+
+ +
+

HQTB Configuration File

+

Below, the configuration file with the underlying default, is listed.

+
# information about the genome to be used to generate the new model
+subject:
+    annotated_genome: __USER__
+    full_sequence: __USER__
+
+# information about the template model/genome
+template:
+    annotated_genome: __USER__
+    model: __USER__
+    namespace: BiGG
+
+# information about the output
+out:
+    dir: ./specimen_run/
+    name: specimen_model
+    memote: False
+
+# data(bases) required to run the program
+data:
+    # if this parameter is set, assumes that the directory structure from setup
+    # is used and uses this path to a directory as the parent folder for the
+    # following paths (assumes all data paths are relative ones)
+    data_direc: null
+    # required
+    diamond: __USER__
+    # needed but potentially downloaded
+    mnx_chem_prop: MetaNetX/chem_prop.tsv
+    mnx_chem_xref: MetaNetX/chem_xref.tsv
+    mnx_reac_prop: MetaNetX/reac_prop.tsv
+    mnx_reac_xref: MetaNetX/reac_xref.tsv
+    # optional, but good and manual
+    ncbi_map: null
+    ncbi_dat: null
+    # optional for directionality control
+    biocyc: null
+    # optional:
+    #   the pan-core model is used for analysis and if no universal model
+    #   is given, also for gapfilling
+    #   if the pan-core model is too small for useful gapfilling, use an
+    #   additional universal model for gapfilling
+    #   if none if given gapfilling (and core-pan analysis) is skipped
+    universal: null
+    pan-core: null
+
+# paramters for the single steps of the pipeline
+parameters:
+    bidirectional_blast:
+        # default should suffice except special cases
+        template_name: null
+        input_name: null
+        temp_header: null
+        in_header: null
+        # can be set by user if wanted, but not necessary
+        sensitivity: more-sensitive
+
+    generate_draft_model:
+        edit_names: no
+        pid: 80.0
+        medium: default
+
+    refinement_extension:
+        # default (usually) fine
+        id: locus_tag
+        # default fine
+        sensitivity: more-sensitive
+        # default alright but good to edit for trying different options
+        coverage: 95.0
+        pid: 90.0
+        # default almost needed, except for special cases
+        exclude_dna: True
+        exclude_rna: True
+
+    refinement_cleanup:
+        # default as standart
+        check_dupl_reac: True
+        check_dupl_meta: default
+        remove_unused_meta: False
+        remove_dupl_reac: True
+        remove_dupl_meta: True
+        # current default means no gapfilling
+        media_gap: null
+
+    refinement_annotation:
+        # for KEGG pathway annotation
+        viaEC: False
+        viaRC: False
+
+    refinement_smoothing:
+        # useful
+        mcc: skip
+        # ECG correction
+        egc: null
+        # depend on organism (current: Klebsiella )
+        dna_weight_frac: 0.023
+        ion_weight_frac: 0.05
+
+    # validation:
+        # default should suffice
+
+    analysis:
+        # default is currently only option
+        pc_based_on: id
+        # can be default but useful to edit
+        media_analysis: __USER__ # edit to fit a default media config file
+        test_aa_auxotrophies: True
+        # perform pathway analysis with KEGG
+        pathway: True
+
+# options for performance
+performance:
+    threads: 2
+    # for the gapfilling, if iterations and chunk_size are set (not null)
+    # use a heuristic for faster performance:
+    #     instead of using all reactions that can be added at once,
+    #     run x interations of gapfilling with n-size randomised chunks of reactions
+    gapfilling:
+        iterations: 3
+        chunk_size: 2000
+
+
+
+ + +
+