hyb_check

Read one or more ‘.hyb’ format files and check for errors.

This utility reads in one or more files in hyb-format (see the hybkit Hyb File Specification) and uses hybkit’s internal file error checking to check for errors. This can be useful as an intial preparation step for further analyses.

Example system calls
hyb_check -i my_file_1.hyb
hyb_check -i ../my_file_2.hyb /path/to/myfile_3.hyb -v --custom_flags myflag
usage: hyb_check [-h] -i PATH_TO/MY_FILE.HYB [PATH_TO/MY_FILE.HYB ...]
                 [-v | -s] [--mirna_types MIRNA_TYPES [MIRNA_TYPES ...]]
                 [--custom_flags CUSTOM_FLAGS [CUSTOM_FLAGS ...]]
                 [--hyb_placeholder HYB_PLACEHOLDER]
                 [--reorder_flags {True,False}]
                 [--allow_undefined_flags [{True,False}]]
                 [--allow_unknown_seg_types [{True,False}]]
                 [--check_complete_seg_types [{True,False}]]
                 [--hybformat_id [{True,False}]]
                 [--hybformat_ref [{True,False}]]

Named Arguments

-i, --in_hyb

REQUIRED path to one or more hyb-format files with a “.hyb” suffix for use in the evaluation.

-v, --verbose

Print verbose output during run.

Default: False

-s, --silent

Print no output during run.

Default: False

Hyb Record Settings

--mirna_types

“seg_type” fields identifying a miRNA

Default: [‘miRNA’, ‘microRNA’]

--custom_flags

Custom flags to allow in addition to those specified in the hybkit specification.

Default: []

--hyb_placeholder

placeholder character/string for missing data in hyb files.

Default: “.”

--reorder_flags

Possible choices: True, False

Re-order flags to the hybkit-specificiation order when writing hyb records.

Default: True

--allow_undefined_flags

Possible choices: True, False

Allow use of flags not definied in the hybkit-specificiation order when reading and writing hyb records. As the preferred alternative to using this setting, the –custom_flags arguement can be be used to supply custom allowed flags.

Default: False

--allow_unknown_seg_types

Possible choices: True, False

Allow unknown segment types when assigning segment types.

Default: False

--check_complete_seg_types

Possible choices: True, False

Check every segment possibility when assigning segment types, rather than breaking after the first match is found. If True, finding segment types is slower but better at catching errors.

Default: False

Hyb File Settings

--hybformat_id

Possible choices: True, False

The Hyb Software Package places further information in the “id” field of the hybrid record that can be used to infer the number of contained read counts. When set to True, the identifiers will be parsed as: “<read_id>_<read_count>”

Default: False

--hybformat_ref

Possible choices: True, False

The Hyb Software Package uses a reference database with identifiers that contain sequence type and other sequence information. When set to True, all hyb file identifiers will be parsed as: “<gene_id>_<transcript_id>_<gene_name>_<seg_type>”

Default: False