Question

我有一个熊猫df：

number  sample  chrom1  start   chrom2  end
1   s1  1   0   2   1500
2   s1  2   10  2   50
19  s2  3   3098318 3   3125700
19  s3  3   3098720 3   3125870
20  s4  3   3125694 3   3126976
20  s1  3   3125694 3   3126976
20  s1  3   3125695 3   3126976
20  s5  3   3125700 3   3126976
21  s3  3   3125870 3   3134920
22  s2  3   3126976 3   3135039
24  s5  3   17286051    3   17311472
25  s2  3   17286052    3   17294628
26  s4  3   17286052    3   17311472
26  s1  3   17286052    3   17311472
27  s3  3   17286405    3   17294550
28  s4  3   17293197    3   17294628
28  s1  3   17293197    3   17294628
28  s5  3   17293199    3   17294628
29  s2  3   17294628    3   17311472

我正在尝试将具有不同数字的行分组，但是其中start在+/- 10内 AND 的末尾也在同一行的+/- 10内染色体。

在此示例中，我想找到这两行：

24  s5  3   17286051    3   17311472
26  s4  3   17286052    3   17311472

其中chrom1 [3]和chrom2 [3]相同，并且start和结束值彼此为+/- 10，并将它们分组为相同的数字：

24  s5  3   17286051    3   17311472
24  s4  3   17286052    3   17311472 # Change the number to the first seen in this series

这就是我要尝试的：

import pandas as pd
from collections import defaultdict


def parse_vars(inFile):

    df = pd.read_csv(inFile, delimiter="\t")
    df = df[['number', 'chrom1', 'start', 'chrom2', 'end']]

    vars = {}

    seen_l = defaultdict(lambda: defaultdict(dict)) # To track the `starts`
    seen_r = defaultdict(lambda: defaultdict(dict)) # To track the `ends`

    for index in df.index:
        event = df.loc[index, 'number']
        c1 = df.loc[index, 'chrom1']
        b1 = int(df.loc[index, 'start'])
        c2 = df.loc[index, 'chrom2']
        b2 = int(df.loc[index, 'end'])

        print [event, c1, b1, c2, b2]

        vars[event] = [c1, b1, c2, b2]

        # Iterate over windows +/- 10
        for i, j in zip( range(b1-10, b1+10), range(b2-10, b2+10) ):
            # if : 
            # i in seen_l[c1] AND
            # j in seen_r[c2] AND
            # the 'number' for these two instances is the same: 

            if i in seen_l[c1] and j in seen_r[c2] and seen_l[c1][i] == seen_r[c2][j]:
                print seen_l[c1][i], seen_r[c2][j]
                if seen_l[c1][i] != event: print"Seen: %s %s in event %s %s" % (event, [c1, b1, c2, b2], seen_l[c1][i], vars[seen_l[c1][i]])

        seen_l[c1][b1] = event
        seen_r[c2][b2] = event

我遇到的问题是，seen_l[3][17286052] numbers和25中都存在26，并且它们各自的seen_r事件都存在（{{ 1}}，seen_r[3][17294628] = 25）不相等，我无法将这些行连接在一起。

是否可以使用seen_r[3][17311472] = 26值列表作为start字典的嵌套键？

Answer 1

在pyranges中，间隔重叠很容易。下面的大多数代码是将开始和结束分成两个不同的df。然后根据+ -10的时间间隔重叠将其合并：

from io import StringIO
import pandas as pd
import pyranges as pr

c = """number  sample  chrom1  start   chrom2  end
1   s1  1   0   2   1500
2   s1  2   10  2   50
19  s2  3   3098318 3   3125700
19  s3  3   3098720 3   3125870
20  s4  3   3125694 3   3126976
20  s1  3   3125694 3   3126976
20  s1  3   3125695 3   3126976
20  s5  3   3125700 3   3126976
21  s3  3   3125870 3   3134920
22  s2  3   3126976 3   3135039
24  s5  3   17286051    3   17311472
25  s2  3   17286052    3   17294628
26  s4  3   17286052    3   17311472
26  s1  3   17286052    3   17311472
27  s3  3   17286405    3   17294550
28  s4  3   17293197    3   17294628
28  s1  3   17293197    3   17294628
28  s5  3   17293199    3   17294628
29  s2  3   17294628    3   17311472"""

df = pd.read_table(StringIO(c), sep="\s+")

df1 = df[["chrom1", "start", "number", "sample"]]
df1.insert(2, "end", df.start + 1)

df2 = df[["chrom2", "end", "number", "sample"]]
df2.insert(2, "start", df.end - 1)

names = ["Chromosome", "Start", "End", "number", "sample"]
df1.columns = names
df2.columns = names

gr1, gr2 = pr.PyRanges(df1), pr.PyRanges(df2)

j = gr1.join(gr2, slack=10)
# +--------------+-----------+-----------+-----------+------------+-----------+-----------+------------+------------+
# | Chromosome   | Start     | End       | number    | sample     | Start_b   | End_b     | number_b   | sample_b   |
# | (category)   | (int32)   | (int32)   | (int64)   | (object)   | (int32)   | (int32)   | (int64)    | (object)   |
# |--------------+-----------+-----------+-----------+------------+-----------+-----------+------------+------------|
# | 3            | 3125694   | 3125695   | 20        | s4         | 3125700   | 3125699   | 19         | s2         |
# | 3            | 3125694   | 3125695   | 20        | s1         | 3125700   | 3125699   | 19         | s2         |
# | 3            | 3125695   | 3125696   | 20        | s1         | 3125700   | 3125699   | 19         | s2         |
# | 3            | 3125700   | 3125701   | 20        | s5         | 3125700   | 3125699   | 19         | s2         |
# | ...          | ...       | ...       | ...       | ...        | ...       | ...       | ...        | ...        |
# | 3            | 17294628  | 17294629  | 29        | s2         | 17294628  | 17294627  | 25         | s2         |
# | 3            | 17294628  | 17294629  | 29        | s2         | 17294628  | 17294627  | 28         | s5         |
# | 3            | 17294628  | 17294629  | 29        | s2         | 17294628  | 17294627  | 28         | s1         |
# | 3            | 17294628  | 17294629  | 29        | s2         | 17294628  | 17294627  | 28         | s4         |
# +--------------+-----------+-----------+-----------+------------+-----------+-----------+------------+------------+
# Unstranded PyRanges object has 13 rows and 9 columns from 1 chromosomes.
# For printing, the PyRanges was sorted on Chromosome.

# to get the data as a pandas df:
jdf = j.df

对列的值在pandas df

1 个答案: