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我正在使用这个脚本：

import csv
import time
import sys
from ete3 import NCBITaxa

ncbi = NCBITaxa()

def get_desired_ranks(taxid, desired_ranks):
    lineage = ncbi.get_lineage(taxid)   
    names = ncbi.get_taxid_translator(lineage)
    lineage2ranks = ncbi.get_rank(names)
    ranks2lineage = dict((rank,taxid) for (taxid, rank) in lineage2ranks.items())
    return{'{}_id'.format(rank): ranks2lineage.get(rank, '<not present>') for rank in desired_ranks}

if __name__ == '__main__':
    file = open(sys.argv[1], "r")    
    taxids = []
    contigs = []
    for line in file:
        line = line.split("\n")[0]
        taxids.append(line.split(",")[0])
        contigs.append(line.split(",")[1])

    desired_ranks = ['superkingdom', 'phylum']
    results = list()
    for taxid in taxids:
        results.append(list())
        results[-1].append(str(taxid))
        ranks = get_desired_ranks(taxid, desired_ranks)
        for key, rank in ranks.items():
            if rank != '<not present>':
                results[-1].append(list(ncbi.get_taxid_translator([rank]).values())[0])
            else:
                results[-1].append(rank)

    i = 0
    for result in results:
        print(contigs[i] + ','),
        print(','.join(result))
        i += 1

    file.close()

该脚本从文件中提取样本，并从 NCBI 分类数据库的本地副本中获取它们各自的谱系。奇怪的是，当我在少量出租车（~​​70，~100）上运行该脚本时，它运行良好，但我的大多数数据集都超过 280k 出租车，这些破坏了脚本。

我得到这个完整的错误：

Traceback (most recent call last):
  File "/data1/lstout/blast/scripts/getLineageByETE3.py", line 31, in <module>
    ranks = get_desired_ranks(taxid, desired_ranks)
  File "/data1/lstout/blast/scripts/getLineageByETE3.py", line 11, in get_desired_ranks
    lineage = ncbi.get_lineage(taxid)   
  File "/data1/lstout/.local/lib/python2.7/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 227, in get_lineage
    result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %taxid)
sqlite3.Warning: You can only execute one statement at a time.

回溯中的前两个文件只是我上面引用的脚本，第三个文件是 ete3 的一个。正如我所说，该脚本适用于小型数据集。

我试过的：

  • 导入时间模块并在第 11 行和第 31 行我的违规代码行之前/之后休眠几毫秒/百分之一秒。没有效果。

  • 转到ete3代码中的第227行......

    result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %merged_conversion[taxid])

并将“执行”功能更改为“执行脚本”，以便能够一次处理多个查询（这似乎是问题所在）。这产生了一个新的错误，并导致我在他们的脚本中更改一些小东西试图让它起作用。没有结果。这是完整的违规功能：

    def get_lineage(self, taxid):
    """Given a valid taxid number, return its corresponding lineage track as a
    hierarchically sorted list of parent taxids.
    """
    if not taxid:
        return None
    result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %taxid)
    raw_track = result.fetchone()
    if not raw_track:
        #perhaps is an obsolete taxid
        _, merged_conversion = self._translate_merged([taxid])
        if taxid in merged_conversion:
            result = self.db.execute('SELECT track FROM species WHERE taxid=%s' %merged_conversion[taxid])
            raw_track = result.fetchone()
        # if not raise error
        if not raw_track:
            #raw_track = ["1"]
            raise ValueError("%s taxid not found" %taxid)
        else:
            warnings.warn("taxid %s was translated into %s" %(taxid, merged_conversion[taxid]))

    track = list(map(int, raw_track[0].split(",")))
    return list(reversed(track))

令我困扰的是，这适用于少量数据！我正在我学校的高性能计算机上运行这些脚本，并尝试在他们的头节点和交互式 moab 调度程序中运行。没有任何帮助。

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