2B, AU085_gp41; Enterobacteria phage VT2phi_272; Shiga toxin 2 B subunit; K11007 shiga toxin subunit B +vg:26516283 stxB, phi191_00011, AU083_gp11; Escherichia phage phi191; shiga toxin subunit B precursor; K11007 shiga toxin subunit B +vg:26516284 stxA, phi191_00012, AU083_gp12; Escherichia phage phi191; shiga toxin subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26519429 AU154_gp39; Shigella phage Ss-VASD; Stx1 A subunit; K11006 shiga toxin subunit A +vg:26519430 AU154_gp40; Shigella phage Ss-VASD; Stx1 B subunit; K11007 shiga toxin subunit B +vg:1261950 stxA2, L0103, sltIIA, stx2A, 933Wp40; Enterobacteria phage 933W; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262010 stxB2, L0104, sltIIB, stx2B, 933Wp41; Enterobacteria phage 933W; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:2641645 stxA1, phi4795p38, PBV4795_ORF40; Enterobacteria phage BP-4795; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:2641657 stxB1, phi4795p39, PBV4795_ORF41; Enterobacteria phage BP-4795; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:929695 stxA2e, P27p25; Enterobacteria phage phiP27; shiga toxin 2e A-subunit; K11006 shiga toxin subunit A +vg:929727 stxB2e, P27p26; Enterobacteria phage phiP27; shiga toxin 2e B-subunit; K11007 shiga toxin subunit B +vg:4397483 stx2A, Stx2-86_gp01; Stx2-converting phage 86; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:4397484 stx2B, Stx2-86_gp02; Stx2-converting phage 86; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:6159405 stx2A, pMIN27_41; Enterobacteria phage Min27; ORF44; K11006 shiga toxin subunit A +vg:6159351 stx2B, pMIN27_42; Enterobacteria phage Min27; ORF45; K11007 shiga toxin subunit B +vg:6973138 Stx2-1717_gp41; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit A; K11006 shiga toxin subunit A +vg:6972909 stx2cB, Stx2-1717_gp42; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit B; K11007 shiga toxin subunit B +vg:6973079 YYZ_gp39; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:6973080 YYZ_gp40; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:13828571 stx2A, D300_gp43; Escherichia phage P13374; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:13828535 stx2B, D300_gp42; Escherichia phage P13374; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:14005228 F366_gp36; Escherichia phage TL-2011c; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:14005229 F366_gp37; Escherichia phage TL-2011c; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:1262249 stx2A, VT2-Sap42; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262250 stx2B, VT2-Sap43; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/test-data/shiga-toxin-example-AND-broken Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,88 @@ +ece:Z1464 stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W; K11006 shiga toxin subunit A +ece:Z1465 stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W; K11007 shiga toxin subunit B +ece:Z3343 stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V; K11007 shiga toxin subunit B +ece:Z3344 stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V; K11006 shiga toxin subunit A +ecs:ECs1205 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecs:ECs1206 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +ecs:ECs2973 Shiga toxin I subunit B; K11007 shiga toxin subunit B +ecs:ECs2974 Shiga toxin I subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_2905 shigatoxin 2, subunit B; K11007 shiga toxin subunit B +ecf:ECH74115_2906 shiga toxin subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_3532 shiga toxin 2 B subunit; K11007 shiga toxin subunit B +ecf:ECH74115_3533 shiga toxin subunit A; K11006 shiga toxin subunit A +etw:ECSP_2722 stx2cB; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +etw:ECSP_2723 stx2A1; Shiga-like toxin II subunit A precursor; K11006 shiga toxin subunit A +etw:ECSP_3252 stx2B; shiga toxin II subunit B; K11007 shiga toxin subunit B +etw:ECSP_3253 stx2A2; shiga toxin II subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1154 