How to use the pomoxis.pyscrap.pyscrap function in pomoxis

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github nanoporetech / pomoxis / pomoxis / apps / read_until_filter.py View on Github external
logger.debug("Skipping because I've seen before.")
                    continue
                else:
                    logger.debug("Analysing {} samples".format(len(read_block)))
                    sample_rate = read_block.sample_rate
                    events = minknow_event_detect(
                        read_block, read_block.sample_rate, **{
                            'window_lengths':[3, 6], 'thresholds':[1.4, 1.1],
                            'peak_height':0.2
                        }
                    )
                    if len(events) < 100:
                        continue

                    #TODO: do this in a process pool
                    score, basecall = pyscrap.basecall_events(events)
                    #TODO: check sanity of basecall
                    if len(basecall) < 100:
                        continue

                    alignment, returncode = yield from align_client.call.align(basecall)
                    hits = []
                    if returncode != 0:
                        logger.warning('Alignment failed for {}'.format(read_block.info))
                    else:
                        recs = [x for x in alignment.split('\n') if len(x) > 0 and x[0] != '@']
                        for r in recs:
                            fields = r.split('\t')
                            if fields[2] != '*':
                                hits.append(fields[2])
                    logger.debug('{} aligns to {}'.format(read_block.info, hits))