Index

_

__init__() (blacktie.utils.calls.BaseCall method) (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CufflinksCall method) (blacktie.utils.calls.CuffmergeCall method) (blacktie.utils.calls.CummerbundCall method) (blacktie.utils.calls.TophatCall method) (blacktie.utils.errors.MissingArgumentError method) (blacktie.utils.errors.SystemCallError method) (blacktie.utils.misc.Bunch method)

_flag_out_dir() (blacktie.utils.calls.BaseCall method)

B

BaseCall (class in blacktie.utils.calls) blacktie.utils.calls (module) blacktie.utils.errors (module) blacktie.utils.externals (module) blacktie.utils.misc (module)

BlacktieError build_out_dir_path() (blacktie.utils.calls.BaseCall method) build_qsub() (blacktie.utils.calls.BaseCall method) Bunch (class in blacktie.utils.misc) bunchify() (in module blacktie.utils.misc)

C

construct_options_list() (blacktie.utils.calls.BaseCall method) CuffdiffCall (class in blacktie.utils.calls) CufflinksCall (class in blacktie.utils.calls)

CuffmergeCall (class in blacktie.utils.calls) CummerbundCall (class in blacktie.utils.calls)

E

email_notification() (in module blacktie.utils.misc)

execute() (blacktie.utils.calls.BaseCall method)

G

get_accepted_hits() (blacktie.utils.calls.CufflinksCall method) get_bam_path() (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CufflinksCall method) get_bt_idx() (blacktie.utils.calls.TophatCall method) get_condition_id() (blacktie.utils.calls.BaseCall method) get_cuffdiff_dir() (blacktie.utils.calls.CummerbundCall method) get_cuffGTF_path() (blacktie.utils.calls.CuffmergeCall method) get_cufflinks_gtfs() (blacktie.utils.calls.CuffmergeCall method) get_cuffmerge_gtf() (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CummerbundCall method) get_genome() (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CufflinksCall method) (blacktie.utils.calls.CuffmergeCall method) get_gtf_anno() (blacktie.utils.calls.CufflinksCall method) (blacktie.utils.calls.CuffmergeCall method) (blacktie.utils.calls.TophatCall method)

get_gtf_anno_guide() (blacktie.utils.calls.CufflinksCall method) get_labels() (blacktie.utils.calls.CuffdiffCall method) get_lt_reads() (blacktie.utils.calls.TophatCall method) get_mask_file() (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CufflinksCall method) get_out_dir() (blacktie.utils.calls.CuffdiffCall method) (blacktie.utils.calls.CufflinksCall method) (blacktie.utils.calls.CuffmergeCall method) (blacktie.utils.calls.CummerbundCall method) (blacktie.utils.calls.TophatCall method) get_rt_reads() (blacktie.utils.calls.TophatCall method) get_sample_bams() (blacktie.utils.calls.CuffdiffCall method) get_time() (in module blacktie.utils.misc) get_version_number() (in module blacktie.utils.misc)

I

init_log_file() (blacktie.utils.calls.BaseCall method) init_opt_dict() (blacktie.utils.calls.BaseCall method)

InvalidFileFormatError

L

log_end() (blacktie.utils.calls.BaseCall method) log_msg() (blacktie.utils.calls.BaseCall method)

log_start() (blacktie.utils.calls.BaseCall method)

M

map_condition_groups() (in module blacktie.utils.misc) MissingArgumentError

mkdirp() (in module blacktie.utils.externals)

N

notify_end_of_call() (blacktie.utils.calls.BaseCall method)

notify_start_of_call() (blacktie.utils.calls.BaseCall method)

P

purge_progress_bars() (blacktie.utils.calls.BaseCall method)

R

runExternalApp() (in module blacktie.utils.externals)

S

SanityCheckError set_call_id() (blacktie.utils.calls.BaseCall method)

SystemCallError

T

TophatCall (class in blacktie.utils.calls)

U

UnexpectedValueError

V

verify_options() (blacktie.utils.calls.CufflinksCall method)

W

whereis() (in module blacktie.utils.externals)

whoami() (in module blacktie.utils.misc)