snsxt
latest
Introduction
snsxt package
snsxt
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
_
__init__() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
(snsxt.util.qsub.Job method)
_completions() (snsxt.util.qsub.Job method)
_debug_update() (snsxt.util.qsub.Job method)
_init_analysis_attrs() (snsxt.sns_classes.classes.SnsAnalysisSample method)
_init_attrs() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
_init_dirs() (snsxt.sns_classes.classes.SnsAnalysisSample method)
(snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
_init_files() (snsxt.sns_classes.classes.SnsAnalysisSample method)
(snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
_init_static_files() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
_setup_report() (in module snsxt.sns_tasks.task_classes)
_update() (snsxt.util.qsub.Job method)
A
add_file() (snsxt.util.classes.AnalysisItem method)
add_files() (snsxt.util.classes.AnalysisItem method)
add_handlers() (in module snsxt.util.log)
add_missing_console_handler() (in module snsxt.util.log)
analysis_complete() (in module snsxt.cleanup)
AnalysisItem (class in snsxt.util.classes)
B
background_jobs (in module snsxt.job_management)
background_output_files (in module snsxt.validation)
backup_file() (in module snsxt.util.tools)
build_console_handler() (in module snsxt.util.log)
build_logger() (in module snsxt.util.log)
C
check_default_address() (in module snsxt.mail)
check_qsub_log_errors_present() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
compare() (in module snsxt.util.tools)
compile_RMD_report() (in module snsxt.setup_report)
configs (in module snsxt.run)
Container (class in snsxt.util.template)
(class in snsxt.util.tools)
copy_and_overwrite() (in module snsxt.util.tools)
create_main_filehandler() (in module snsxt.util.log)
D
default_probes (in module snsxt.run)
default_targets (in module snsxt.run)
default_task_list (in module snsxt.run)
demo_multi_qsub() (in module snsxt.util.qsub)
demo_qsub() (in module snsxt.util.qsub)
DirHop (class in snsxt.util.tools)
E
email_error_output() (in module snsxt.mail)
email_files (in module snsxt.mail)
email_log_filehandler() (in module snsxt.util.log)
email_logpath() (in module snsxt.run)
email_output() (in module snsxt.mail)
error() (snsxt.util.qsub.Job method)
expected_static_files() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
extra_handlers (in module snsxt.run)
F
filter_qacct() (in module snsxt.util.qsub)
(snsxt.util.qsub.Job method)
find() (in module snsxt.util.find)
find_all_job_id_names() (in module snsxt.util.qsub)
find_files() (in module snsxt.util.find)
find_gen() (in module snsxt.util.find)
G
get_all_handlers() (in module snsxt.util.log)
get_analysis_config() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
get_dirs() (snsxt.util.classes.AnalysisItem method)
get_file_contents() (in module snsxt.util.mutt)
get_files() (snsxt.util.classes.AnalysisItem method)
get_handler_paths() (snsxt.util.classes.LoggedObject method)
get_is_error() (snsxt.util.qsub.Job method)
get_is_present() (snsxt.util.qsub.Job method)
get_is_running() (snsxt.util.qsub.Job method)
get_job() (snsxt.util.qsub.Job method)
get_job_ID_name() (in module snsxt.util.qsub)
get_log_file() (snsxt.util.qsub.Job method)
get_logger_handler() (in module snsxt.util.log)
get_main_report_file() (in module snsxt.setup_report)
get_output_files() (snsxt.sns_classes.classes.SnsAnalysisSample method)
get_qacct() (in module snsxt.util.qsub)
(snsxt.util.qsub.Job method)
get_qacct_job_failed_status() (in module snsxt.util.qsub)
(snsxt.util.qsub.Job method)
get_qsub_logfiles() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
get_reply_to_address() (in module snsxt.util.mutt)
get_report_files() (in module snsxt.setup_report)
get_samples() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
get_samplesIDs_from_samples_fastq_raw() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
get_state() (snsxt.util.qsub.Job method)
get_status() (snsxt.util.qsub.Job method)
get_summary_combined_contents() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
get_task_list() (in module snsxt.run)
H
has_console_handler() (in module snsxt.util.log)
I
item_exists() (in module snsxt.util.tools)
J
Job (class in snsxt.util.qsub)