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1155 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +elx:CDCO157_2738 Shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +elx:CDCO157_2739 Shiga toxin I subunit A precursor; K11006 shiga toxin subunit A +eoj:ECO26_1599 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoj:ECO26_1600 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2429 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2430 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3361 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3362 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2844 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2845 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5197 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5198 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eso:O3O_09170 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eso:O3O_09165 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esm:O3M_16105 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esm:O3M_16110 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esl:O3K_16130 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esl:O3K_16135 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecoo:ECRM13514_3144 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoo:ECRM13514_3145 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +ecoh:ECRM13516_2315 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoh:ECRM13516_2316 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +setc:CFSAN001921_15985 Shiga toxin A subunit +seni:CY43_01420 Shiga toxin A subunit +seen:SE451236_07435 Shiga toxin A subunit +senh:CFSAN002069_07720 Shiga toxin A subunit +seec:CFSAN002050_07960 Shiga toxin A subunit +sene:IA1_01505 Shiga toxin A subunit +senc:SEET0819_08350 Shiga toxin A subunit +sdy:SDY_1389 stxA; Shiga toxin subunit A; K11006 shiga toxin subunit A +sdy:SDY_1390 stxB; Shiga toxin subunit B; K11007 shiga toxin subunit B +sdz:Asd1617_01826 Shiga toxin subunit A (EC:3.2.2.22); K11006 shiga toxin subunit A +ssab:SSABA_v1c03870 hypothetical protein; K11006 shiga toxin subunit A +ssab:SSABA_v1c09020 hypothetical protein; K11006 shiga toxin subunit A +calt:Cal6303_2132 ribosome-inactivating protein; K11006 shiga toxin subunit A +vg:22277199 PI30_gp34; Shigella phage POCJ13; shiga toxin A-chain precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:22277200 PI30_gp35; Shigella phage POCJ13; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +vg:1262301 APSE-1_07; Endosymbiont phage APSE-1; P7; K11007 shiga toxin subunit B +vg:1481747 stx1A, Stx1_p142; Escherichia Stx1 converting phage; Shiga toxin1 subunit A; K11006 shiga toxin subunit A +vg:1481748 stx1B, Stx1_p143; Escherichia Stx1 converting phage; Shiga toxin1 subunit B; K11007 shiga toxin subunit B +vg:1481767 stx2A, Stx2II_p143; Stx2 converting phage II; Shiga toxin2 subunit A; K11006 shiga toxin subunit A +vg:1481768 stx2B, Stx2II_p144; Stx2 converting phage II; Shiga toxin2 subunit B; K11007 shiga toxin subunit B +vg:26228052 AS349_gp84; Escherichia phage PA2; shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26228100 AS349_gp83; Escherichia phage PA2; shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +vg:26516496 stx2A, AU085_gp42; Enterobacteria phage VT2phi_272; Shiga toxin 2 A subunit; K11006 shiga toxin subunit A +vg:26516448 stx2B, AU085_gp41; Enterobacteria phage VT2phi_272; Shiga toxin 2 B subunit; K11007 shiga toxin subunit B +vg:26516283 stxB, phi191_00011, AU083_gp11; Escherichia phage phi191; shiga toxin subunit B precursor; K11007 shiga toxin subunit B +vg:26516284 stxA, phi191_00012, AU083_gp12; Escherichia phage phi191; shiga toxin subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26519429 AU154_gp39; Shigella phage Ss-VASD; Stx1 A subunit; K11006 shiga toxin subunit A +vg:26519430 AU154_gp40; Shigella phage Ss-VASD; Stx1 B subunit; K11007 shiga toxin subunit B +vg:1261950 stxA2, L0103, sltIIA, stx2A, 933Wp40; Enterobacteria phage 