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 |