gffmunger-config.yml

# This file contains configuration for the gffmunger application
# All options intended for the end user are specified via the CLI
# The options here are for whomsoever maintains a particular installation of the application


# When attributes *values* are lists (e.g. a 'product' that has more than one 'term' within the value),
# gffutils will by default sort the list. Set this flag to true to preserve the original order.
# (This does *not* affect the order of the attributes themselves)
keep_attr_value_order   : True

# By default, attributes are cut from the polypeptide feature and pasted to the feature from which the polypeptide
# derives (e.g. mRNA).
# List here any attribites that should *not* be transferred, but should instead be left in the polypeptide feature.
attr_not_transferred : 
                        - 'ID'
                        - 'Derives_from'
                        - 'Parent'

# The fields used to sort the features in the GFF3 output
# (seqid, source, featuretype, start, end, score, strand, frame, attributes, extra)
output_feature_sort  :
                        - 'seqid'
                        - 'start'
                        
# Features of these types are checked to see if anotations have been transferred to them.
# If not, a warning is sent to the logger.
# List of features that are expected to have annotation.
# Warnings are logged in the event that
# - an annotation is transferred to a feature of a type *not* in this list
# - the output GFF3 contains a feature of a type in this list which
#   did not have an annotation transferred to it from a polypeptide
annotated_feature_types :  
                           - 'mRNA'
                           - 'pseudogenic_transcript'

# This flag can be used to restrict the transfer of annotations from polypeptides only to mRNA.
# Set it to flase to transfer annotations from polypeptides to features of all types.
# Expect that this will be False, but this flag exists because of a slight ambiguity in the spec.,
# which makes it desirable to switch behaviour in a hurry ;-)
only_transfer_anot_to_mRNA : False

# For use of genometools to validate GFF3 input.
gt_path                 : '/usr/bin/gt'
gff3_validator_tool     : 'gff3validator'
gff3_validation_timeout : 60

# Working filenames; shouldn't need to edit these unless their location offends.
# A UUID is substituted for <uid> to avoid clashes if there are concurrent gffmunder processes.
gffutils_db_filename : '/tmp/gffutils.<uid>.db'
temp_input_file      : '/tmp/gffmunger_input.<uid>.gff3'

# Causes features in the input GFF3 to be read into a read_features_to_buffer.
# currently Features are imported to and exported from gffutils so this should be False, but if you find a reason
# for storing "raw" Features in memory you can make this true (you'll see the necessary code is all still in place)
read_features_to_buffer : False