Mercurial > repos > greg > validate_affy_metadata
changeset 0:80d672b3e6dd draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 15 Aug 2019 13:17:41 -0400 |
| parents | |
| children | b5f5c3d0f349 |
| files | .shed.yml test-data/affy_metadata.tabular validate_affy_metadata.py validate_affy_metadata.xml |
| diffstat | 4 files changed, 361 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Aug 15 13:17:41 2019 -0400 @@ -0,0 +1,11 @@ +name: validate_affy_metadata +owner: greg +description: | + Contains a tool that validates an Affymetrix metadata file for 96 well plate data. +homepage_url: http://baumslab.org +long_description: | + Contains a tool that validates an Affymetrix metadata file for 96 well plate data. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/corals/validate_affy_metadata +type: unrestricted +categories: + - Micro-array Analysis
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/affy_metadata.tabular Thu Aug 15 13:17:41 2019 -0400 @@ -0,0 +1,97 @@ +#user_specimen_id field_call bcoral_genet_id bsym_genet_id reef region latitude longitude geographic_origin colony_location depth disease_resist bleach_resist mortality tle spawning collector_last_name collector_first_name organization collection_date email seq_facility array_version public public_after_date sperm_motility healing_time dna_extraction_method dna_concentration registry_id result_folder_name plate_barcode +1090 palmata Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-04-05 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 7.636 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1091 palmata Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-04-05 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 24.082 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1092 palmata Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-04-05 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 43.933 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1096 palmata Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-07-02 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 10.16 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1099 palmata Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 32.792 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1112 palmata P1012 Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-04-05 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 10.827 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1113 palmata P1013 Western Sambo Florida 24.479867 -81.718667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-04-05 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 8.922 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1146 palmata P1019 RockKey Florida 24.456017 -81.859633 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-07-16 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 30.495 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1151 palmata P1020 RockKey Florida 24.456017 -81.859633 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2002-07-16 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 22.163 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +1446 cervicornis C1015 CRF Florida 25.022308 -80.402375 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2005-05-07 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 6.277 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +2869 palmata P2582 GR1 Florida 25.091146 -80.40632 Reef unknown -9 -9 -9 -9 -9 No Williams Dana University of Miami 2010-08-17 d.williams5@miami.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 16.959 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +2905 palmata P2598 KL4NOAA Florida 25.022308 -80.402375 Reef unknown -9 -9 -9 -9 -9 No Williams Dana University of Miami 2010-08-20 d.williams5@miami.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 9.667 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15624 prolifera Sandbores Belize 16.7791333 -88.11755 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.473 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +3846 cervicornis C1548 Flat Cay USVI 18.31822 -64.99104 Reef unknown -9 -9 -9 -9 -9 No TNC TNC The Nature Conservancy 2011-11-11 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.008 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +3847 cervicornis C1548 Flat Cay USVI 18.31822 -64.99104 Reef unknown -9 -9 -9 -9 -9 No TNC TNC The Nature Conservancy 2011-11-11 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 3.641 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +4917 cervicornis C1492 Little Conch Florida 24.946333 -80.470166 Colony unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2011-11-22 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 5.574 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +4918 cervicornis C1494 Plantation Key Florida 24.9509 -80.4936166 Colony unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2011-11-22 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.433 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +5130 prolifera P1872 San Cristobal PuertoRico 17.56493 -67.04515 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2004-06-18 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 54.198 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +6898 palmata P2427 Looe Key Florida 24.54585 -81.4050667 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2009-07-14 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 20.179 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15625 prolifera Sandbores Belize 16.7791333 -88.11755 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 40.298 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +8952 prolifera H59 Glovers Belize 