Mercurial > repos > jackcurragh > trips_viz_bam_to_sqlite
comparison trips_bam_to_sqlite/bam_to_sqlite.py @ 2:c8d8675697c6 draft
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author | jackcurragh |
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date | Wed, 20 Apr 2022 15:18:00 +0000 |
parents | 3ac12b611d7f |
children |
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1:3ac12b611d7f | 2:c8d8675697c6 |
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226 three_ok = True | 226 three_ok = True |
227 | 227 |
228 return (pos_modifier, readlen_modifier, mismatches) | 228 return (pos_modifier, readlen_modifier, mismatches) |
229 | 229 |
230 | 230 |
231 def process_bam(bam_filepath, transcriptome_info_dict_path, outputfile): | 231 def process_bam(bam_filepath, transcriptome_info_dict_path, outputfile, desc): |
232 desc = "NULL" | 232 desc = desc |
233 start_time = time.time() | 233 start_time = time.time() |
234 study_dict = {} | 234 study_dict = {} |
235 nuc_count_dict = {"mapped": {}, "unmapped": {}} | 235 nuc_count_dict = {"mapped": {}, "unmapped": {}} |
236 dinuc_count_dict = {} | 236 dinuc_count_dict = {} |
237 threeprime_nuc_count_dict = {"mapped": {}, "unmapped": {}} | 237 threeprime_nuc_count_dict = {"mapped": {}, "unmapped": {}} |
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 os.system(f'samtools sort -n {bam_filepath} -o {bam_filepath}_n_sorted.bam') |
292 pysam.set_verbosity(0) | |
292 infile = pysam.Samfile(f"{bam_filepath}_n_sorted.bam", "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": |
719 "Usage: python bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)>" | 720 "Usage: python bam_to_sqlite.py <path_to_bam_file> <path_to_organism.sqlite> <file_description (optional)>" |
720 ) | 721 ) |
721 sys.exit() | 722 sys.exit() |
722 bam_filepath = sys.argv[1] | 723 bam_filepath = sys.argv[1] |
723 annotation_sqlite_filepath = sys.argv[2] | 724 annotation_sqlite_filepath = sys.argv[2] |
724 # try: | 725 try: |
725 # desc = sys.argv[3] | 726 desc = sys.argv[3] |
726 # except: | 727 except: |
727 # desc = bam_filepath.split("/")[-1] | 728 desc = bam_filepath.split("/")[-1] |
728 outputfile = bam_filepath + "v2.sqlite" | 729 |
729 process_bam(bam_filepath, annotation_sqlite_filepath, outputfile) | 730 outputfile = sys.argv[4] |
731 process_bam(bam_filepath, annotation_sqlite_filepath, outputfile, desc) |