pyrpipe_engine module

The pyrpipe_engine module is the key module responsible for handling execution of all the Unix commands. The Runnable class calls the execute_comand() function in the pyrpipe_engine module. All the commands executed via the pyrpipe_engine module are automatically logged. All the functions responsible for executing Unix command are “decorated” with the dryable method, which allows using the –dry-run flag on any function using the pyrpipe_engine module.

The pyrpipe_engine can be directly used to execute Unix command or to import output of a Unix command in python. The functions defined in the pyrpipe_engine module are described below.

Function Description
dryable() A decorater to make Unix functions dry when –dry-run is specified
parse_cmd() Parse a Unix command and return command as string
get_shell_output() Execute a command and return return code and output. These commands are not logged
get_return_status() Execute command and return status of the command
execute_commandRealtime() Execute a command and print output in realtime
execute_command() Execute a command and log the status. This is the function used by the Runnable class.
is_paired() Check is sra file paired or single end. Uses fastq-dump
get_program_path() Return path to a Unix command
check_dependencies() Check a list of dependencies are present in Unix path
delete_files() Delete files, rm command
move_file() Moves files, mv command

pyrpipe_utils module

The pyrpipe_utils module define multiple helpful functions. Functions defined in the pyrpipe_utils modules are extensively used throughout pyrpipe modules. Users can directly utilize these fuctions in their code and expedite development. A description of these functions is provided below.

Function Description
pyrpipe_print() Prints in color
get_timestamp() Return current timestamp
check_paths_exist() Return true is paths are valid
check_files_exist() Return True if files are valid
check_hisatindex() Verify valid Hisat2 index
check_kallistoindex() Verify kallisto index
check_salmonindex() Verify salmon index
check_starindex() Verify STAR index
check_bowtie2index() Verify Bowtie2 index
get_file_size() Return file size in human readable format
parse_java_args() Parse tool options in JAVA style format
parse_unix_args() Parse tool options in Unix style format
get_file_directory() Return a file’s directory
get_filename() Return filename with extension
get_fileext() Return file extension
get_file_basename() Return filename, without extension
mkdir() Create a directory
get_union() Return union of lists
find_files() Search files using regex patterns
get_mdf() Compute and return MD5 checksum of a file