python - 使用数据框更改 fasta 文件中的序列名称

Question

我有问题，我解释一下。

我有一个 fasta 文件:

>seqA
AAAAATTTGG
>seqB
ATTGGGCCG
>seqC
ATTGGCC
>seqD
ATTGGACAG

和一个数据框:

seq name      New name seq
seqB            BOBO
seqC            JOHN

如果我的数据框中有相同的 seq 名称，我想在 fasta 文件中更改我的 ID seq 名称并将其更改为新名称 seq，它会给出:

新法斯塔:

>seqA
AAAAATTTGG
>BOBO
ATTGGGCCG
>JOHN
ATTGGCC
>seqD
ATTGGACAG

非常感谢

编辑:我使用了这个脚本:

blast=pd.read_table("matches_Busco_0035_0042.m8",header=None)
blast.columns = ["qseqid", "Busco_ID", "pident", "length", "mismatch", "gapopen","qstart", "qend", "sstart", "send", "evalue", "bitscore"]

repl = blast[blast.pident > 95]

print(repl)

#substituion dataframe

newfile = []
count = 0

for rec in SeqIO.parse("concatenate_0035_0042_aa2.fa", "fasta"):
    #get corresponding value for record ID from dataframe
    x = repl.loc[repl.seq == rec.id, "Busco_ID"]
    #change record, if not empty
    if x.any():
        rec.name = rec.description = rec.id = x.iloc[0]
        count += 1
    #append record to list
    newfile.append(rec)

#write list into new fasta file
SeqIO.write(newfile, "changedtest.faa", "fasta")
#tell us, how hard you had to work for us
print("I changed {} entries!".format(count))

我得到了以下错误:

Traceback (most recent call last):
  File "Get_busco_blast.py", line 74, in <module>
    x = repl.loc[repl.seq == rec.id, "Busco_ID"]
  File "/usr/local/lib/python3.6/site-packages/pandas/core/generic.py", line 3614, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'seq'

Answer 1

用 BioPython 之类的东西更容易做到这一点.

先创建字典

names = Series(df['seq name'].values,index=df['New seq name']).to_dict()

现在迭代

from Bio import SeqIO
outs = []
for record in SeqIO.parse("orig.fasta", "fasta"):
    record.id = names.get(record.id, default=record.id)
    outs.append(record)
SeqIO.write(open("new.fasta", "w"), outs, "fasta")