# HG changeset patch # User galaxyp # Date 1488389410 18000 # Node ID 5e6e9b779e4db6a69b50dbeb52b14e4395980589 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8 diff -r 000000000000 -r 5e6e9b779e4d SKIP_TOOLS_FILE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer diff -r 000000000000 -r 5e6e9b779e4d TOFCalibration.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TOFCalibration.xml Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,220 @@ + + + + + Applies time of flight calibration. + + TOFCalibration + macros.xml + + + + + TOFCalibration + +#if $param_in: + -in $param_in +#end if +#if $param_out: + -out $param_out +#end if +#if $param_ext_calibrants: + -ext_calibrants $param_ext_calibrants +#end if +#if $param_ref_masses: + -ref_masses $param_ref_masses +#end if +#if $param_tof_const: + -tof_const $param_tof_const +#end if +#if $param_peak_data: + -peak_data +#end if +#if $param_algorithm_PeakPicker_signal_to_noise: + -algorithm:PeakPicker:signal_to_noise $param_algorithm_PeakPicker_signal_to_noise +#end if +#if $param_algorithm_PeakPicker_peak_width: + -algorithm:PeakPicker:peak_width $param_algorithm_PeakPicker_peak_width +#end if +#if $param_algorithm_PeakPicker_estimate_peak_width: + -algorithm:PeakPicker:estimate_peak_width +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if + #if $adv_opts.param_algorithm_PeakPicker_centroid_percentage: + -algorithm:PeakPicker:centroid_percentage $adv_opts.param_algorithm_PeakPicker_centroid_percentage +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor: + -algorithm:PeakPicker:fwhm_lower_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_lower_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor: + -algorithm:PeakPicker:fwhm_upper_bound_factor $adv_opts.param_algorithm_PeakPicker_fwhm_upper_bound_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_iterations: + -algorithm:PeakPicker:optimization:iterations $adv_opts.param_algorithm_PeakPicker_optimization_iterations +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position: + -algorithm:PeakPicker:optimization:penalties:position $adv_opts.param_algorithm_PeakPicker_optimization_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width: + -algorithm:PeakPicker:optimization:penalties:left_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width: + -algorithm:PeakPicker:optimization:penalties:right_width $adv_opts.param_algorithm_PeakPicker_optimization_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height: + -algorithm:PeakPicker:optimization:penalties:height $adv_opts.param_algorithm_PeakPicker_optimization_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz: + -algorithm:PeakPicker:optimization:2d:tolerance_mz $adv_opts.param_algorithm_PeakPicker_optimization_2d_tolerance_mz +#end if + #if $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance: + -algorithm:PeakPicker:optimization:2d:max_peak_distance $adv_opts.param_algorithm_PeakPicker_optimization_2d_max_peak_distance +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound: + -algorithm:PeakPicker:thresholds:peak_bound $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level: + -algorithm:PeakPicker:thresholds:peak_bound_ms2_level $adv_opts.param_algorithm_PeakPicker_thresholds_peak_bound_ms2_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_correlation: + -algorithm:PeakPicker:thresholds:correlation $adv_opts.param_algorithm_PeakPicker_thresholds_correlation +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level: + -algorithm:PeakPicker:thresholds:noise_level $adv_opts.param_algorithm_PeakPicker_thresholds_noise_level +#end if + #if $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius: + -algorithm:PeakPicker:thresholds:search_radius $adv_opts.param_algorithm_PeakPicker_thresholds_search_radius +#end if + #if $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing: + -algorithm:PeakPicker:wavelet_transform:spacing $adv_opts.param_algorithm_PeakPicker_wavelet_transform_spacing +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_deconvolution: + -algorithm:PeakPicker:deconvolution:deconvolution +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold: + -algorithm:PeakPicker:deconvolution:asym_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_asym_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width: + -algorithm:PeakPicker:deconvolution:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width: + -algorithm:PeakPicker:deconvolution:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling: + -algorithm:PeakPicker:deconvolution:scaling $adv_opts.param_algorithm_PeakPicker_deconvolution_scaling +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold: + -algorithm:PeakPicker:deconvolution:fitting:fwhm_threshold $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_fwhm_threshold +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs: + -algorithm:PeakPicker:deconvolution:fitting:eps_abs $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_abs +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel: + -algorithm:PeakPicker:deconvolution:fitting:eps_rel $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_eps_rel +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration: + -algorithm:PeakPicker:deconvolution:fitting:max_iteration $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_max_iteration +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position: + -algorithm:PeakPicker:deconvolution:fitting:penalties:position $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_position +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height: + -algorithm:PeakPicker:deconvolution:fitting:penalties:height $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_height +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:left_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_left_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width: + -algorithm:PeakPicker:deconvolution:fitting:penalties:right_width $adv_opts.param_algorithm_PeakPicker_deconvolution_fitting_penalties_right_width +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:max_intensity $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_max_intensity +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_stdev_factor $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_stdev_factor +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_max_percentile $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_max_percentile +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:auto_mode $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_auto_mode +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:win_len $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_win_len +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:bin_count $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_bin_count +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:stdev_mp $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_stdev_mp +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:min_required_elements $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_min_required_elements +#end if + #if $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window: + -algorithm:PeakPicker:SignalToNoiseEstimationParameter:noise_for_empty_window $adv_opts.param_algorithm_PeakPicker_SignalToNoiseEstimationParameter_noise_for_empty_window +#end if +#end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Applies time of flight calibration. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_TOFCalibration.html + diff -r 000000000000 -r 5e6e9b779e4d datatypes_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 5e6e9b779e4d filetypes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,29 @@ +# CTD type # Galaxy type # Long Galaxy data type # Mimetype +csv tabular galaxy.datatypes.tabular:Tabular +fasta fasta galaxy.datatypes.sequence:Fasta +FASTA fasta galaxy.datatypes.sequence:Fasta +ini txt galaxy.datatypes.data:Text +txt txt galaxy.datatypes.data:Text +options txt galaxy.datatypes.data:Text +grid grid galaxy.datatypes.data:Grid +html html galaxy.datatypes.text:Html text/html +HTML html galaxy.datatypes.text:Html text/html +TraML traml galaxy.datatypes.proteomics:TraML application/xml +traML traml galaxy.datatypes.proteomics:TraML application/xml +XML xml galaxy.datatypes.xml:GenericXml application/xml +consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml +edta tabular galaxy.datatypes.tabular:Tabular +featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml +idXML idxml galaxy.datatypes.proteomics:IdXM application/xml +mzML mzml galaxy.datatypes.proteomics:MzML application/xml +mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml +pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml +qcML qcml galaxy.datatypes.xml:GenericXml application/xml +trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml +tsv tabular galaxy.datatypes.tabular:Tabular +xsd txt galaxy.datatypes.data:Text +mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml +msp msp galaxy.datatypes.proteomics:Msp +mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml +png png galaxy.datatypes.images:Png image/png +mgf mgf galaxy.datatypes.proteomics:Mgf \ No newline at end of file diff -r 000000000000 -r 5e6e9b779e4d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,35 @@ + + + + + openms + xtandem + fido + msgf_plus + + + + + + + + + + + + doi:10.1186/1471-2105-9-163 + + + + + + + + + + + + + + + diff -r 000000000000 -r 5e6e9b779e4d readme.