Get how many new RNA-seq have been downloaded and mapped

1 files changed, 59 insertions, 0 deletions

diff --git a/Code/get_new_runs.py b/Code/get_new_runs.py
new file mode 100644
index 0000000..502c568
--- /dev/null
+++ b/Code/get_new_runs.py
@@ -0,0 +1,59 @@
+# 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)
+