(tf%ddlZddlmcmZddlZddlmZddl Z ddl m Z ddl m Z ddl m Z ddlmZej ej"dej$ddd ej$d dd ej$d dd ej$ddd ej$ddd ej$ddd ej$ddddej$ddd ej$ddddej$ddd  d#d Z d#d!Zd"Zy)$N)fill_filetype_and_datatype) import_file) get_temp_dir)_startfilenamez --hg-namedefaultz8The name of the higlass container to import this file to)rhelpz --filetypez(The type of file to ingest (e.g. cooler)z --datatypez0The data type of in the input file (e.g. matrix)z --assemblyz(The assembly that this data is mapped toz--namezThe name to use for this filez--uidzThe uuid to use for this filez --no-uploadTzYDo not copy the file to the media directory. File must already be in the media directory.)ris_flagr z--chromsizes-filenamez8A set of chromosome sizes to use for bed and bedpe filesz --has-headerFzYDoes the input file have column header information (only relevant for bed or bedpe files)z--project-namez;Group this tileset with others by specifying a project namec .t|||||||||| | y)z Ingest a dataset N)_ingest) rhg_namefiletypedatatypeassemblynamechromsizes_filename has_headeruid no_upload project_names _/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/higlass_manage/ingest.pyingestr s.p    c | t|| sGt j |s2t j |std|tjyt|||\}}t|} t|||||| | \} }t|| |||||| | S#t$rtdt|YwxYw)Nz HiGlass not running. Starting...)r zFile not found:file) r Exceptionprintropexistsislinksysstderrraggregate_filer) rr rrrrrrrrrtemp_dir to_imports rr r Ts W bii1"))H:M  ;6h(SXxG$H*Y     -   01w s B B;:B;c |dk(r|rtdtj||tdtjyt j |t j|dz}tdtj|||d|ddd|d d |}d }||fS|d k(r|rtdtj||tdtjyt j ||dz}tdj|tj|||d|dd|d  |}d}||fS||fS)NbedfilezcBedfile files need to be aggregated and cannot be linked. Consider not using the --link-file optionrzAn assembly or set of chromosome sizes is required when importing bed files. Please specify one or the other using the --assembly or --chromsizes-filename parametersz.beddbzAggregating bedfilerandom2ri)importance_columnr chromosome max_per_tile delimiterroffset tile_sizebeddbbedpezaBedpe files need to be aggregated and cannot be linked. Consider not using the --link-file optionz.bed2ddbz"Aggregating bedpe (output_file: {})r+rr,r-rr0bed2ddb) rr"r#rrjoinntpathbasenamecca_bedfileformat_bedpe) rrrrrrtmp_dir output_filer&s rr$r$sy9 uZZ    3 ; xZZ  gggvx'@8'KL  #$   &! 3  8$$ W  sZZ    3 ; xZZ  gggx*'<=  299+FG   &! 3  8$$(##r) NNNNNFNNN)clickclodius.cli.aggregatecli aggregater7r5os.pathpathrr"higlass_manage.commonrrrhiglass_manage.startrcommandargumentoptionrr r$rrrIs ##  <-.'    C $%O$%W$%Oh+JK gt*IJ    d    C    d    F        KL PD    0fI$r