933W; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262010 stxB2, L0104, sltIIB, stx2B, 933Wp41; Enterobacteria phage 933W; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:2641645 stxA1, phi4795p38, PBV4795_ORF40; Enterobacteria phage BP-4795; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:2641657 stxB1, phi4795p39, PBV4795_ORF41; Enterobacteria phage BP-4795; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:929695 stxA2e, P27p25; Enterobacteria phage phiP27; shiga toxin 2e A-subunit; K11006 shiga toxin subunit A +vg:929727 stxB2e, P27p26; Enterobacteria phage phiP27; shiga toxin 2e B-subunit; K11007 shiga toxin subunit B +vg:4397483 stx2A, Stx2-86_gp01; Stx2-converting phage 86; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:4397484 stx2B, Stx2-86_gp02; Stx2-converting phage 86; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:6159405 stx2A, pMIN27_41; Enterobacteria phage Min27; ORF44; K11006 shiga toxin subunit A +vg:6159351 stx2B, pMIN27_42; Enterobacteria phage Min27; ORF45; K11007 shiga toxin subunit B +vg:6973138 Stx2-1717_gp41; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit A; K11006 shiga toxin subunit A +vg:6972909 stx2cB, Stx2-1717_gp42; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit B; K11007 shiga toxin subunit B +vg:6973079 YYZ_gp39; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:6973080 YYZ_gp40; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:13828571 stx2A, D300_gp43; Escherichia phage P13374; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:13828535 stx2B, D300_gp42; Escherichia phage P13374; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:14005228 F366_gp36; Escherichia phage TL-2011c; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:14005229 F366_gp37; Escherichia phage TL-2011c; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:1262249 stx2A, VT2-Sap42; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262250 stx2B, VT2-Sap43; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/test-data/shiga-toxin-example-OR Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,88 @@ +ece:Z1464 stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W; K11006 shiga toxin subunit A +ece:Z1465 stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W; K11007 shiga toxin subunit B +ece:Z3343 stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V; K11007 shiga toxin subunit B +ece:Z3344 stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V; K11006 shiga toxin subunit A +ecs:ECs1205 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecs:ECs1206 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +ecs:ECs2973 Shiga toxin I subunit B; K11007 shiga toxin subunit B +ecs:ECs2974 Shiga toxin I subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_2905 shigatoxin 2, subunit B; K11007 shiga toxin subunit B +ecf:ECH74115_2906 shiga toxin subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_3532 shiga toxin 2 B subunit; K11007 shiga toxin subunit B +ecf:ECH74115_3533 shiga toxin subunit A; K11006 shiga toxin subunit A +etw:ECSP_2722 stx2cB; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +etw:ECSP_2723 stx2A1; Shiga-like toxin II subunit A precursor; K11006 shiga toxin subunit A +etw:ECSP_3252 stx2B; shiga toxin II subunit B; K11007 shiga toxin subunit B +etw:ECSP_3253 stx2A2; shiga toxin II subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1154 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1155 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +elx:CDCO157_2738 Shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +elx:CDCO157_2739 Shiga toxin I subunit A precursor; K11006 shiga toxin subunit A +eoj:ECO26_1599 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoj:ECO26_1600 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2429 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2430 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3361 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3362 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2844 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2845 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5197 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5198 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eso:O3O_09170 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eso:O3O_09165 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esm:O3M_16105 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esm:O3M_16110 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esl:O3K_16130 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esl:O3K_16135 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecoo:ECRM13514_3144 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoo:ECRM13514_3145 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +ecoh:ECRM13516_2315 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoh:ECRM13516_2316 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +setc:CFSAN001921_15985 Shiga toxin A subunit +seni:CY43_01420 Shiga toxin A subunit +seen:SE451236_07435 Shiga toxin A subunit +senh:CFSAN002069_07720 Shiga toxin A subunit +seec:CFSAN002050_07960 Shiga toxin A subunit +sene:IA1_01505 Shiga toxin A subunit +senc:SEET0819_08350 Shiga toxin A subunit +sdy:SDY_1389 stxA; Shiga toxin subunit A; K11006 shiga toxin subunit A +sdy:SDY_1390 stxB; Shiga toxin subunit B; K11007 shiga toxin subunit B +sdz:Asd1617_01826 Shiga toxin subunit A (EC:3.2.2.22); K11006 shiga toxin subunit A +ssab:SSABA_v1c03870 hypothetical protein; K11006 shiga toxin subunit A +ssab:SSABA_v1c09020 hypothetical protein; K11006 shiga toxin subunit A +calt:Cal6303_2132 ribosome-inactivating protein; K11006 shiga toxin subunit A +vg:22277199 PI30_gp34; Shigella phage POCJ13; shiga toxin A-chain precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:22277200 PI30_gp35; Shigella phage POCJ13; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +vg:1262301 APSE-1_07; Endosymbiont phage APSE-1; P7; K11007 shiga toxin subunit B +vg:1481747 stx1A, Stx1_p142; Escherichia Stx1 converting phage; Shiga toxin1 subunit A; K11006 shiga toxin subunit A +vg:1481748 stx1B, Stx1_p143; Escherichia Stx1 converting phage; Shiga toxin1 subunit B; K11007 shiga toxin subunit B +vg:1481767 stx2A, Stx2II_p143; Stx2 converting phage II; Shiga toxin2 subunit A; K11006 shiga toxin subunit A +vg:1481768 stx2B, Stx2II_p144; Stx2 converting phage II; Shiga toxin2 subunit B; K11007 shiga toxin subunit B +vg:26228052 AS349_gp84; Escherichia phage PA2; shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26228100 AS349_gp83; Escherichia phage PA2; shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +vg:26516496 stx2A, AU085_gp42; Enterobacteria phage VT2phi_272; Shiga toxin 2 A subunit; K11006 shiga toxin subunit A +vg:26516448 stx2B, AU085_gp41; Enterobacteria phage VT2phi_272; Shiga toxin 2 B subunit; K11007 shiga toxin subunit B +vg:26516283 stxB, phi191_00011, AU083_gp11; Escherichia phage phi191; shiga toxin subunit B precursor; K11007 shiga toxin subunit B +vg:26516284 stxA, phi191_00012, AU083_gp12; Escherichia phage phi191; shiga toxin subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26519429 AU154_gp39; Shigella phage Ss-VASD; Stx1 A subunit; K11006 shiga toxin subunit A +vg:26519430 AU154_gp40; Shigella phage Ss-VASD; Stx1 B subunit; K11007 shiga toxin subunit B +vg:1261950 stxA2, L0103, sltIIA, stx2A, 933Wp40; Enterobacteria phage 933W; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262010 stxB2, L0104, sltIIB, stx2B, 933Wp41; Enterobacteria phage 933W; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:2641645 stxA1, phi4795p38, PBV4795_ORF40; Enterobacteria phage BP-4795; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:2641657 stxB1, phi4795p39, PBV4795_ORF41; Enterobacteria phage BP-4795; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:929695 stxA2e, P27p25; Enterobacteria phage phiP27; shiga toxin 2e A-subunit; K11006 shiga toxin subunit A +vg:929727 stxB2e, P27p26; Enterobacteria phage phiP27; shiga toxin 2e B-subunit; K11007 shiga toxin subunit B +vg:4397483 stx2A, Stx2-86_gp01; Stx2-converting