16.908817 -87.773467 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2012-09-13 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 33.666 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9003 prolifera H8 JudyLang Cuba 23.220565 -82.346683 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2005-05-19 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 6.834 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9005 prolifera H9 JudyLang Cuba 23.220565 -82.346683 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2005-05-19 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 1.612 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9372 prolifera H10 Nain Cay Bahamas 22.35199 -75.79612 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret SECORE 2008-01-16 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.015 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9395 cervicornis C1170 LowerKeys Florida 24.517654 -81.62134 Reef unknown -9 -9 -9 -9 -9 No TNC TNC The Nature Conservancy 2008-02-26 unknown@unknown.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.197 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9585 cervicornis C1213 Biscayne National Park Florida 25.39894 -80.16032 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret ACRRE 2008-06-12 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 0.231 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9592 cervicornis C1215 Biscayne National Park Florida 25.37236 -80.17155 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret ACRRE 2008-06-12 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 25.613 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9609 cervicornis C1218 Biscayne National Park Florida 25.42616 -80.14175 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret ACRRE 2008-06-12 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 5.716 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9749 cervicornis C1224 Margara PuertoRico 17.949552 -66.727433 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret SECORE 2008-08-25 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 0.747 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +9759 cervicornis C1142 Margara PuertoRico 17.949552 -66.727433 Reef unknown -9 -9 -9 -9 -9 No Miller Margaret SECORE 2008-08-25 m.miller@secore.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.315 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11954 palmata P1007 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 18.468 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11956 palmata P1002 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 5.338 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11955 palmata P2819 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 41.167 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11957 palmata P2817 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 22.121 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11958 palmata P2816 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 12.93 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11962 palmata P2818 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 17.122 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +11963 palmata P2815 CRF Florida 24.710868 -80.947981 Reef unknown -9 -9 -9 -9 -9 No Nedimyer Ken CRF 2014-04-21 info@coralrestoration.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 20.695 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13692 prolifera H110 Botany2 USVI 18.357883 -65.032967 Colony unknown 8 -9 -9 -9 -9 No Baums Iliana Penn State 2015-10-27 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 5.582 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13694 palmata P2963 Botany2 USVI 18.357883 -65.032967 Colony unknown 8 -9 -9 -9 -9 No Baums Iliana Penn State 2015-10-27 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 24.272 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13710 palmata P2966 Botany2 USVI 18.359033 -65.032833 Colony unknown 2 -9 -9 -9 -9 No Baums Iliana Penn State 2015-10-28 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 12.101 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13734 prolifera H107 Sapphire USVI 18.3349 -64.848 Colony unknown 5 -9 -9 -9 -9 No Baums Iliana Penn State 2015-10-30 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 9.935 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13756 cervicornis C1343 FlatKey USVI 18.316367 -64.98855 Colony unknown 17 -9 -9 -9 -9 No Baums Iliana Penn State 2015-10-31 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.504 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13786 cervicornis C1569 SouthCarrieBowCay Belize 16.801383 -88.082783 Colony unknown 4 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-06 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 11.766 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13805 palmata P2956 Sandbores2 Belize 16.772567 -88.1111 Colony unknown 3 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-07 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 16.571 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13809 palmata P2958 SouthCarrieBowCay Belize 16.8013222 -88.0825 Reef unknown 2 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-06 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 47.491 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13811 palmata P2948 GloversAtoll Belize 16.92005 -87.767217 Colony unknown 1 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-08 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 18.526 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13835 palmata P2950 GloversAtoll Belize 16.9084 -87.767217 Colony unknown 1 