def data_list(wanted_data): """ Retrieves information of additional files under folder ``BacterialTyper/data``. """ data = os.path.dirname(os.path.realpath(__file__)) list_data = HCGB_main.get_fullpath_list(data) for f in list_data: name = os.path.splitext(os.path.basename(f))[0] if (name == wanted_data): return (f)
def R_scripts(script, Debug):
"""
Lists files within ``other_tools/R`` directory and returns path to given script
"""
RDir = os.path.dirname(os.path.realpath(__file__))
list_R = main_functions.get_fullpath_list(RDir, Debug)
dict_R = {}
for f in list_R:
name = os.path.splitext(os.path.basename(f))[0]
if (name == script):
return (f)
def R_scripts(script):
"""Lists files within ``other_tools/R`` directory and returns path to given script
.. seealso:: This function depends on other BacterialTyper functions called:
- :func:`HCGB.functions.main_functions.get_fullpath_list`
"""
RDir = os.path.dirname(os.path.realpath(__file__)) + '/R/'
list_R = HCGB_main.get_fullpath_list(RDir)
dict_R = {}
for f in list_R:
name = os.path.splitext(os.path.basename(f))[0]
if (name == script):
return (f)
def print_available_BUSCO():
HCGB_aes.print_sepLine("-", 100, False)
busco_bin = set_config.get_exe('busco')
## get datasets
busco_bin_call = busco_bin + ' --list-datasets > tmp'
HCGB_sys.system_call(busco_bin_call, message=False)
## dump in screen
with open("./tmp", 'r') as f:
print(f.read())
## clean
list_files = HCGB_main.get_fullpath_list("./busco_downloads", False)
list_files + ['tmp']
for i in list_files:
os.remove(i)
os.rmdir("./busco_downloads/information")
os.rmdir("./busco_downloads/")
HCGB_aes.print_sepLine("-", 100, False)
print ("\n")
def agrvate_call(sample, assembly_file, folder, debug=False):
"""agrvate call and check results."""
## prepare call
log_call = os.path.join(folder, "agrvate_cmd.log")
err_call = os.path.join(folder, "agrvate_cmd.err")
agrvate_bin = set_config.get_exe('agrvate')
## system call
cmd_call = "%s -i %s -m -f > %s 2> %s " %(agrvate_bin,
assembly_file,
log_call, err_call) ## use mummer (-m) and force results folder (-f)
status = HCGB_sys.system_call(cmd_call)
## check results
## see https://github.com/VishnuRaghuram94/AgrVATE#results for additional details
results = pd.DataFrame()
## check folder is created
assembly_file_name = os.path.basename(assembly_file).split('.fna')[0]
original_results_folder = os.path.join(folder, assembly_file_name + '-results')
results_folder = os.path.join(folder, 'agrvate_results')
if os.path.isdir(original_results_folder):
print("+ Results folder generated OK")
print("+ Check results generated:")
## rename folder
os.rename(original_results_folder, results_folder)
os.rename(os.path.join(folder, assembly_file_name + '.fna-error-report.tab'), os.path.join(results_folder, 'error_report.tab'))
## write to excel
file_name_Excel = os.path.join(folder, sample + '_agr_results.xlsx')
writer_Excel = pd.ExcelWriter(file_name_Excel, engine='xlsxwriter') ## open excel handle
## get all files
list_files = HCGB_main.get_fullpath_list(results_folder)
## summary tab
summary_tab_file = [s for s in list_files if s.endswith("summary.tab")][0]
summary_tab = HCGB_main.get_data(summary_tab_file, '\t', options="")
summary_tab['sample'] = sample
## columns
#agr_group: gp1/gp2/gp3/gp4. 'u' means unknown.