phage 86; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:4397484 stx2B, Stx2-86_gp02; Stx2-converting phage 86; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:6159405 stx2A, pMIN27_41; Enterobacteria phage Min27; ORF44; K11006 shiga toxin subunit A +vg:6159351 stx2B, pMIN27_42; Enterobacteria phage Min27; ORF45; K11007 shiga toxin subunit B +vg:6973138 Stx2-1717_gp41; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit A; K11006 shiga toxin subunit A +vg:6972909 stx2cB, Stx2-1717_gp42; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit B; K11007 shiga toxin subunit B +vg:6973079 YYZ_gp39; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:6973080 YYZ_gp40; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:13828571 stx2A, D300_gp43; Escherichia phage P13374; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:13828535 stx2B, D300_gp42; Escherichia phage P13374; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:14005228 F366_gp36; Escherichia phage TL-2011c; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:14005229 F366_gp37; Escherichia phage TL-2011c; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:1262249 stx2A, VT2-Sap42; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262250 stx2B, VT2-Sap43; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_data/kegg_glycan/test-data/shiga-toxin-example-OR-broken Fri May 06 08:05:48 2016 -0400 @@ -0,0 +1,103 @@ +ece:Z1464 stx2A; shiga-like toxin II A subunit encoded by bacteriophage BP-933W; K11006 shiga toxin subunit A +ece:Z1465 stx2B; shiga-like toxin II B subunit encoded by bacteriophage BP-933W; K11007 shiga toxin subunit B +ece:Z3343 stx1B; shiga-like toxin 1 subunit B encoded within prophage CP-933V; K11007 shiga toxin subunit B +ece:Z3344 stx1A; shiga-like toxin 1 subunit A encoded within prophage CP-933V; K11006 shiga toxin subunit A +ecs:ECs1205 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecs:ECs1206 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +ecs:ECs2973 Shiga toxin I subunit B; K11007 shiga toxin subunit B +ecs:ECs2974 Shiga toxin I subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_2905 shigatoxin 2, subunit B; K11007 shiga toxin subunit B +ecf:ECH74115_2906 shiga toxin subunit A; K11006 shiga toxin subunit A +ecf:ECH74115_3532 shiga toxin 2 B subunit; K11007 shiga toxin subunit B +ecf:ECH74115_3533 shiga toxin subunit A; K11006 shiga toxin subunit A +etw:ECSP_2722 stx2cB; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +etw:ECSP_2723 stx2A1; Shiga-like toxin II subunit A precursor; K11006 shiga toxin subunit A +etw:ECSP_3252 stx2B; shiga toxin II subunit B; K11007 shiga toxin subunit B +etw:ECSP_3253 stx2A2; shiga toxin II subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1154 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +elx:CDCO157_1155 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +elx:CDCO157_2738 Shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +elx:CDCO157_2739 Shiga toxin I subunit A precursor; K11006 shiga toxin subunit A +eoj:ECO26_1599 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoj:ECO26_1600 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2429 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoi:ECO111_2430 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3361 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoi:ECO111_3362 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2844 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eoh:ECO103_2845 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5197 Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +eoh:ECO103_5198 Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +eso:O3O_09170 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +eso:O3O_09165 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esm:O3M_16105 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esm:O3M_16110 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +esl:O3K_16130 Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +esl:O3K_16135 Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +ecoo:ECRM13514_3144 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoo:ECRM13514_3145 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +ecoh:ECRM13516_2315 stx2B; Shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +ecoh:ECRM13516_2316 stx2A; Shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +stm:STM0284 shiga-like toxin A subunit +seo:STM14_0332 putative Shiga-like toxin A subunit +sev:STMMW_02891 putative shiga-like toxin A subunit +sem:STMDT12_C02790 putative Shiga-like toxin A subunit +sej:STMUK_0287 putative Shiga-like toxin A subunit +setu:STU288_13325 putative shiga-like toxin A subunit +setc:CFSAN001921_15985 Shiga toxin A subunit +send:DT104_02831 sciR; shiga-like toxin a subunit, type VI secretion system SciR protein flags: precursor +seni:CY43_01420 Shiga toxin A subunit +seen:SE451236_07435 Shiga toxin A subunit +spt:SPA2480 putative shiga-like toxin A subunit +sek:SSPA2315 shiga-like toxin A subunit +sei:SPC_0292 putative shiga-like toxin A subunit +sec:SCH_0277 putative shiga-like toxin A subunit +shb:SU5_0926 SciR Shiga-like toxin A subunit +senh:CFSAN002069_07720 Shiga toxin A subunit +seeh:SEEH1578_10515 putative shiga-like toxin A subunit +seec:CFSAN002050_07960 Shiga toxin A subunit +sene:IA1_01505 Shiga toxin A subunit +senc:SEET0819_08350 Shiga toxin A subunit +sdy:SDY_1389 stxA; Shiga toxin subunit A; K11006 shiga toxin subunit A +sdy:SDY_1390 stxB; Shiga toxin subunit B; K11007 shiga toxin subunit B +sdz:Asd1617_01826 Shiga toxin subunit A (EC:3.2.2.22); K11006 shiga toxin subunit A +ebi:EbC_13780 Putative shiga-like toxin A subunit +psos:POS17_2009 P9; putative Shiga-like toxin alpha subunit +ssab:SSABA_v1c03870 hypothetical protein; K11006 shiga toxin subunit A +ssab:SSABA_v1c09020 hypothetical protein; K11006 shiga toxin subunit A +calt:Cal6303_2132 ribosome-inactivating protein; K11006 shiga toxin subunit A +vg:22277199 PI30_gp34; Shigella phage POCJ13; shiga toxin A-chain precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:22277200 PI30_gp35; Shigella phage POCJ13; shiga toxin I subunit B precursor; K11007 shiga toxin subunit B +vg:1262301 APSE-1_07; Endosymbiont phage APSE-1; P7; K11007 shiga toxin subunit B +vg:1481747 stx1A, Stx1_p142; Escherichia Stx1 converting phage; Shiga toxin1 subunit A; K11006 shiga toxin subunit A +vg:1481748 stx1B, Stx1_p143; Escherichia Stx1 converting phage; Shiga toxin1 subunit B; K11007 shiga toxin subunit B +vg:1481767 stx2A, Stx2II_p143; Stx2 converting phage II; Shiga toxin2 subunit A; K11006 shiga toxin subunit A +vg:1481768 stx2B, Stx2II_p144; Stx2 converting phage II; Shiga toxin2 subunit B; K11007 shiga toxin subunit B +vg:26228052 AS349_gp84; Escherichia phage PA2; shiga-like toxin II subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26228100 AS349_gp83; Escherichia phage PA2; shiga-like toxin II subunit B precursor; K11007 shiga toxin subunit B +vg:26516496 stx2A, AU085_gp42; Enterobacteria phage VT2phi_272; Shiga toxin 2 A subunit; K11006 shiga toxin subunit A +vg:26516448 stx2B, AU085_gp41; Enterobacteria phage VT2phi_272; Shiga toxin 2 B subunit; K11007 shiga toxin subunit B +vg:26516283 stxB, phi191_00011, AU083_gp11; Escherichia phage phi191; shiga toxin subunit B precursor; K11007 shiga toxin subunit B +vg:26516284 stxA, phi191_00012, AU083_gp12; Escherichia phage phi191; shiga toxin subunit A precursor (EC:3.2.2.22); K11006 shiga toxin subunit A +vg:26519429 AU154_gp39; Shigella phage Ss-VASD; Stx1 A subunit; K11006 shiga toxin subunit A +vg:26519430 AU154_gp40; Shigella phage Ss-VASD; Stx1 B subunit; K11007 shiga toxin subunit B +vg:1261950 stxA2, L0103, sltIIA, stx2A, 933Wp40; Enterobacteria phage 933W; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262010 stxB2, L0104, sltIIB, stx2B, 933Wp41; Enterobacteria phage 933W; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:2641645 stxA1, phi4795p38, PBV4795_ORF40; Enterobacteria phage BP-4795; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:2641657 stxB1, phi4795p39, PBV4795_ORF41; Enterobacteria