Package: hca2scea
hca2sceaA tool to assist in the automatic conversion of an hca metadata spreadsheet to scea metadata MAGE-TAB files.Installationpip install hca2sceaDescriptionThe tool takes as input an HCA metadata spreadsheet and converts the metadata to SCEA MAGE-TAB files which are then saved to an output directory.UsageTo run it as a package, after installing it via pip:$hca2scea-husage:hca2scea[-h]-sSPREADSHEET-idPROJECT_UUID-studySTUDY[-name{cs_name,cs_id,sp_name,sp_id,other}]-acACCESSION_NUMBER-cCURATORS[CURATORS...]-et{baseline,differential}[-facs]-fEXPERIMENTAL_FACTORS[EXPERIMENTAL_FACTORS...]-pdPUBLIC_RELEASE_DATE-hdHCA_UPDATE_DATE[-oOUTPUT_DIR][-zip]runhca->sceatool

optionalarguments:-h,--helpshowthishelpmessageandexit-sSPREADSHEET,--spreadsheetSPREADSHEETPleaseprovideapathtotheHCAprojectspreadsheet.-idPROJECT_UUID,--project_uuidPROJECT_UUIDPleaseprovideanHCAingestprojectsubmissionid.-studySTUDYPleaseprovidetheSRAorENAstudyaccession.-name{cs_name,cs_id,sp_name,sp_id,other}Pleaseindicatewhichfieldtouseasthesamplename.cs=cellsuspension,sp=specimen.-acACCESSION_NUMBER,--accession_numberACCESSION_NUMBERProvideanE-HCADaccessionnumber.Pleasefindthenextsuitableaccessionnumberbycheckingthegoogletrackersheet.-cCURATORS[CURATORS...],--curatorsCURATORS[CURATORS...]spaceseparatednamesofcurators-et{baseline,differential},--experiment_type{baseline,differential}Pleaseindicatewhetherthisisabaselineordifferentialexperimentaldesign-facsPleasespecifyifFACSwasusedtoisolatesinglecells.-fEXPERIMENTAL_FACTORS[EXPERIMENTAL_FACTORS...],--experimental_factorsEXPERIMENTAL_FACTORS[EXPERIMENTAL_FACTORS...]spaceseparatedlistofexperimentalfactors-pdPUBLIC_RELEASE_DATE,--public_release_datePUBLIC_RELEASE_DATEPleaseenterthepublicreleasedateinthisformat:YYYY-MM-DD-hdHCA_UPDATE_DATE,--hca_update_dateHCA_UPDATE_DATEPleaseenterthelasttimetheHCAprohectsubmissionwasupdatedinthisformat:YYYY-MM-DD-oOUTPUT_DIR,--output_dirOUTPUT_DIRProvidefullpathtopreferredoutputdir-zip,--zip_formatPleaseindicatewhetheryouwouldlikethescripttooutputalltxtfilesseparatelyortogetherin1zipfile.```Torunitasapythonmodule:```shellscriptcd/path-to/hca2scea
python-mhca-to-scea-tools.hca_to_scea.hca2scea-hArgumentsArgumentArgument nameDescriptionRequired?-sHCA spreadsheetPath to HCA spreadsheet (.xlsx)yes-idHCA project uuidThis is added to the 'secondary accessions' field in idf fileyes-cCurator initialsHCA Curator initials. Space-separated list.yes-acaccession numberProvide an SCEA accession number (integer).yes-etExperiment typeMust be 1 of [differential,baseline]yes-fFactor valueA space-separated list of user-defined factor values e.g. age diseaseyes-pdDataset publication dateprovide in YYYY-MM-DD E.g. from GEOyes-hdHCA last update dateprovide in YYYY-MM-DD The last time the HCA project was updated in ingest  UI (production)yes-studystudy accession (SRPxxx)The study accession will be used to find the paths to the fastq files for the given runsyes-nameHCA name fieldWhich HCA field to use for the biomaterial names columns. Must be 1 ofno[cs_name, cs_id, sp_name, sp_id, other] where cs indicates cell suspension and sp indicatesspecimen from organism. Default is cs_name.-facsoptional argumentIf FACS was used as a single cell isolation method, indicate this by adding the -facs argument.no-ooptional argumentAn output dir path can optionally be provided. If it does not exist, it will be created.no-zipoptional argumentIndicate if you would like the resulting output files to be output in a single zip file.noDefinitionsFactor valuesA factor value is a chosen experimental characteristic which can be used to group or differentiate samples. Multiple factor values can be entered and should be chosen from the following list.Known disease(s)Development stageOrganOrgan partSelected cell type(s)IndividualThere must be at least 1 factor value. If you cannot identify a factor value i.e. all donors and samples share the same metadata with respect to the above list of factor values, then enter 'Individual'.Datasets with more than 1 technolgoy type are not eligible for SCEA. Therefore, technology type is not a valid factor value.Experiment typeAn experiment with samples which can be grouped or differentiatied by a factor value is classified as 'differential'. The list of possible factor values can be found above.If 1 or more factor values other than 'Individual' is identified, then the experiment type should be 'Differential'. If the only factor value is 'Individual', then the experiment type should be 'Baseline'.Related E-HCAD-IDIf the project has been split into two separate E-HCAD datasets, due to different technologies being used in the same project, or any other reason, then enter the E-HCAD-ID for the other dataset here. Example: E-HCAD-50.ExamplesRequired arguments onlypython3 hca2scea.py -s /home/aday/GSE111976-endometrium_MC_SCEA.xlsx -id 379ed69e-be05-48bc-af5e-a7fc589709bf -study SRP135922 -ac 50 -c AD -et differential -f menstrual cycle day -pd 2021-06-29 -hd 2021-02-12Specify optional name argumentpython3 hca2scea.py -s /home/aday/GSE111976-endometrium_MC_SCEA.xlsx -id 379ed69e-be05-48bc-af5e-a7fc589709bf -study SRP135922 -name cs_name -ac 50 -c AD -et differential -f menstrual cycle day -pd 2021-06-29 -hd 2021-02-12Specify that FACS was usedpython3 hca2scea.py -s /home/aday/GSE111976-endometrium_MC_SCEA.xlsx -id 379ed69e-be05-48bc-af5e-a7fc589709bf -study SRP135922 -ac 50 -c AD -et differential -f menstrual cycle day -pd 2021-06-29 -hd 2021-02-12 -facsSpecify optional output dirpython3 hca2scea.py -s /home/aday/GSE111976-endometrium_MC_SCEA.xlsx -id 379ed69e-be05-48bc-af5e-a7fc589709bf -study SRP135922 -ac 50 -c AD -et differential -f menstrual cycle day -pd 2021-06-29 -hd 2021-02-12 -o my_output_dirDeveloper NotesDeveloping Code in Editable ModeUsingpip's editable mode, projects using hca-to-scea as a dependency can refer to the latest code in this repository
directly without installing it through PyPI. This can be done either by manually cloning the code
base:pip install -e path/to/hca2sceaor by havingpipdo it automatically by providing a reference to this repository:pip install -e \
git+https://github.com/ebi-ait/hca-to-scea-tools.git\
#egg=hca2sceaPublish to PyPICreate PyPI Account through theregistration page.Take note that PyPI requires email addresses to be verified before publishing.Package the project for distribution.python setup.py sdistInstallTwinepip install twineUpload the distribution package to PyPI.twine upload dist/*Runningpython setup.py sdistwill create a package in thedistdirectory of the project
base directory.