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 |
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date | Tue, 07 Jun 2022 16:20:36 +0000 |
parents | 4ee95ba271a5 |
children | 2c6f630c732f |
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5:8b059b0a19dc | 6:1be4bbe849e3 |
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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 |