phage BP-4795; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:929695 stxA2e, P27p25; Enterobacteria phage phiP27; shiga toxin 2e A-subunit; K11006 shiga toxin subunit A +vg:929727 stxB2e, P27p26; Enterobacteria phage phiP27; shiga toxin 2e B-subunit; K11007 shiga toxin subunit B +vg:4397483 stx2A, Stx2-86_gp01; Stx2-converting phage 86; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:4397484 stx2B, Stx2-86_gp02; Stx2-converting phage 86; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:6159405 stx2A, pMIN27_41; Enterobacteria phage Min27; ORF44; K11006 shiga toxin subunit A +vg:6159351 stx2B, pMIN27_42; Enterobacteria phage Min27; ORF45; K11007 shiga toxin subunit B +vg:6973138 Stx2-1717_gp41; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit A; K11006 shiga toxin subunit A +vg:6972909 stx2cB, Stx2-1717_gp42; Stx2-converting phage 1717; verocytotoxin 2 variant 2c subunit B; K11007 shiga toxin subunit B +vg:6973079 YYZ_gp39; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit A; K11006 shiga toxin subunit A +vg:6973080 YYZ_gp40; Enterobacteria phage YYZ-2008; Shiga toxin 1 subunit B; K11007 shiga toxin subunit B +vg:13828571 stx2A, D300_gp43; Escherichia phage P13374; shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:13828535 stx2B, D300_gp42; Escherichia phage P13374; shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:14005228 F366_gp36; Escherichia phage TL-2011c; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:14005229 F366_gp37; Escherichia phage TL-2011c; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B +vg:1262249 stx2A, VT2-Sap42; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit A; K11006 shiga toxin subunit A +vg:1262250 stx2B, VT2-Sap43; Enterobacteria phage VT2-Sakai; Shiga toxin 2 subunit B; K11007 shiga toxin subunit B
--- a/get_data/kegg_glycan/test_findKEGG.py Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/test_findKEGG.py Fri May 06 08:05:48 2016 -0400 @@ -41,9 +41,10 @@ m = fk.find_entries_in_KEGG("john", "glucose") def test_unfindable_entry(self): - """should return None""" + """should return an empty string""" m = fk.find_entries_in_KEGG("glycan", "sally") - self.assertIsNone(m) + emptystring="" + self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") def test_find_example(self): m = fk.find_entries_in_KEGG("glycan", "glucose") @@ -52,9 +53,123 @@ def test_query_has_newlines(self): """ - should be fine and return entries + Assume a new line query is an AND query. + """ + m = fk.find_entries_in_KEGG("glycan", "glucose\nUDP") + self.assertIsNotNone(m) + print m + self.assertIn("UDP-D-glucose", m) + + def test_query_has_newlines_and_a_space(self): + """ + glucose\\n UDP. OR's should pass """ m = fk.find_entries_in_KEGG("glycan", "glucose\n UDP") self.assertIsNotNone(m) self.assertIn("UDP-D-glucose", m) + def test_gene_specific_or(self): + """ + test "shiga toxin" returns. + /find/genes/"shiga toxin" for keywords "shiga toxin" + """ + m = fk.find_entries_in_KEGG("genes","shiga toxin") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("shiga", m) + self.assertIn("toxin", m) + self.assertNotIn("stm:STM0284",m) # should not be found in the OR query + + def test_gene_specific_and(self): + """ + test "shiga+toxin" returns. it should + /find/genes/shiga+toxin for keywords "shiga" and "toxin" + """ + m = fk.find_entries_in_KEGG("genes","shiga+toxin") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("shiga", m) + self.assertIn("toxin", m) + self.assertIn("stm:STM0284",m) # should be found in the AND query + + def test_enzyme_specific_1(self): + """ + test 2.4.99.1 returns + """ + m = fk.find_entries_in_KEGG("enzyme","2.4.99.1") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("2.4.99.1", m) + + def test_enzyme_specific_2(self): + """ + test 2.4.99.6 returns + """ + m = fk.find_entries_in_KEGG("enzyme","2.4.99.6") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("2.4.99.6", m) + + def test_enzyme_specific_3(self): + """ + test ec: 2.4.99.6 with space (tests stripping space functionality) + """ + m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.6") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("2.4.99.6", m) + + def test_enzyme_specific_4(self): + """ + test ec: 2.4.99. , should return 2.4.99.