Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

diff trips_bam_to_sqlite/bam_to_sqlite.py @ 1:3ac12b611d7f draft

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author jackcurragh
date Sun, 17 Apr 2022 08:44:20 +0000
parents fef356fa1802
children c8d8675697c6
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line diff
--- a/trips_bam_to_sqlite/bam_to_sqlite.py	Mon Apr 04 09:48:32 2022 +0000
+++ b/trips_bam_to_sqlite/bam_to_sqlite.py	Sun Apr 17 08:44:20 2022 +0000
@@ -288,7 +288,8 @@
     master_offset_dict = {"fiveprime": {}, "threeprime": {}}
     master_metagene_stop_dict = {"fiveprime": {}, "threeprime": {}}
 
-    infile = pysam.Samfile(bam_filepath, "rb")
+    os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam')
+    infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
     header = infile.header["HD"]
     unsorted = False
     if "SO" in header: