Python validated_fns示例

示例#1

文件： ovlp_filter.py 项目： yoshihikosuzuki/FALCON

def try_run_ovlp_filter(n_core, ovl, fofn, max_diff, max_cov, min_cov, min_len,
                        bestn, db_fn):
    io.LOG('starting ovlp_filter')
    file_list = io.validated_fns(ovl) if ovl != None else io.validated_fns(
        fofn)
    io.LOG('fofn %r: %r' % (ovl if ovl != None else fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_filter(exe_pool, ovl, file_list, max_diff, max_cov, min_cov,
                        min_len, bestn, db_fn)
        io.LOG('finished ovlp_filter')
    except:
        io.LOG('terminating ovlp_filter workers...')
        exe_pool.terminate()
        raise

示例#2

文件： ovlp_stats.py 项目： evolvedmicrobe/FALCON

def try_run_ovlp_stats(n_core, fofn, min_len):
    io.LOG('starting ovlp_stats')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn %r: %r' %(fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_stats(exe_pool, file_list, min_len)
        io.LOG('finished ovlp_stats')
    except KeyboardInterrupt:
        io.LOG('terminating ovlp_stats workers...')
        exe_pool.terminate()

示例#3

def try_run_ovlp_stats(n_core, fofn, min_len):
    io.LOG('starting ovlp_stats')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn %r: %r' % (fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_stats(exe_pool, file_list, min_len)
        io.LOG('finished ovlp_stats')
    except KeyboardInterrupt:
        io.LOG('terminating ovlp_stats workers...')
        exe_pool.terminate()

示例#4

文件： ovlp_filter.py 项目： evolvedmicrobe/FALCON

def try_run_ovlp_filter(n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
    io.LOG("starting ovlp_filter")
    file_list = io.validated_fns(fofn)
    io.LOG("fofn %r: %r" % (fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_filter(exe_pool, file_list, max_diff, max_cov, min_cov, min_len, bestn, db_fn)
        io.LOG("finished ovlp_filter")
    except KeyboardInterrupt:
        io.LOG("terminating ovlp_filter workers...")
        exe_pool.terminate()

示例#5

文件： ovlp_filter.py 项目： lpp1985/lpp_Script

def try_run_ovlp_filter(n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
    io.LOG('starting ovlp_filter')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn %r: %r' %(fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_filter(exe_pool, file_list, max_diff, max_cov, min_cov, min_len, bestn, db_fn)
        io.LOG('finished ovlp_filter')
    except:
        io.LOG('terminating ovlp_filter workers...')
        exe_pool.terminate()
        raise

示例#6

文件： ovlp_stats.py 项目： fangzhiyu/falcon3

def try_run_ovlp_stats(n_core, db_fn, fofn, min_len):
    io.LOG('starting ovlp_stats')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn {!r}: {}'.format(fofn, file_list))
    io.LOG('db {!r}; n_core={}'.format(db_fn, n_core))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_stats(exe_pool, db_fn, file_list, min_len)
        io.LOG('finished ovlp_stats')
    except KeyboardInterrupt:
        io.LOG('terminating ovlp_stats workers...')
        exe_pool.terminate()

示例#7

文件： ovlp_stats.py 项目： PacificBiosciences/FALCON

def try_run_ovlp_stats(n_core, db_fn, fofn, min_len):
    io.LOG('starting ovlp_stats')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn {!r}: {}'.format(fofn, file_list))
    io.LOG('db {!r}; n_core={}'.format(db_fn, n_core))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    try:
        run_ovlp_stats(exe_pool, db_fn, file_list, min_len)
        io.LOG('finished ovlp_stats')
    except KeyboardInterrupt:
        io.LOG('terminating ovlp_stats workers...')
        exe_pool.terminate()

示例#8

def try_run_ovlp_filter(out_fn, n_core, fofn, max_diff, max_cov, min_cov, min_len, min_idt, ignore_indels, bestn, db_fn):
    io.LOG('starting ovlp_filter')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn %r: %r' % (fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    tmp_out_fn = out_fn + '.tmp'
    try:
        with open(tmp_out_fn, 'w') as outs:
            run_ovlp_filter(outs, exe_pool, file_list, max_diff, max_cov,
                            min_cov, min_len, min_idt, ignore_indels, bestn, db_fn)
        os.rename(tmp_out_fn, out_fn)
        io.LOG('finished ovlp_filter')
    except:
        io.LOG('terminating ovlp_filter workers...')
        exe_pool.terminate()
        raise

示例#9

文件： ovlp_filter.py 项目： PacificBiosciences/FALCON

def try_run_ovlp_filter(out_fn, n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
    io.LOG('starting ovlp_filter')
    file_list = io.validated_fns(fofn)
    io.LOG('fofn %r: %r' % (fofn, file_list))
    n_core = min(n_core, len(file_list))
    exe_pool = Pool(n_core)
    tmp_out_fn = out_fn + '.tmp'
    try:
        with open(tmp_out_fn, 'w') as outs:
            run_ovlp_filter(outs, exe_pool, file_list, max_diff, max_cov,
                            min_cov, min_len, bestn, db_fn)
            outs.write('---\n')
        os.rename(tmp_out_fn, out_fn)
        io.LOG('finished ovlp_filter')
    except:
        io.LOG('terminating ovlp_filter workers...')
        exe_pool.terminate()
        raise