Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

comparison trips_bam_to_sqlite/bam_to_sqlite.py @ 6:1be4bbe849e3 draft

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author jackcurragh
date Tue, 07 Jun 2022 16:20:36 +0000
parents 4ee95ba271a5
children 2c6f630c732f
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5:8b059b0a19dc 6:1be4bbe849e3
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')
292 pysam.set_verbosity(0) 291 pysam.set_verbosity(0)
293 infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb") 292 infile = pysam.Samfile(f"{bam_filepath}", "rb")
294 header = infile.header["HD"] 293 header = infile.header["HD"]
295 unsorted = False 294 unsorted = False
296 if "SO" in header: 295 if "SO" in header:
297 if header["SO"] != "queryname": 296 if header["SO"] != "queryname":
298 unsorted = True 297 unsorted = True