subtom_cat_motls

Concatenate motive lists and print on the standard output.

This MOTL manipulation script uses one MATLAB compiled scripts below:

subtom_cat_motls

Options

Directories

scratch_dir: Absolute path to the folder with the input to be processed. Other paths are relative to this one.
mcr_cache_dir: Absolute path to MCR directory for the processing.
exec_dir: Directory for executables

Variables

cat_exec: Concatenate MOTLs executable

File Options

input_motl_fns: Relative path and filename(s) of the input MOTL files to be concatenated. You can use shell wildcard characters * and ? to specify a given number of files and they will be expanded or you can just list the files one by one.
output_motl_fn: Relative path and name of the output MOTL file. If you are not going to write an output file just set this variable to ‘’
output_star_fn: Relative path and name of the output STAR file. If you are not going to write an output file just set this variable to ‘’

Concatenate Options

write_motl: If you want to write out the concatenated MOTL files set this to 1, however if you just want to print the MOTL contents to the screen, set this to 0.
write_star: If you want to write out the concatenated STAR file set this to 1, however if you just want to print the MOTL contents to the screen, set this to 0.
sort_row: If you want to have the output MOTL file sorted by a particular field then specify it here. If the given value is not a value between 1-20 then the output MOTL file will be sorted arbitrarily based on the dir command in Matlab.
do_quiet: If you just want to write output to files and not print to the screen set this to 1, however if you want to see the output printed to the screen leave this set to 0.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

cat_exec="${exec_dir}/MOTL/subtom_cat_motls"

input_motl_fns=("combinedmotl/allmotl_1_tomo_1.em" \
                "combinedmotl/allmotl_1_tomo_2.em" \
                "combinedmotl/allmotl_1_tomo_3.em" \
                "combinedmotl/allmotl_1_tomo_4.em" \
                "combinedmotl/allmotl_1_tomo_5.em")

output_motl_fn="combinedmotl/allmotl_1.em"

output_star_fn="combinemotl/allmotl_1.star"

write_motl=1

write_star=0

sort_row=4

do_quiet=1