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,165 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * http://open-ms.sourceforge.net + + +Generating OpenMS wrappers +========================== + + * install OpenMS (you can do this automatically through the Tool Shed) + * create a folder called CTD + * inside of your new installed openms/bin folder, execute the following command: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + + * clone or install CTDopts + + ```bash + git clone https://github.com/genericworkflownodes/CTDopts + ``` + + * add CTDopts to your `$PYTHONPATH` + + ```bash + export PYTHONPATH=/home/user/CTDopts/ + ``` + + * clone or install CTD2Galaxy + + ```bash + git clone https://github.com/blankclemens/CTD2Galaxy.git + ``` + + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. + + ```bash + python generator.py \ + -i /PATH/TO/YOUR/CTD/*.ctd \ + -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ + -d datatypes_conf.xml -g openms \ + -b version log debug test no_progress threads \ + in_type executable myrimatch_executable \ + fido_executable fidocp_executable \ + omssa_executable pepnovo_executable \ + xtandem_executable param_model_directory \ + java_executable java_memory java_permgen \ + -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ + -s PATH/TO/SKIP_TOOLS_FILES.txt + ``` + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + + ``` + sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml + sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml + sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml + sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml + ``` + + * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + + ``` + * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit + + and change it to + + -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + + * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + + + + * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. + + ``` + + + + + + + ``` + + + * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`: + * SeedListGenerator + * SpecLibSearcher + * MapAlignerIdentification + * MapAlignerPoseClustering + * MapAlignerSpectrum + * MapAlignerRTTransformer + + * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: + * OMSSAAdapter + * MyrimatchAdapter + + * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: + * PepNovoAdapter + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + diff -r 000000000000 -r 5e6e9b779e4d repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,4 @@ + + + + diff -r 000000000000 -r 5e6e9b779e4d test-data/DecoyDatabase_input.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_input.fasta Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,146 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK +QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ +NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR +SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG +DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM +TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL +DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE +NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE +EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW +KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT +IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF +MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK +EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ +DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS +TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI +ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA +CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS +DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP +PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR +RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY +VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN +VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT +KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC +LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA +YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR +QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK +YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT +PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA +MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV +ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS +EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN +FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG +YQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS +GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG +SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK +SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS +LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR +LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV +KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL +ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED +IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV +QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE +TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG +VLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGLFLRYDNLNHSGEDFLGTKEV +SLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDE +LLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKH +SFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGRIQVPEETYLIL +KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ +LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP +DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR +DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI +LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC +ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV +NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT +TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL +PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP +LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK +QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL +PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL +HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG +AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL +NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI +LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED +FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA +PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS +ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL +LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE +IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR +ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF +EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP +ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF +FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK +ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR +RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE +QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL +SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV +AASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR +QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD +GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ +NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF +SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA +NHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ +EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK +EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP +AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA +LLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD +LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT +TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY +IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE +GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ +TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC +HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI +FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR +NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR +SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI diff -r 000000000000 -r 5e6e9b779e4d test-data/DecoyDatabase_output.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_output.fasta Wed Mar 01 12:30:10 2017 -0500 @@ -0,0 +1,228 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES +RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT +MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG +CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK +REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS +GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW +CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL +EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE +HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ +FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR +QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL +VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD +YAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK +ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV +LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE +TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL +VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK +EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL +RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA +PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET +FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA +SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST +GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA +PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS +FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ +VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH +QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN +GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA +ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA +ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGL +FLRYDNLNHSGEDFLGTKEVSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTY +MAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKHSFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASR +MDSTGVSGRIQVPEETYLILKDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 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