输入

我有2个输入：一个fasta文件和一个熊猫数据框。

fasta文件如下所示：

> sp|P00001| some text here 1
MKLLILTCLVAVALARPKHPIKKVSPTFDTNMVGKHQGLPQEVLNENLLRFFVAPFPEVFGKEKVSLDAGPGMCSRNE
>sp|P00002| some text here 2
MSSGNAKIGHPAPNFKATAVMPDGQFKDISLSDYKGKYVVFFFYPLDFTFVCPTGLGRSSYRATSCLPALCLP
>sp|P00003| some text here 3
MSVLDSGNFSWKMTEACMKVKIPLVKKKSLRQNLIENGKLKEFMRTHKYNLGSKYIREAATLVSEQPLQN

这是我的第二个输入，一个大熊猫数据框（2列＆＃39; ProteinID＆＃39;和＃39; Phosphopeptide＆＃39;）

ProteinID  -- Phosphopeptide
P00001   --   KVSPT*FDTNMVGK
P00001  --    SLDAGPGMCS*R
P00003   --   LDS*GNFSWKMTEACMK

目标

我需要做的是以下内容。对于每种磷酸肽，我需要在fasta文件头中找到蛋白质（ProteinID）（从＆＃39;＆gt;＆＃39;开始）。然后我需要用星号标记提取氨基酸之前和之后的6个氨基酸。

输出

我的输出是写入数据框的新列，如下所示：

ProteinID  -- Phosphopeptide  --   NewColumn
P00001   --   KVSPT*FDTNMVGK  --   IKKVSPTFDTNMV 
P00001   --   SLDAGPGMCS*R    --   AGPGMCSRNE
P00003   --   LDS*GNFSWKMTEACMK -- MSVLDSGNFSWK

请注意，后两行在其各自蛋白质的末端或开头含有肽，因此在这些情况下我们不需要提取12个氨基酸。

我很难（编程经验很少）编写这个程序，非常感谢任何帮助（建议，提示，功能等）。

Answer 1

这是一个提取相关子字符串的函数：

def flank(seq, pp):
    # 1: find the position of the AA preceding the '*' marker in the
    # phosphopeptide
    marked_pos = pp.find('*') - 1
    if (marked_pos < 0):
        raise ValueError("invalid phosphopeptide string")

    # 2: find the phosphopeptide (without '*') in the sequence
    pp_pos = s.find(pp.replace('*', ''))
    if pp_pos == -1:
        raise ValueError("phosphopeptide not found in the sequence")

    # avoid a negative starting index
    start = max(0, pp_pos + marked_pos - 6)

    # 3: use slicing to produce the result
    return seq[start : pp_pos + marked_pos + 7]

示例：

seq = "MKLLILTCLVAVALARPKHPIKKVSPTFDTNMVGKHQGLPQEVLNENLLRFFVAPFPEVFGKEKVSLDAGPGMCSRNE"
pp = "KVSPT*FDTNMVGK"
print(flank(seq, pp))

打印：

IKKVSPTFDTNMV

Answer 2

嗨请检查一下：我的fasta文件名为'txt'：

段：

#!/usr/bin/python
import re

protein_dict = [
    ('P00001', 'KVSPT*FDTNMVGK'),
    ('P00001', 'SLDAGPGMCS*R'),
    ('P00003', 'LDS*GNFSWKMTEACMK')
    ]

protein_id = None

def prepare_structure_from_fasta(file):
    fasta_structure = dict()
    with open(file, 'r') as fh:
        for line in fh:
            if '>' in line:
                protein_id = line.split('|')[1]
            else:
                if not protein_id:
                    raise Exception("Wrong fasta file structure")
                fasta_structure[protein_id] = line.strip()
    return fasta_structure


def match(pattern, string):
    matc = re.search(pattern, string)
    if matc:
        return matc.groups()[0]
    return None

fasta_struct = prepare_structure_from_fasta('txt')
final_struct = []

for pro_d in protein_dict:

    pro_id = pro_d[0]
    pep_id = pro_d[1]
    first, second = pep_id.split('*')

    if len(first) <= 6:
        f_count = 7 - len(first)
    else:
        first = first[len(first) - 7:]
        f_count = 0
    if len(second) <= 6:
        s_count = 7 - len(second)
    else:
        second = second[0:6]
        s_count = 0

    _regex = '([A-Z]{0,%d}%s%s[A-Z]{0,%d})' % (f_count,first,second,s_count)
    final_struct.append((pro_id, pep_id, match(_regex, fasta_struct[pro_id])))

for pro in final_struct:
    print pro

输出：

('P00001', 'KVSPT*FDTNMVGK', 'IKKVSPTFDTNMV')
('P00001', 'SLDAGPGMCS*R', 'AGPGMCSRNE')
('P00003', 'LDS*GNFSWKMTEACMK', 'MSVLDSGNFSWK')

提取侧翼氨基酸的fasta序列

输入

目标

输出

2 个答案: