diff script.py @ 0:2ed60a09d6b6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/script.py	Mon Jul 15 05:11:46 2019 -0400
@@ -0,0 +1,80 @@
+import os
+import argparse
+from collections import Counter
+from jinja2 import Template
+
+
+def main():
+    # --workdir `pwd` --output-dir `pwd`/output --input 
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("--workdir", "-w", required=True)
+    parser.add_argument("--output-dir", "-o", required=True)
+    parser.add_argument("--template", "-t", required=True)
+    parser.add_argument("--output-conf", "-c", required=True)
+    parser.add_argument("--input", "-i", action="append", required=True)
+    parser.add_argument("--bed", "-b", default=None)
+
+    
+
+    args = parser.parse_args()
+
+    workdir = args.workdir
+    output_dir = args.output_dir
+    input_files_raw = args.input
+    template_file_path = args.template
+    output_config_path = args.output_conf
+    bed_file_path = args.bed
+    
+    
+    if bed_file_path:
+        bed_new_name = "bed_file.bed"
+        bed_new_file_path = os.path.join(
+            workdir,
+            bed_new_name
+        )
+        os.symlink(bed_file_path, bed_new_file_path)
+        bed_file_path = bed_new_file_path
+    
+    input_files = []
+    phenotype_counter = Counter()
+    for input_file in input_files_raw:
+        if input_file.find(":"):
+            forward_file, reverse_file, phenotype = input_file.split(":")
+            phenotype_counter.update(phenotype)
+            phenotype_count = phenotype_counter[phenotype]
+
+            forward_new_name = "{phenotype}_{phenotype_count}_R1.fastq.gz".format(phenotype=phenotype, phenotype_count=phenotype_count)
+            forward_new_file_path = os.path.join(
+                workdir,
+                forward_new_name
+            )
+            os.symlink(forward_file, forward_new_file_path)
+
+            reverse_new_name = "{phenotype}_{phenotype_count}_R2.fastq.gz".format(phenotype=phenotype, phenotype_count=phenotype_count)
+            reverse_new_file_path = os.path.join(
+                workdir,
+                reverse_new_name
+            )
+            os.symlink(reverse_file, reverse_new_file_path)
+            
+            input_files.append(
+                {
+                    "forward": forward_new_file_path, 
+                    "reverse": reverse_new_file_path, 
+                    "description": "{phenotype}_{phenotype_index}".format(phenotype=phenotype, phenotype_index=phenotype_count),
+                    "phenotype": phenotype
+                }
+            )
+        
+    with open(output_config_path, 'w') as config_file_handle, open(template_file_path, 'r') as template_file_handle:
+        template = Template(template_file_handle.read())
+        config_file_handle.write(template.render(
+            samples=input_files,
+            output_dir=output_dir,
+            bed_file_path=bed_file_path
+        ))
+
+
+if __name__ == "__main__":
+    main()
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