download_srx_rename.py

'''
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')