Question

我想用带有.tsv部分的列表来更改我的fasta标头的部分。

我不是生物信息学家，而是具有bash和python初学者技能的微生物学家。谢谢。

示例：

标题：

Prevalence_Sequence_ID：1 | ARO：3003072 | RES：mphL |蛋白质同源模型

使用

.tsv

ARO：3003072 mphL mphL是一种染色体编码的大环内酯磷酸转移酶，可灭活14和15元大环内酯，例如红霉素，克拉霉素，阿奇霉素。

到

新标题

Prevalence_Sequence_ID：1 | mphL mphL是一种染色体编码的大环内酯磷酸转移酶，可灭活14和15元大环内酯，例如红霉素，克拉霉素，阿奇霉素。 | RES：mphL |蛋白质同源模型

.tsv中没有给出fasta标头中的ARO，然后就忽略它。

快速法示例

>Prevalence_Sequence_ID:1|ARO:3003072|RES:mphL|Protein Homolog Model
MTTLKVKQLANKKGLNILEDS
>gb|ARO:3004145|RES:AxyZ|Achromobacter_insuavis_AXX-A_
MARKTKEESQRTRDRILDAAEHVFLSKG
>Prevalence_Sequence_ID:31298|ARO:3000777|RES:adeF|Protein Homolog Model
MDFSRFFIDRPIFAAVLSILIFI

.tsv

示例

ARO:3003072 mphL    mphL is a chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.
ARO:3004145 AxyZ    AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.
ARO:3000777 adeF    AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.

Answer 1

如果序列不需要排序，我们可以用第二个字段对fasta进行排序，用|作为分隔符替换.tsv中的第一个空格，然后通过第一个字段对其进行排序，然后使用适当的输出进行合并格式：

cat <<EOF >fasta
>Prevalence_Sequence_ID:1|ARO:3003072|RES:mphL|Protein Homolog Model
MTTLKVKQLANKKGLNILEDS
>gb|ARO:3004145|RES:AxyZ|Achromobacter_insuavis_AXX-A_
MARKTKEESQRTRDRILDAAEHVFLSKG
>Prevalence_Sequence_ID:31298|ARO:3000777|RES:adeF|Protein Homolog Model
MDFSRFFIDRPIFAAVLSILIFI
EOF
cat <<EOF >tsv
ARO:3003072 mphL    mphL is a chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.
ARO:3004145 AxyZ    AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.
ARO:3000777 adeF    AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.
EOF

join -t'|' -12 -21 -o1.1,2.2,1.3 <(
    <fasta sort -t'|' -k2) <(
    <tsv sed 's/ /|/' | sort -t'|' -k1)

如果您需要根据Fasta对输出进行排序，我们可以使用nl -w1对行进行编号，然后进行合并，然后使用数字对输出进行排序，并删除数字：

join -t'|' -12 -21 -o1.1,2.2,1.3 <(
    <fasta nl -w1 | sort -t'|' -k2) <(
    <tsv sed 's/ /|/' | sort -t'|' -k1) |
sort -t $'\t' -n -k2 | cut -f2-

Answer 2

如果您使用awk，则可以执行以下步骤：

读取完整的EventProcessingConfigurer文件并将所有值存储到由第一列索引的数组中。
解析fasta文件：
- 如果遇到标题（以tsv开头），则
  - 从标题（>之后的第一个字符串）中提取密钥
  - 用数组的内容替换键
- 打印当前行

这些步骤也可以在python中完成，但是您可以使用以下行在awk中轻松完成此操作：

Answer 3

import pandas as pd
from Bio import SeqIO

tsvdata = pd.read_csv('example.tsv', sep='/t', header=None, names=['aro','_', 'description'])

for record in SeqIO.parse("example.fasta", "fasta"): 
    fasta_record = str(record).split('|')
    key = fasta_record[1]
    fasta_record[1]=tsvdata[tsvdata['aro']==key]['description'].values[0] 
    print('|'.join(fasta_record))

Answer 4

我将您的示例Fasta和TSV数据保存到example.fasta和example.tsv中。这是输入文件的内容-

$ cat example.fasta
>Prevalence_Sequence_ID:1|ARO:3003072|RES:mphL|Protein Homolog Model
MTTLKVKQLANKKGLNILEDS
>gb|ARO:3004145|RES:AxyZ|Achromobacter_insuavis_AXX-A_
MARKTKEESQRTRDRILDAAEHVFLSKG
>Prevalence_Sequence_ID:31298|ARO:3000777|RES:adeF|Protein Homolog Model
MDFSRFFIDRPIFAAVLSILIFI

$ cat example.tsv
ARO:3003072 mphL    mphL is a chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.
ARO:3004145 AxyZ    AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.
ARO:3000777 adeF    AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.

# import biopython, bioython needs to be installed in your environment/machine
from Bio.SeqIO.FastaIO import SimpleFastaParser as sfp

# read in the tsv data into a dict
with open("example.tsv") as tsvdata:
    tsv_data = {line.strip().split("\t")[0]: " ".join(line.strip().split("\t")[1:])
                for line in tsvdata}

# read input fasta file contents and write to a separate file in real time
with open("example_out.fasta", "w") as outfasta:
    with open("example.fasta") as infasta:
        for header, seq in sfp(infasta):
            aro = header.strip().split("|")[1]  # get ARO for header
            header = header.replace(aro, tsv_data.get(aro, aro))  # lookup ARO in dict and replace if found, otherwise ignore it
            outfasta.write(">{0}\n{1}\n".format(header, seq))

这是输出文件的内容-

$ cat example_out.fasta
>Prevalence_Sequence_ID:1|mphL mphL is a chromosomally-encoded macrolide phosphotransferases that inactivate 14- and 15-membered macrolides such as erythromycin, clarithromycin, azithromycin.|RES:mphL|Protein Homolog Model
MTTLKVKQLANKKGLNILEDS
>gb|AxyZ AxyZ is a transcriptional regulator of the AxyXY-OprZ efflux pump system.|RES:AxyZ|Achromobacter_insuavis_AXX-A_
MARKTKEESQRTRDRILDAAEHVFLSKG
>Prevalence_Sequence_ID:31298|adeF AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH.|RES:adeF|Protein Homolog Model
MDFSRFFIDRPIFAAVLSILIFI

根据.csv

4 个答案: