Console Mode Cheat-Sheet

TRANSIT has the capability of running in Console mode, without depending on libraries for GUI elements. More hands-on users can utilize transit in this manner to quickly run multiple jobs in parallel. Below is brief

Analysis Methods

TRANSIT has the capacity of determining essentiality within a single condition, or between conditions to determine conditional essentiality.

Single Condition Essentiality

Analysis methods in a single condition require at least 4 positional arguments followed by optional flags.

python transit.py <method> <wig-files> <annotation> <output>

Positional Arguments	Definition
<method>	Short name of the desired analysis method e.g. gumbel, resampling, hmm
<wig-files>	Comma-separated list of paths read-count datasets in .wig format
<annotation>	Path to the annotation in .prot_table or .GFF3 format.
<output>	Desired path and name of the output file

Example

python transit.py gumbel glycerol_H37Rv_rep1.wig,glycerol_H37Rv_rep2.wig H37Rv.prot_table glycerol_TTR.txt -r Sum -s 10000

Conditional Essentiality

Analysis methods between two conditions require at least 5 positional arguments followed by optional flags.

Positional Arguments	Definition
<method>	Short name of the desired analysis method e.g. gumbel, resampling, hmm
<control-files>	Comma-separated list of paths read-count files in .wig format for the control datasets
<experimental-files>	Comma-separated list of paths read-count files in .wif format for the experimental datasets
<annotation>	Path to the annotation in .prot_table or .GFF3 format.
<output>	Desired path and name of the output file

Example

python transit.py resampling glycerol_H37Rv_rep1.wig,glycerol_H37Rv_rep2.wig cholesterol_H37Rv_rep1.wig,cholesterol_H37Rv_rep2.wig H37Rv.prot_table glycerol_TTR.txt -n TTR -s 10000

Normalizing datasets

TRANSIT also allows users to normalize datasets and export them afterwards. To normalize datasets, 3 positional arguments followed by optional flags.

Positional Arguments

Positional Arguments	Definition
<wig-files>	Comma-separated list of paths read-count datasets in .wig format
<annotation>	Path to the annotation in .prot_table or .GFF3 format.
<output>	Desired path and name of the output file

Optional Arguments

Argument	Definition
-n <String>	Short name of the normalization method, e.g. -n TTR

Example

python transit.py norm glycerol_H37Rv_rep1.wig,glycerol_H37Rv_rep2.wig H37Rv.prot_table glycerol_TTR.txt -n TTR