Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite

comparison trips_bam_to_sqlite/bam_to_sqlite.py @ 12:02874b1b2015 draft

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author jackcurragh
date Wed, 02 Nov 2022 15:23:28 +0000
parents 3d2b1532a1b0
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11:3d2b1532a1b0 12:02874b1b2015
249 master_trip_dict = {"fiveprime":{}, "threeprime":{}} 249 master_trip_dict = {"fiveprime":{}, "threeprime":{}}
250 master_offset_dict = {"fiveprime":{}, "threeprime":{}} 250 master_offset_dict = {"fiveprime":{}, "threeprime":{}}
251 master_metagene_stop_dict = {"fiveprime":{}, "threeprime":{}} 251 master_metagene_stop_dict = {"fiveprime":{}, "threeprime":{}}
252 252
253 253
254 os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam') 254 os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam 2> /dev/null')
255 255
256 pysam.set_verbosity(0) 256 pysam.set_verbosity(0)
257 infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb") 257 infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "rb")
258 header = infile.header["HD"] 258 header = infile.header["HD"]
259 259