## If multiple agr groups were found (col 5 = m),
## the displayed agr group is the majority/highest confidence.
# match_score: maximum 15; 0 means untypeable; < 5 means low confidence.
# canonical_agrD: 1 means canonical; 0 means non-canonical; u means unknown.
# multiple_agr: s means single, m means multiple, u means unknown )
## Multiple groups are found likely due to multiple S. aureus isolates in sequence
# frameshifts: Number found in CDS of extracted agr operon ('u' if agr operon not extracted)
## debug messages
if debug:
HCGB_aes.debug_message("agrvate results: Summary tab file", 'yellow')
print(summary_tab_file)
print(summary_tab)
## add summary results to all results
del summary_tab['#filename']
results = summary_tab.copy()
## save summary_tab into excel
## tab summary
summary_tab.to_excel(writer_Excel, sheet_name='summary') ## write excel handle
## agr_gp tab
agr_gp_tab_file = [s for s in list_files if s.endswith("agr_gp.tab")][0]
if HCGB_files.is_non_zero_file(agr_gp_tab_file):
agr_gp_tab = HCGB_main.get_data(agr_gp_tab_file, '\t', options='header=None')
agr_gp_tab.columns = ['contig', 'agr', 'evalue', 'identity', 'start', 'end']
agr_gp_tab['sample'] = sample
## columns
## Assembly Contig ID
## ID of matched agr group kmer
## evalue
## Percentage identity of match
## Start position of kmer alignment on input sequence
## End position of kmer alignment on input sequence
## debug messages
if debug:
HCGB_aes.debug_message("agrvate results: agr_gp file", 'yellow')
print(agr_gp_tab_file)
print(agr_gp_tab)
## save agr_gp_tab file into excel
## tab operon
agr_gp_tab.to_excel(writer_Excel, sheet_name='operon') ## write excel handle
## agr_operon fna
try:
agr_operon_fna_file = [s for s in list_files if s.endswith("agr_operon.fna")][0]
## debug messages
if debug:
HCGB_aes.debug_message("agrvate results: agr_operon file", 'yellow')
print(agr_operon_fna_file)
results['operon_fna'] = agr_operon_fna_file
except:
results['operon_fna'] = ''
## agr_operon fna
error_report_file = [s for s in list_files if s.endswith("error_report.tab")][0]
error_report = HCGB_main.get_data(error_report_file, '\t', options="")
del error_report['#input_name']
## debug messages
if debug:
HCGB_aes.debug_message("agrvate results: error_report.tab file", 'yellow')
print(error_report_file)
print(error_report)
## save error_report file into excel
## tab steps
error_report.to_excel(writer_Excel, sheet_name='steps') ## write excel handle
## merge results
results = pd.concat([results, error_report], axis=1)
## close xlsx file
writer_Excel.save() ## close excel handle
## add to pandas dataframe
results['agr_operon_xlsx'] = file_name_Excel
## debug messages
if debug:
HCGB_aes.debug_message("agrvate results", 'yellow')
HCGB_main.print_all_pandaDF(results)
return (results)
def install(software, min_version, install_path, Debug):
(path2Export, versionInstalled) = install_soft(software, min_version, install_path, Debug)
## failed to install:
if not path2Export:
print(colored("**Check paths or install it in the system and add it to $PATH environment variable.",'yellow'))
return ()
else:
## add to $PATH: include in environment bin
env_bin_directory = os.path.dirname(os.environ['_'])
print ("\n+ Add software to path")
file_list = []
## unique file to export
if (software == 'fastqc' or software == 'trimmomatic'):
file_list.append(path2Export)
else:
## all folder
if (software == 'spades'):
pathToExport = os.path.join(path2Export, 'bin')
if (software == 'prokka'):
pathToExport = os.path.join(path2Export, 'bin')
file_list = HCGB_main.get_fullpath_list(path2Export)
## add binaries compiled for linux
if (software == 'prokka'):
pathToExport2 = os.path.join(path2Export, 'binaries', 'linux')
file_list = file_list + HCGB_main.get_fullpath_list(pathToExport2)
## discard some files obtain
file_list = [s for s in file_list if '.a' not in s]
file_list = [s for s in file_list if '.c' not in s]
file_list = [s for s in file_list if '.o' not in s]
file_list = [s for s in file_list if '.h' not in s]
file_list = [s for s in file_list if '.git' not in s]
file_list = [s for s in file_list if '.git/' not in s]
file_list = [s for s in file_list if '.gitignore' not in s]
file_list = [s for s in file_list if 'Makefile' not in s]
file_list = [s for s in file_list if '.pdf' not in s]
file_list = [s for s in file_list if '.tar.gz' not in s]
file_list = [s for s in file_list if 'README.md' not in s]
file_list = [s for s in file_list if '__pycache__' not in s]
file_list = [s for s in file_list if 'db/' not in s]
file_list = [s for s in file_list if 'doc/' not in s]
file_list = [s for s in file_list if 'test/' not in s]
file_list = [s for s in file_list if 'aux/' not in s]
## debug messages
if Debug:
print(colored("** Debug: list to include in path",'yellow'))
print (file_list)
print()
## create symbolic link in bin directory in environment
HCGB_main.get_symbolic_link(file_list, env_bin_directory)
print(colored("**Software (%s - Version: %s) installed in the system and add it to $PATH environment variable." %(software, versionInstalled),'green'))
return (versionInstalled)