python - 去除重复行并保留得分最高的行

Question

第一列（scaffold这一列）相同，则根据第AS列（AS:i:xx）数字 xx的大小，保留数字最大的行。如果数字大小相同则都保留。

举例，
输入文件

scaffold_010679_1AL.2    16    chr1A    429400034    119    3272M    *    GACACAAGAGACTCTTTG    *    AS:i:3268    XS:i:2147    XF:i:0    XE:i:29    NM:i:1
scaffold_010679_1AL.2    16    chr1A    429400034    119    3272M    *    GACACAAGAGACTCTTTG    *    AS:i:3268    XS:i:2147    XF:i:0    XE:i:29    NM:i:1 
scaffold_010679_1AL.2    16    chr1A    429400034    119    3272M    *    GACACAAGAGACTCTTTG    *    AS:i:1268    XS:i:2147    XF:i:0    XE:i:29    NM:i:1
scaffold_010679_1AL.3    16    chr1A    429397743    19    599S1730M1I279M    *    0    0    TGCCGAGGTTTTTGA    *    AS:i:1998    XS:i:1877    XF:i:3    XE:i:20    NM:i:2    XN:i:1
scaffold_010679_1AL.3    16    chr1A    429397743    19    599S1730M1I279M    *    0    0    TGCCGAGGTTTTTGA    *    AS:i:1098    XS:i:1877    XF:i:3    XE:i:20    NM:i:2    XN:i:1

结果文件

scaffold_010679_1AL.2    16    chr1A    429400034    119    3272M    *    GACACAAGAGACTCTTTG    *    AS:i:3268    XS:i:2147    XF:i:0    XE:i:29    NM:i:1
scaffold_010679_1AL.2    16    chr1A    429400034    119    3272M    *    GACACAAGAGACTCTTTG    *    AS:i:3268    XS:i:2147    XF:i:0    XE:i:29    NM:i:1 
scaffold_010679_1AL.3    16    chr1A    429397743    19    599S1730M1I279M    *    0    0    TGCCGAGGTTTTTGA    *    AS:i:1998    XS:i:1877    XF:i:3    XE:i:20    NM:i:2    XN:i:1

Answer 1

# coding: utf-8

from itertools import groupby

with open('a.txt') as f:
    data = [line for line in f]

    #因为数据的列数不相同, 只能以AS:i:为开头来识别
    #取第一列为key, AS:i:列为value
    lst = [(l.split()[0], _) for l in data for _ in l.split() if _.startswith('AS:i:')]
    
    #找出同key下的max(value)
    max_lst = [max(list(g)) for k, g in groupby(lst, lambda x: x[0])]
    
    #从原数据里找到同时包含key和value的行
    print [line for line in data for _ in max_lst if _[0] in line and _[1] in line]

Answer 2

awk '{n=gensub(".*AS:i:([0-9]+).*","\\1","g")}n>=k[$1]{c[$1]=n==k[$1]?c[$1]"\n"$0:$0;k[$1]=n}END{for(i in c)print c[i]}' file

Answer 3

grep "`sort -r -t "*" -k 3 b.txt | head -1 |awk -F "*" '{split(,a," ");print a[1]}'
`" b.txt

The idea file is divided into 3 columns according to the asterisk *, sorted in descending order according to the third column, take out the first row, take out the AS:i: maximum number, search it with grep, and get the result.

I didn’t read the question carefully and made a mistake~~The result is wrong