job_state_key (in module snsxt.util.qsub)
json_dumps() (in module snsxt.util.tools)
K
kill_background_jobs() (in module snsxt.job_management)
kill_job_ids() (in module snsxt.util.qsub)
kill_jobs() (in module snsxt.util.qsub)
L
list_none() (snsxt.util.classes.AnalysisItem method)
load_json() (in module snsxt.util.tools)
log_all_handler_filepaths() (in module snsxt.util.log)
log_exception() (in module snsxt.util.log)
log_handler_paths() (snsxt.util.classes.LoggedObject method)
log_setup() (in module snsxt.util.log)
LoggedObject (class in snsxt.util.classes)
logger_filepath() (in module snsxt.util.log)
logpath() (in module snsxt.run)
(in module snsxt.util.log)
M
main() (in module snsxt.run)
(in module snsxt.util.template)
make_attachement_string() (in module snsxt.util.mutt)
mkdirs() (in module snsxt.util.tools)
monitor_jobs() (in module snsxt.util.qsub)
monitor_validate_background_jobs() (in module snsxt.job_management)
monitor_validate_jobs() (in module snsxt.job_management)
multi_filter() (in module snsxt.util.find)
mutt_mail() (in module snsxt.util.mutt)
my_debugger() (in module snsxt.util.tools)
N
num_lines() (in module snsxt.util.tools)
P
parse() (in module snsxt.run)
parse_git() (in module snsxt.util.git)
present() (snsxt.util.qsub.Job method)
print_dict() (in module snsxt.util.tools)
print_filehandler_filepaths_to_log() (in module snsxt.util.log)
print_iter() (in module snsxt.util.git)
print_json() (in module snsxt.util.tools)
Q
qacct2dict() (in module snsxt.util.qsub)
(snsxt.util.qsub.Job method)
R
remove_all_handlers() (in module snsxt.util.log)
remove_handlers() (in module snsxt.util.log)
reply_to_address() (in module snsxt.util.tools)
run() (in module snsxt.util.mutt)
(in module snsxt.util.template)
(snsxt.util.tools.SubprocessCmd method)
running() (snsxt.util.qsub.Job method)
S
save_configs() (in module snsxt.cleanup)
set_dir() (snsxt.util.classes.AnalysisItem method)
set_dirs() (snsxt.util.classes.AnalysisItem method)
set_file() (snsxt.util.classes.AnalysisItem method)
set_files() (snsxt.util.classes.AnalysisItem method)
setUp() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
(snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
(snsxt.util.test_qsub.TestJob method)
setup_report() (in module snsxt.setup_report)
sns_start_email() (in module snsxt.mail)
SnsAnalysisSample (class in snsxt.sns_classes.classes)
SnsWESAnalysisOutput (class in snsxt.sns_classes.classes)
snsxt (module)
snsxt.cleanup (module)
snsxt.config (module)
snsxt.job_management (module)
snsxt.mail (module)
snsxt.report (module)
snsxt.run (module)
snsxt.setup_report (module)
snsxt.sns_classes (module)
snsxt.sns_classes.classes (module)
snsxt.sns_classes.config (module)
snsxt.sns_classes.test (module)
snsxt.sns_classes.test_sns_classes (module)
snsxt.sns_tasks (module)
snsxt.sns_tasks.scripts (module)
snsxt.sns_tasks.task_classes (module)
snsxt.test (module)
snsxt.util (module)
snsxt.util.classes (module)
snsxt.util.find (module)
snsxt.util.git (module)
snsxt.util.log (module)
snsxt.util.mutt (module)
snsxt.util.qsub (module)
snsxt.util.sh (module)
snsxt.util.template (module)
snsxt.util.test (module)
snsxt.util.test_find (module)
snsxt.util.test_qsub (module)
snsxt.util.test_tools (module)
snsxt.util.tools (module)
snsxt.validation (module)
startup() (in module snsxt.run)
submit() (in module snsxt.util.qsub)
submit_job() (in module snsxt.util.qsub)
subprocess_cmd() (in module snsxt.util.mutt)
(in module snsxt.util.qsub)
(in module snsxt.util.tools)
SubprocessCmd (class in snsxt.util.tools)
summary_combined_contains_errors() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
super_filter() (in module snsxt.util.find)
T
tearDown() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
(snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
(snsxt.util.test_qsub.TestJob method)
test_AnalysisItem_files_entry1() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
test_AnalysisItem_files_entry_listnone() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
test_AnalysisItem_files_entry_missingkey() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
test_AnalysisItem_files_type() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
test_cmd_echo_stdout() (snsxt.util.test_tools.TestSubprocessCmd method)
