add samplesheet.py

docs/usage.md

@@ -31,6 +31,16 @@ CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz
 CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz
 ```
 
+### Create `samplesheet.csv` using helper script
+
+When you have many samples, manually creating `samplesheet.csv` can be tedious and error-prone. There is a python script [samplesheet.py](../scripts/samplesheet.py) in the scripts directory that can help you extract the path of all paired-end fastq files in the specified folders and create a samplesheet.csv file.
+
+```
+python scripts/samplesheet.py folder1,folder2
+```
+
+The sample name is extracted from the prefix of the fastq files. You may still need to manually change the sample column.
+
 ## Running the pipeline
 
 The typical command for running the pipeline is as follows:

scripts/samplesheet.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+"""
+samplesheet.py folder1,folder2
+read all paired fastq files in folders and create a samplesheet.csv file.
+"""
+import csv
+import os
+import argparse
+
+def get_read(folder):
+    read1_list = [f'_1', f'R1', f'R1_001']
+    read2_list = [f'_2', f'R2', f'R2_001']
+    fq_list = ['fq', 'fastq']
+    suffix1_list = [
+        f'{x}.{y}.gz'
+        for x in read1_list
+        for y in fq_list
+    ]
+    suffix2_list = [
+        f'{x}.{y}.gz'
+        for x in read2_list
+        for y in fq_list
+    ]
+
+    for file in os.listdir(folder):
+        r1 = os.path.join(folder, file)
+        if os.path.isfile(r1):
+            for suffix1, suffix2 in zip(suffix1_list, suffix2_list):
+                if file.endswith(suffix1):
+                    prefix = file[:-len(suffix1)]
+                    r2 = os.path.join(folder, prefix+suffix2)
+                    if not os.path.exists(r2):
+                        print("warning: {r1} exists, but {r2} not exists. continue")
+                        continue
+                    prefix = prefix.split("_")[0]
+                    print(prefix, r1, r2)
+                    yield prefix,r1,r2
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('folders')
+    args = parser.parse_args()
+    with open('samplesheet.csv', 'w', newline='') as f:
+        writer = csv.writer(f)
+        writer.writerow(['sample', 'fastq_1', 'fastq_2'])
+        for folder in args.folders.split(','):
+            folder = os.path.abspath(folder)
+            for prefix, r1, r2 in get_read(folder):
+                writer.writerow([prefix, r1, r2])
+    print("samplesheet.csv created")
+
+