* + """ + m = fk.find_entries_in_KEGG("enzyme","ec: 2.4.99.") + self.assertIsNotNone(m) + #. not matching to all entries - that is silly, the db get updated! + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + self.assertIn("2.4.99.11", m) + + def test_enzyme_specific_5(self): + """ + test ec: 2.4.99.1+2.4.99.6 . AND function, so returns nothing here. Do not expect an enzyme to be doubly classified. + """ + m = fk.find_entries_in_KEGG("enzyme","2.4.99.1+2.4.99.6") + self.assertIsNotNone(m) + emptystring="" + self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") + + def test_enzyme_specific_6(self): + """ + test ec: 2.4.99.1 2.4.99.6 . OR function, should return something but does not (KEGG FAILURE?). + note that trying this without "" will return the AND function result which is incorrect. + """ + m = fk.find_entries_in_KEGG("enzyme","2.4.99.1 2.4.99.6") + self.assertIsNotNone(m) + #self.assertIn("2.4.99.1", m) + emptystring="" + print m + self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") + + + def test_enzyme_specific_7(self): + """ + test deoxy+1.1.1. . AND function, that should return something + """ + m = fk.find_entries_in_KEGG("enzyme","deoxy+1.1.1") + self.assertIsNotNone(m) + print m + self.assertIn("deoxy", m) + self.assertIn("1.1.1", m) + + def test_enzyme_specific_8(self): + """ + test deoxy 1.1.1. . OR function. should return deoxy or 1.1.1. but does not (KEGG FAILURE?). i + note that trying this without "" will return the AND function result which is incorrect. + """ + m = fk.find_entries_in_KEGG("enzyme","deoxy 1.1.1") + self.assertIsNotNone(m) + emptystring="" + print m + self.assertItemsEqual(m,emptystring,"Expected Empty String for non-existent entry") +
--- a/get_data/kegg_glycan/test_linkKEGG.py Wed Mar 23 14:35:56 2016 -0400 +++ b/get_data/kegg_glycan/test_linkKEGG.py Fri May 06 08:05:48 2016 -0400 @@ -40,3 +40,76 @@ m = lk.linked_entries_from_kegg("br", "gl:G10496") self.assertEquals(m,"") + def test_enzyme_glycan_search_1(self): + """ + test "2.4.99.1 ec: " returns + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1 ec:") + self.assertIn("2.4.99.1", m) + + + def test_enzyme_glycan_search_2(self): + """ + test "2.4.99.1 ec: 2.4.99.6" returns + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1 ec: 2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_3(self): + """ + test "2.4.99.1 ec:2.4.99.6" returns + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1 ec:2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_4(self): + """ + test "2.4.99.1+2.4.99.6" returns. This time '+' is or. + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1+2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_4b(self): + """ + test "2.4.99.1+ 2.4.99.6" returns. This time '+' is or. + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1+ 2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_5(self): + """ + test "2.4.99.1 2.4.99.6" returns. Space also means or for the link db. + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1 2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + + def test_enzyme_glycan_search_6(self): + """ + test "2.4.99.1+nana+2.4.99.6" returns. strangely when inserting junk it still works. + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1+nana+2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_6b(self): + """ + test "2.4.99.1 nana 2.4.99.6" returns. strangely when inserting junk it still works. + """ + m = lk.linked_entries_from_kegg("glycan", "2.4.99.1+nana+2.4.99.6" ) + self.assertIn("2.4.99.1", m) + self.assertIn("2.4.99.6", m) + + def test_enzyme_glycan_search_7(self): + """ + test "\"2.4.99.1\"" is a bad request as it includes quotes. + """ + from urllib2 import HTTPError + with self.assertRaises(HTTPError): + m = lk.linked_entries_from_kegg("glycan", "\"2.4.99.1\"" ) +