给定另一个包含来自ListA的部分字符串的ListB的代码,改进TSV字符串的代码排序ListA并返回每个模式的第一顺序

时间:2019-02-15 12:36:27

标签: python python-3.x list sorting

继上一个问题here之后,我面临另一个挑战。

我有以下新的listA

listA = ['rs141130360\tchr1:16495\tC\t653635\tNC_024540.1\tTranscript\tintron_variant,non_coding_transcript_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t-\t-1\t-\tSNV\tWASH7P\tEntrezGene\tHGNC:38034\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\tOK\t-\t-\t-\t-\t8/10\t-\t-\tNR_024540.1:n.1080+112C>G\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs141130360\tchr1:16495\tC\t100287102\tNR_046018.2\tTranscript\tframeshift_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t2086\t1\t-\tSNV\tDDX11L1\tEntrezGene\tHGNC:37102\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs141130360\tchr1:16495\tC\t102466751\tNG_106918.1\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t874\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs141130360\tchr1:16495\tC\t102466751\tNG_106918.1\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t874\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs62636367\tchr1:16719\tA\t653635\tNR_024540.1\tTranscript\tnon_coding_transcript_exon_variant\t968\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t-\t-1\t-\tSNV\tWASH7P\tEntrezGene\tHGNC:38034\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\tOK\t-\t-\t-\t8/11\t-\t-\t-\tNR_024540.1:n.968A>T\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs62636367\tchr1:16719\tA\t100287102\tNR_046018.2\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t2310\t1\t-\tSNV\tDDX11L1\tEntrezGene\tHGNC:37102\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
         'rs62636367\tchr1:16719\tA\t102466751\tNC_106918.1\tTranscript\tframeshift_variant\t-\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t650\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n']

和相同的listB和空白的listC

ListB = ["NC", "NG", "NM", "NP", "NR", "XM", "XP", "XR", "WP"]
listC = []

使用以下代码,我可以通过将listA中的字符串匹配到listB的第五列来根据listBlistA重新排序:

d = {x: i for i, x in enumerate(listB)}

def get_index(s):
    by_tabs = s.split('\t')
    by_underscore = by_tabs[4].split('_')
    return d[by_underscore[0]]

listC = sorted(listA, key=get_index)

listC将输出:

print(listC)
['rs141130360\tchr1:16495\tC\t653635\tNC_024540.1\tTranscript\tintron_variant,non_coding_transcript_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t-\t-1\t-\tSNV\tWASH7P\tEntrezGene\tHGNC:38034\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\tOK\t-\t-\t-\t-\t8/10\t-\t-\tNR_024540.1:n.1080+112C>G\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n', 
'rs62636367\tchr1:16719\tA\t102466751\tNC_106918.1\tTranscript\tframeshift_variant\t-\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t650\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n', 
'rs141130360\tchr1:16495\tC\t102466751\tNG_106918.1\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t874\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
'rs141130360\tchr1:16495\tC\t102466751\tNG_106918.1\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t874\t-1\t-\tSNV\tMIR6859-1\tEntrezGene\tHGNC:50039\tmiRNA\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
'rs141130360\tchr1:16495\tC\t100287102\tNR_046018.2\tTranscript\tframeshift_variant\t-\t-\t-\t-\t-\trs3210724\tG\tMODIFIER\t2086\t1\t-\tSNV\tDDX11L1\tEntrezGene\tHGNC:37102\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tG\tG\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
'rs62636367\tchr1:16719\tA\t653635\tNR_024540.1\tTranscript\tnon_coding_transcript_exon_variant\t968\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t-\t-1\t-\tSNV\tWASH7P\tEntrezGene\tHGNC:38034\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\tOK\t-\t-\t-\t8/11\t-\t-\t-\tNR_024540.1:n.968A>T\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n',
'rs62636367\tchr1:16719\tA\t100287102\tNR_046018.2\tTranscript\tdownstream_gene_variant\t-\t-\t-\t-\t-\trs62636367\tT\tMODIFIER\t2310\t1\t-\tSNV\tDDX11L1\tEntrezGene\tHGNC:37102\ttranscribed_pseudogene\t-\t-\t-\t-\t-\t-\t-\t-\t-\tRefSeq\tT\tT\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\t-\n']

我想返回listC中每个listB根据key排序的dictionary中的第一个元素。我尝试快速获得所需的输出如下:我有一个附加的词典,其中包含来自第一TSV列(dictionary = { 'rs141130360': 'value', 'rs62636367': 'value', etc...}

for i in list(dictionary.keys()):
    print(next((x for x in listC if i in x), ""))

将正确打印:

rs141130360 chr1:16495  C   653635  NC_024540.1 Transcript  intron_variant,non_coding_transcript_variant    -   -   -   -   -   rs3210724   G   MODIFIER    -   -1  -   SNV WASH7P  EntrezGene  HGNC:38034  transcribed_pseudogene  -   -   -   -   -   -   -   -   -   RefSeq  G   G   OK  -   -   -   -   8/10    -   -   NR_024540.1:n.1080+112C>G   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
rs62636367  chr1:16719  A   102466751   NC_106918.1 Transcript  frameshift_variant  -   -   -   -   -   rs62636367  T   MODIFIER    650 -1  -   SNV MIR6859-1   EntrezGene  HGNC:50039  miRNA   -   -   -   -   -   -   -   -   -   RefSeq  T   T   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -

但是,问题是我的真实listA包含532493个元素。遍历这个庞大的列表需要花费很多时间。

我希望在上面获得相同的输出,但需要的运行时间更少(30 mins之后,它正在运行,但仍未完成。如果我猜对了,应该对函数{{ 1}},但目前还不确定该怎么办。

0 个答案:

没有答案