moritzschaefer · October 17, 2020 23:57 · Oct 17, 2020
diff --git a/download_srx_rename.py b/download_srx_rename.py
@@ -0,0 +1,59 @@
+'''
+Download a file from SRA (using SRX accessions or anything else that 
+is queryable by esearch) and rename them according to a yaml file.
+
+Example yaml file:
+
+CXXC1:
+  signal:
+    - SRX373166
+  control:
+    - SRX373169
+E2F1: 
+  signal:
+  - SRX2897263
+  - SRX2897262
+  control: 
+
+'''
+
+
+import os
+import subprocess
+
+import yaml
+
+with open('samples.yaml') as f:
+    data = yaml.load(f)
+
+for tf, samples in data.items():
+    for sample_type in ['signal', 'control']:
+        for srx in samples[sample_type]:
+            print(f'Downloading {srx}')
+            p = subprocess.Popen(f'esearch  -db sra -query {srx} | efetch --format runinfo | cut -d "," -f 1 | grep SRR',
+                                shell=True,
+                                stdin=subprocess.PIPE,
+                                stdout=subprocess.PIPE,
+                                stderr=subprocess.PIPE)
+
+            srrs = [s.strip() for s in p.stdout.readlines()]
+
+            p2 = subprocess.Popen(f'fasterq-dump --split-files {" ".join(srrs)}',
+                                  shell=True,
+                                  stdin=subprocess.PIPE,
+                                  stdout=subprocess.PIPE,
+                                  stderr=subprocess.PIPE)
+
+            if p.result != 0:
+                nl = "\n"
+                print(f'downloading {srx} failed: {nl.join(p.stdout.readlines(-1))}\n\n{nl.join(p.stderr.readlines(-1))}')
+            else:
+                print(f'Succesfully downloaded {srx}')
+
+            for i, srr in enumerate(srrs):
+                try:
+                    os.rename(f'{srr}.fastq', f'{tf}_{sample_type}_{i+1}_R1.fastq')
+                except Exception as e:
+                    print(e)
+                    for r in range(1,3):
+                        os.rename(f'{srr}_{r}.fastq', f'{tf}_{sample_type}_{i+1}_R{r}.fastq')