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# Purpose: check what are the newly added run ids, and how many.
# Usage: python3 get_new_runs.py
# 23 Apr 2025, zjnu, hui
import os, glob, gzip
from configure import MAPPED_RDATA_DIR, TPM_FILE, UPDATE_NETWORK_LOG_FILE
from log import write_log_file
def convert_to_ena_run_id(x):
''' Check section Sample ID naming convention from ../brain.documentation/QUICKSTART.rst '''
index = max(x.find('DRR'), x.find('ERR'), x.find('SRR'))
if index > 0:
return x[index:].rstrip('X')
else:
return x
def get_run_ids_from_quant_file_names(path_to_quant_files):
result = set()
quant_files = glob.glob(os.path.join(path_to_quant_files, '*_quant.txt'))
for filepath in quant_files:
fname = os.path.basename(filepath)
result.add(fname.strip('_quant.txt'))
return result
def get_run_ids_from_tpm_files(path_to_tpm_files):
tpm_files = glob.glob(os.path.join(path_to_tpm_files, 'TPM*'))
run_ids = set()
for filename in tpm_files:
if filename.endswith('txt'):
with open(filename) as f:
line = f.readlines()[0]
line = line.strip()
lst = line.split('\t')
for runid in lst[1:]:
run_ids.add(convert_to_ena_run_id(runid))
elif filename.endswith('gz'):
with gzip.open(filename, 'rt') as f:
line = f.readlines()[0]
line = line.strip()
lst = line.split('\t')
for runid in lst[1:]:
run_ids.add(convert_to_ena_run_id(runid))
return run_ids
if __name__ == '__main__':
# Get all run IDs in MAPPED_RDATA_DIR
new_run_ids = get_run_ids_from_quant_file_names(MAPPED_RDATA_DIR)
# Get all run IDs in PATH_TO_TPM
PATH_TO_TPM = os.path.dirname(TPM_FILE)
existing_run_ids = get_run_ids_from_tpm_files(PATH_TO_TPM)
set_diff = new_run_ids.difference(existing_run_ids)
print('Total new run IDs in the quant files from %s: %d' % (MAPPED_RDATA_DIR, len(new_run_ids)))
print('Total existing run IDs in the TPM files from %s: %d' % (PATH_TO_TPM, len(existing_run_ids)))
print('Diff: %d' % (len(set_diff)))
write_log_file('[get_new_runs.py] %d new RNA-seq downloaded and mapped.' % (len(set_diff)), UPDATE_NETWORK_LOG_FILE)
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