test_cmd_echo_success() (snsxt.util.test_tools.TestSubprocessCmd method)
test_cmd_fail() (snsxt.util.test_tools.TestSubprocessCmd method)
test_cwd_change() (snsxt.util.test_tools.TestDirHop method)
test_cwd_change_fail() (snsxt.util.test_tools.TestDirHop method)
test_debug_init_Job() (snsxt.util.test_qsub.TestJob method)
test_error() (snsxt.util.test_find.TestSuperFilter method)
(snsxt.util.test_qsub.TestJob method)
test_fail() (snsxt.util.test_find.TestSuperFilter method)
(snsxt.util.test_qsub.TestJob method)
test_find_all_job_id_names1() (snsxt.util.test_qsub.TestJob method)
test_full_overlap() (snsxt.util.test_tools.TestWriteTabularOverlap method)
test_get_bam_dir_exists() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_get_job1() (snsxt.util.test_qsub.TestJob method)
test_get_samples() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_invalid_path() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_item_should_exist_any() (snsxt.util.test_tools.TestItemExists method)
test_item_should_exist_dir() (snsxt.util.test_tools.TestItemExists method)
test_item_should_exist_file() (snsxt.util.test_tools.TestItemExists method)
test_item_should_not_exist_file() (snsxt.util.test_tools.TestItemExists method)
test_item_wrong_type() (snsxt.util.test_tools.TestItemExists method)
test_job_Eqw() (snsxt.util.test_qsub.TestJob method)
test_job_Eqw_not_running() (snsxt.util.test_qsub.TestJob method)
test_no_settings() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_num_lines1() (snsxt.util.test_tools.TestNumLines method)
test_partial_overlap() (snsxt.util.test_tools.TestWriteTabularOverlap method)
test_qsub_errors() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_running_job1() (snsxt.util.test_qsub.TestJob method)
test_skip() (snsxt.util.test_tools.TestNumLines method)
test_summary_combined_errors() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_super_filter_all_Eqw() (snsxt.util.test_find.TestSuperFilter method)
test_super_filter_all_Eqw_fail() (snsxt.util.test_find.TestSuperFilter method)
test_true() (snsxt.sns_classes.test_sns_classes.TestAnalysisItem method)
(snsxt.util.test_find.TestSuperFilter method)
(snsxt.util.test_qsub.TestJob method)
(snsxt.util.test_tools.TestDirHop method)
(snsxt.util.test_tools.TestWriteTabularOverlap method)
test_update_json1() (snsxt.util.test_tools.TestUpdateJSON method)
test_update_missingfile() (snsxt.util.test_tools.TestUpdateJSON method)
test_valid_analysis_output() (snsxt.sns_classes.test_sns_classes.TestSnsWESAnalysisOutput method)
test_validate_qacct_killed1() (snsxt.util.test_qsub.TestJob method)
test_validate_qacct_normal1() (snsxt.util.test_qsub.TestJob method)
test_validate_qacct_normal1_too_old() (snsxt.util.test_qsub.TestJob method)
test_validate_qacct_normal_wrongusername() (snsxt.util.test_qsub.TestJob method)
TestAnalysisItem (class in snsxt.sns_classes.test_sns_classes)
TestDirHop (class in snsxt.util.test_tools)
TestItemExists (class in snsxt.util.test_tools)
TestJob (class in snsxt.util.test_qsub)
TestNumLines (class in snsxt.util.test_tools)
TestSnsWESAnalysisOutput (class in snsxt.sns_classes.test_sns_classes)
TestSubprocessCmd (class in snsxt.util.test_tools)
TestSuperFilter (class in snsxt.util.test_find)
TestUpdateJSON (class in snsxt.util.test_tools)
TestWriteTabularOverlap (class in snsxt.util.test_tools)
timestamp() (in module snsxt.util.log)
(in module snsxt.util.tools)
U
update_completion_validations() (snsxt.util.qsub.Job method)
update_json() (in module snsxt.util.tools)
update_log_files() (snsxt.util.qsub.Job method)
V
validate() (snsxt.sns_classes.classes.SnsWESAnalysisOutput method)
validate_background_output_files() (in module snsxt.validation)
validate_branch() (in module snsxt.util.git)
validate_completion() (snsxt.util.qsub.Job method)
validate_email_files() (in module snsxt.mail)
validate_items() (in module snsxt.validation)
validate_job_completion() (in module snsxt.util.qsub)
W
walklevel() (in module snsxt.util.find)
write_dicts_to_csv() (in module snsxt.util.tools)
write_json() (in module snsxt.util.tools)
write_tabular_overlap() (in module snsxt.util.tools)
Read the Docs
v: latest
Versions
latest
Downloads
pdf
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.