Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

comparison trips_bam_to_sqlite/bam_to_sqlite.py @ 7:2c6f630c732f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jackcurragh
date Tue, 07 Jun 2022 16:49:36 +0000
parents 1be4bbe849e3
children 0e88342d5794
comparison
equal deleted inserted replaced
6:1be4bbe849e3 7:2c6f630c732f
286 ambiguously_mapped_reads = 0 286 ambiguously_mapped_reads = 0
287 master_trip_dict = {"fiveprime": {}, "threeprime": {}} 287 master_trip_dict = {"fiveprime": {}, "threeprime": {}}
288 master_offset_dict = {"fiveprime": {}, "threeprime": {}} 288 master_offset_dict = {"fiveprime": {}, "threeprime": {}}
289 master_metagene_stop_dict = {"fiveprime": {}, "threeprime": {}} 289 master_metagene_stop_dict = {"fiveprime": {}, "threeprime": {}}
290 290
291 os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam')
291 pysam.set_verbosity(0) 292 pysam.set_verbosity(0)
292 infile = pysam.Samfile(f"{bam_filepath}", "rb") 293 infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
293 header = infile.header["HD"] 294 header = infile.header["HD"]
294 unsorted = False 295 unsorted = False
295 if "SO" in header: 296 if "SO" in header:
296 if header["SO"] != "queryname": 297 if header["SO"] != "queryname":
297 unsorted = True 298 unsorted = True