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-08 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 32.604 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13841 palmata P2965 Sandbores2 Belize 16.763667 -88.113967 Colony unknown 4 -9 -9 -9 -9 No Baums Iliana Penn State 2015-11-07 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 23.21 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13909 palmata P2982 SeaAquarium2 Curacao 12.083133 -68.895567 Colony unknown 8 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-03 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 17.442 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13921 palmata P2973 DirectorsBay Curacao 12.0633 -68.859033 Colony unknown 6 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-04 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 23.66 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13923 cervicornis C1652 East Point Curacao 12.043117 -68.762433 Colony unknown 18 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-05 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 3.405 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13927 palmata P2696 EastPoint2 Curacao 12.043367 -68.762517 Colony unknown 7 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-05 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 62.191 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13929 palmata P2971 EastPoint2 Curacao 12.043467 -68.76315 Colony unknown 5 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-05 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 37.543 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13931 palmata P2980 EastPoint2 Curacao 12.043317 -68.763533 Colony unknown 17 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-05 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 29.898 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13935 cervicornis C1522 WaterFactory Curacao 12.109283 -68.954933 Colony unknown 16 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-06 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 34.711 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13937 palmata P2975 WaterFactory2 Curacao 12.109517 -68.955367 Colony unknown 16 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2016-02-06 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 32.487 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +13972 palmata P2985 WaterFactory2 Curacao 12.109617 -68.954517 Colony unknown 6 -9 -9 -9 -9 No Baums Iliana Penn State 2016-02-06 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 42.685 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15364 cervicornis C1333 site 12 Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 1.784 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15371 cervicornis C1671 Carne Nursery Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.363 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15372 cervicornis C1674 dory channel Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.979 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15373 cervicornis C1675 wypt 112 Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 0.687 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15375 cervicornis C1677 False Caye Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 8.068 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15377 cervicornis C1679 by_RHT1 Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 14.315 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15378 cervicornis C1680 BBC_patch Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 38.132 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15391 palmata P2267 1D Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 18.102 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15395 palmata P3053 CBC wypt 51 Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 37.925 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15626 prolifera Curlew Belize 16.7909389 -88.0830056 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 7.46 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15397 palmata P3055 SWCB2 Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 8.958 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15398 palmata P3056 N of bath room Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 18.42 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15400 prolifera H124 south dory Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Carne Lisa Fragments of Hope 2018-04-20 info@fragmentsofhope.org Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.535 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15610 palmata SouthCarrieBow Belize 16.80132222 -88.0825 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 4.45 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15611 palmata SouthCarrieBow Belize 16.80132222 -88.0825 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 3.718 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15612 palmata SouthCarrieBow Belize 16.80132222 -88.0825 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 23.437 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15613 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 32.171 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15614 palmata Sandbores Belize 16.7791333 -88.11755 Reef unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 11.302 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15615 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 14.209 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15616 palmata Glovers-118 Belize 16.182848 -88.65966 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 5.777 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15617 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.692 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15618 palmata Glovers-118 Belize 16.182848 -88.65966 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 3.014 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15619 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 17.031 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15620 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 29.548 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15621 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Reef unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 28.366 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15622 palmata SouthCarrieBowCaye Belize 16.80145 -88.0827 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 13.49 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15623 palmata BigAcervPatch Belize 16.731183 -88.07823 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 2.964 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15719 palmata Belize Belize 16.182848 -88.65966 Reef unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2017-08-01 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 21.066 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15721 prolifera E rocks Antigua 17.09476 -61.43875 Reef unknown 2 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 24.012 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15722 prolifera E rocks Antigua 17.09476 -61.43875 Reef unknown 2 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 62.918 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15723 prolifera E rocks Antigua 17.09476 -61.43875 Reef unknown 12 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 53.169 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15724 prolifera E rocks Antigua 17.09476 -61.43875 Reef unknown 10 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 43.791 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15725 prolifera E rocks Antigua 17.09476 -61.43875 Reef unknown 9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 48.219 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15726 prolifera N rocks Antigua 17.09476 -61.43875 Reef unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 34.925 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15727 prolifera N rocks Antigua 17.09476 -61.43875 Reef unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 107.991 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15728 prolifera N rocks Antigua 17.09476 -61.43875 Reef unknown 2 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2018-05-31 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 31.269 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15720 cervicornis Belize Belize 16.182848 -88.65966 Colony unknown -9 -9 -9 -9 -9 No Fogarty Nicole NOVA Southeastern 2017-08-01 nf121@nova.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 17.184 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +15729 prolifera JudyLang Cuba 23.220565 -82.346683 Reef unknown -9 -9 -9 -9 -9 No Baums Iliana Penn State 2005-05-19 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Qiagen DNeasy 7.878 -9 PRO100175_PSU175_SAX_b02 P9SR10074 +14225 palmata P1000 F100 Horseshoe Florida 25.139467 -80.29435 Reef sperm -9 -9 -9 -9 -9 Yes Kitchen Sheila Penn State 2016-08-20 ibb3@psu.edu Affymetrix 1 Yes No -9 -9 Nucleon Phytopure 11.469 -9 PRO100175_PSU175_SAX_b02 P9SR10074
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validate_affy_metadata.py Thu Aug 15 13:17:41 2019 -0400 @@ -0,0 +1,178 @@ +#!/usr/bin/env python +""" +Validate the metadata file associated with Affymetrix 96 well plate data. +""" +import argparse +import datetime +import decimal +import re +import shutil +import sys + +parser = argparse.ArgumentParser() +parser.add_argument('--input', dest='input', help='Metadata file for Affymetrix 96 well plate data') +parser.add_argument('--output', dest='output', help='Output dataset'), +args = parser.parse_args() + +EMAIL_MAX_LEN = 255 +VALID_EMAIL_RE = re.compile("[^@]+@[^@]+\.[^@]+") + + +def add_error_msg(accumulated_msgs, msg): + return "%s\n%s" % (accumulated_msgs, msg) + + +def empty_value(line_no, label, accumulated_msgs): + return add_error_msg(accumulated_msgs, "The required %s value is missing on line %d." % (label, line_no)) + + +def stop_error(msg): + sys.exit(msg) + + +def string_as_boolean_string(string): + if str(string).lower() in ['true', 'yes', 'on', '1']: + return 'True' + else: + return 'False' + + +def validate_date_string(line_no, date_string, column, accumulated_msgs): + if len(date_string) == 0: + return accumulated_msgs + try: + datetime.datetime.strptime(date_string, '%Y-%m-%d') + return accumulated_msgs + except ValueError: + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect date format (%s must be YYYY-MM-DD) for column %s." % (line_no, date_string, column)) + + +def validate_decimal(line_no, decimal_string, column, accumulated_msgs): + try: + decimal.Decimal(decimal_string) + return accumulated_msgs + except Exception: + return add_error_msg(accumulated_msgs, "Line %d contains an incorrect decimal value (%s) for column %s." % (line_no, decimal_string, column)) + + +def validate_email(line_no, email, accumulated_msgs): + if not (VALID_EMAIL_RE.match(email)): + return add_error_msg(accumulated_msgs, "Line %d contains an invalid email address (%s). " % (line_no, email)) + elif len(email) > EMAIL_MAX_LEN: + return add_error_msg(accumulated_msgs, "Line %d contains an email address (%) that is longer than the maximum length, %d characters." % (line_no, email)) + return accumulated_msgs + + +accumulated_msgs = "" +# Parse the input file, skipping the header, and validating +# that each data line consists of 31 comma-separated items. +with open(args.input, "r") as ih: + for i, line in enumerate(ih): + if i == 0: + # Skip the header. + continue + # Keep 1-based line value for error messages. + line_no = i + 1 + line = line.rstrip("\r\n") + if i > 97: + accumulated_msgs = add_error_msg(accumulated_msgs, "The input file contains more than 97 lines (must be 1 header line and no more than 96 data lines).") + stop_error(accumulated_msgs) + items = line.split("\t") + if len(items) != 32: + accumulated_msgs = add_error_msg(accumulated_msgs, "Line %d contains %s columns, (must be 32)." % (line_no, len(items))) + stop_error(accumulated_msgs) + # Required and validated. + # Required. + user_specimen_id = items[0] + if len(user_specimen_id) == 0: + accumulated_msgs = empty_value(line_no, "user_specimen_id", accumulated_msgs) + # Optional. + field_call = items[1] + # Optional. + bcoral_genet_id = items[2] + # Optional. + bsym_genet_id = items[3] + # Required. + reef = items[4] + if len(reef) == 0: + accumulated_msgs = empty_value(line_no, "reef", accumulated_msgs) + # Required. + region = items[5] + if len(region) == 0: + accumulated_msgs = empty_value(line_no, "region", accumulated_msgs) + # Required and validated. + latitude = items[6] + accumulated_msgs = validate_decimal(line_no, latitude, "latitude", accumulated_msgs) + # Required and validated. + longitude = items[7] + accumulated_msgs = validate_decimal(line_no, longitude, "longitude", accumulated_msgs) + # Optional. + geographic_origin = items[8] + # Optional. + colony_location = items[9] + # Optional. + depth = items[10] + # Optional. + disease_resist = items[11] + # Optional. + bleach_resist = items[12] + # Optional. + mortality = items[13] + # Optional. + tle = items[14] + # Optional. + spawning = string_as_boolean_string(items[15]) + # Required. + collector_last_name = items[16] + if len(collector_last_name) == 0: + accumulated_msgs = empty_value(line_no, "collector_last_name", accumulated_msgs) + # Required. + collector_first_name = items[17] + if len(collector_first_name) == 0: + accumulated_msgs = empty_value(line_no, "collector_first_name", accumulated_msgs) + # Required. + org = items[18] + if len(org) == 0: + accumulated_msgs = empty_value(line_no, "org", accumulated_msgs) + # Required and validated. + collection_date = items[19] + accumulated_msgs = validate_date_string(line_no, collection_date, "collection_date", accumulated_msgs) + # Required and validated. + contact_email = items[20] + accumulated_msgs = validate_email(line_no, contact_email, accumulated_msgs) + # Required. + seq_facility = items[21] + if len(seq_facility) == 0: + accumulated_msgs = empty_value(line_no, "seq_facility", accumulated_msgs) + # Optional. + array_version = items[22] + # Optional. + public = string_as_boolean_string(items[23]) + # Optional. + public_after_date = items[24] + accumulated_msga = validate_date_string(line_no, public_after_date, "public_after_date", accumulated_msgs) + # Required and validated. + sperm_motility = items[25] + accumulated_msgs = validate_decimal(line_no, sperm_motility, "sperm_motility", accumulated_msgs) + # Required and validated. + healing_time = items[26] + accumulated_msgs = validate_decimal(line_no, healing_time, "healing_time", accumulated_msgs) + # Optional. + dna_extraction_method = items[27] + # Optional. + dna_concentration = items[28] + # If dna_concentration has a value, then it must be decimal. + if len(dna_concentration) > 0: + accumulated_msgs = validate_decimal(line_no, dna_concentration, "dna_concentration", accumulated_msgs) + # Optional. + registry_id = items[29] + # Optional. + result_folder_name = items[30] + # Optional. + plate_barcode = items[31] + + +if len(accumulated_msgs) > 0: + stop_error(accumulated_msgs) + +shutil.copyfile(args.input, args.output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/validate_affy_metadata.xml Thu Aug 15 13:17:41 2019 -0400 @@ -0,0 +1,75 @@ +<tool id="validate_affy_metadata" name="Validate Affymetrix metadata" version="1.0.0"> + <description>for 96 well plate</description> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/validate_affy_metadata.py' +--input '$input' +--output '$output']]></command> + <inputs> + <param name="input" type="data" format="tabular" label="Affymetrix 96 well plate metadata file"> + <validator type="expression" message="96 well plate data must have 32 columns and no more than 96 lines of data"><![CDATA[value is not None and value.metadata.columns==32 and value.metadata.data_lines<=96]]></validator> + </param> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input" value="affy_metadata.tabular" ftype="tabular"/> + <output name="output" file="affy_metadata.tabular" ftype="tabular"/> + </test> + </tests> + <help> +**What it does** + +Validates an Affymetrix metadata file for 96 well plate data. These files consist of 32 columns and no more than 96 data lines. +The tool will output the input file if it is valid. + +----- + +**Columns** + + * user_specimen_id + * field_call + * bcoral_genet_id + * bsym_genet_id + * reef + * region + * latitude + * longitude + * geographic_origin + * colony_location + * depth + * disease_resist + * bleach_resist + * mortality + * tle + * spawning + * collector_last_name + * collector_first_name + * org + * collection_date + * contact_email + * seq_facility + * array_version + * public + * public_after_date + * sperm_motility + * healing_time + * dna_extraction_method + * dna_concentration + * registry_id + * result_folder_name + * plate_barcode + </help> + <citations> + <citation type="bibtex"> + @misc{None, + journal = {None}, + author = {Baums I}, + title = {Manuscript in preparation}, + year = {None}, + url = {http://baumslab.org} + </citation> + </citations> +</tool> +