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reformat-smartseq.py

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+#!/usr/bin/env python
+
+##Written by Haynes Heaton to reformat SS2 files to mimic 10x format for Souporcell
+
+
+import argparse
+
+parser = argparse.ArgumentParser(description = "convert smartseq data to a format souporcell can use")
+parser.add_argument("-i", "--input_dir", required = True, help = "directory with smartseq bams")
+parser.add_argument("-o", "--output_prefix", required= True, help = "outputs bam and barcode files with this prefix")
+args = parser.parse_args()
+
+import glob
+
+import pysam
+
+bamfiles = glob.glob(args.input_dir+"/*.BAM")
+assert len(bamfiles) > 0, "I don't see bam files in directory" + args.input_dir
+template = pysam.AlignmentFile(bamfiles[0])
+outbam = pysam.AlignmentFile(args.output_prefix+".bam",'wb', template = template)
+cell_barcode = 0
+
+with open(args.output_prefix +".tsv", "w") as barcodes:
+    for (cell_barcode, bamfile) in enumerate(bamfiles):
+        umi = 0
+        inbam = pysam.AlignmentFile(bamfile)
+        barcode = bamfile.split('/')[-1]
+        barcodes.write(barcode+"\n")
+        for read in inbam:
+            read.set_tag("UB", str(umi))
+            umi += 1
+            read.set_tag("CB", str(barcode))
+            outbam.write(read)
+
+import subprocess
+
+with open(args.output_prefix+"_sorted.bam",'w') as bamout2:
+    subprocess.check_call(["samtools","sort",args.output_prefix+".bam"],stdout = bamout2)
+
+subprocess.check_call(["rm", args.output_prefix+".bam"])
+subprocess.check_call(["mv", args.output_prefix+"_sorted.bam",args.output_prefix+".bam"])
+