get-gtf-from-predictions

Convert Rp-Bp ORF predictions (BED12+) into GTF. The “thick_start” and “thick_end” fields are used to determine the CDS GTF entries. Only creates “exon” and “CDS” entries. Additional columns are included as attributes.

usage: get-gtf-from-predictions [-h] [--log-file LOG_FILE]
                                [--enable-ext-logging] [--log-stdout]
                                [--no-log-stderr]
                                [--logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                [--file-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                [--stdout-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                [--stderr-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                [--num-cpus NUM_CPUS] [--mem MEM]
                                [--time TIME] [--partitions PARTITIONS]
                                [--no-output] [--no-error]
                                [--stdout-file STDOUT_FILE]
                                [--stderr-file STDERR_FILE] [--do-not-call]
                                [--use-slurm]
                                [--mail-type [{NONE,BEGIN,END,FAIL,REQUEUE,ALL,STAGE_OUT,TIME_LIMIT,TIME_LIMIT_90,TIME_LIMIT_80,TIME_LIMIT_50,ARRAY_TASKS} ...]]
                                [--mail-user MAIL_USER]
                                bed gtf

Positional Arguments

bed

The bed12 file. It must conform to the style expected by utils.bed_utils.

gtf

The (output) gtf file.

logging options

--log-file

Log file (logging is redirected to this file, in addition to stdout and stderr, if specified).

Default: ''

--enable-ext-logging

Enable logging for external programs that may be disabled by default, e.g. CmdStanPy.

Default: False

--log-stdout

Log to stdout (in addition to a file and stderr, if specified).

Default: False

--no-log-stderr

Do not send logging to stderr.

Default: False

--logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for all logs.

Default: 'WARNING'

--file-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for the log file. This option overrides --logging-level.

Default: 'NOTSET'

--stdout-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stdout. This option overrides --logging-level.

Default: 'NOTSET'

--stderr-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stderr. This option overrides --logging-level.

Default: 'NOTSET'

slurm options

--num-cpus

The number of CPUs to use (not only for SLURM). For STAR, --num-cpus are threads, but in general, this is number of processes to spawn. This value should not be greater than the number of cores available. When used with SLURM, this is equivalent to: --ntasks 1 --cpus-per-task <num-cpus>.

Default: 1

--mem

Real memory required (per node), mostly for STAR genome indexing (not only for SLURM). When used with SLURM, this is equivalent to: --mem=<mem>.

Default: '2G'

--time

Set a limit on the total run time of the job allocation. This is equivalent to: --time <time>.

--partitions

Request a partition for the resource allocation. This is equivalent to: -p <partitions>.

--no-output

Redirect stdout to /dev/null. This is equivalent to: --output=/dev/null. By default, stdout is redirected to --output=slurm-*.out.

Default: False

--no-error

Redirect stderr to /dev/null. This is equivalent to: --output=/dev/null. By default, stderr is redirected to --output=slurm-*.err.

Default: False

--stdout-file

Log file (stdout) if not --no-output. This is equivalent to: --output=stdout-file.

--stderr-file

Log file (stderr) if not --no-error. This is equivalent to: --output=stderr-file.

--do-not-call

Do not execute the program (dry run).

Default: False

--use-slurm

Submitted calls to SLURM.

Default: False

--mail-type

Possible choices: NONE, BEGIN, END, FAIL, REQUEUE, ALL, STAGE_OUT, TIME_LIMIT, TIME_LIMIT_90, TIME_LIMIT_80, TIME_LIMIT_50, ARRAY_TASKS

Notify user by email when certain event types occur, if --mail-user is specified.

Default: ['FAIL', 'TIME_LIMIT']

--mail-user

User to receive email notification of state changes as defined by --mail-type.