Python 解析GTF基因文件

我有一个试图解析的基因GTF文件，因此“基因id”、“基因类型”、“基因状态”、“基因名称”和级别都在单独的列中

因此，对于我的原始文件：

chr1 |  ENSEMBL gene|   17369|  17436|  .   -   .   |gene_id "ENSG00000278267.1"; gene_type "miRNA"; gene_status "KNOWN"; gene_name "MIR6859-1"; level 3;
chr1 |  ENSEMBL gene|   30366|  30503|  .   +   .   |gene_id "ENSG00000274890.1"; gene_type "miRNA"; gene_status "KNOWN"; gene_name "MIR1302-2"; level 3;
chr1 |  ENSEMBL gene|   157784| 157887| .   -   .   |gene_id "ENSG00000222623.1"; gene_type "snRNA"; gene_status "KNOWN"; gene_name "RNU6-1100P"; level 3;
chr1 |  ENSEMBL gene|   187891| 187958| .   -   .   |gene_id "ENSG00000273874.1"; gene_type "miRNA"; gene_status "KNOWN"; gene_name "MIR6859-2"; level 3;

我希望它看起来像这样，“基因id”、“基因类型”、“基因状态”、“基因名称”和级别都在单独的列中：

 chr1   |ENSEMBL    |gene|  17369|  |17436  |.  -   .   |gene_id "ENSG00000278267.1"   |gene_type "miRNA"   |gene_status "KNOWN"   |gene_name "MIR6859-1"   |level 3
 chr1   |ENSEMBL    |gene|  30366|  30503   |.  +   .   |gene_id "ENSG00000274890.1"   |gene_type "miRNA"   |gene_status "KNOWN"   |gene_name "MIR1302-2"   |level 3 
 chr1   |ENSEMBL    |gene|  157784| 157887  |.  -   .   |gene_id "ENSG00000222623.1"   |gene_type "snRNA"   |gene_status "KNOWN"   |gene_name "RNU6-1100P"  |level 3  
 chr1   |ENSEMBL    |gene|  187891| 187958  |.  -   .   |gene_id "ENSG00000273874.1"   |gene_type "miRNA"   |gene_status "KNOWN"   |gene_name "MIR6859-2"   |level 3 

我已经尝试使用gffutils解析它，使用它们提供的基本代码：

import gffutils


db = gffutils.create_db("sRNA.gene.gtf", dbfn='sRNA.gene.gtf.db')

print(list(db.featuretypes()))

# Here's how to write genes out to file
with open('sRNA.gene.gtf', 'w') as fout:
  for gene in db.features_of_type('gene'):
    fout.write(str(gene) + '\n')

但是，我收到一个“ImportError:无法导入名称”功能：'

ImportError                               Traceback (most recent call last)
<ipython-input-26-4dd7cd5c7e24> in <module>()
      2 
      3 
----> 4 db = gffutils.create_db("sRNA.gene.gtf", dbfn='sRNA.gene.gtf.db')
      5 
      6 #db = gffutils.FeatureDB('sRNA.gene.gtf.db')

ImportError回溯（最近一次调用）
在（）
2.
3.
---->4db=gffutils.create_db（“sRNA.gene.gtf”，dbfn='sRNA.gene.gtf.db'）
5.
6#db=gffutils.FeatureDB（'sRNA.gene.gtf.db'））

我不确定这里出了什么问题，现在我正在考虑尝试使用命令行解析它。谁能提供一些关于解析GTF文件的最佳方法的建议

---

先谢谢你

要将GTF文件中的多个分隔符更改为单个制表符分隔符。完成此操作后，该文件不再是GTF文件

以下代码将GTF文件的内容转换为文本文件

import gffutils
try:
    db = gffutils.create_db("sample.gtf", dbfn='sample.db')
except:
    pass
db = gffutils.FeatureDB('sample.db', keep_order=True)
with open('sample.txt', 'w') as fout:
    for line in db.all_features():
        line = str(line)
        line = line.split(";") #make your parsing changes here
        fout.write(str(line) + '\n')

请注意，只能使用

create_db（）

方法一次。这就是我把它注释掉的原因

编辑

添加了try语句

您可以使用该库解析gtf/gff，然后将属性列中的每个条目作为一个列获取

安装说明：

# pip install pyranges
# or 
# conda install -c bioconda pyranges

示例文件：

# !head ensembl.gtf
# #!genome-build GRCh38.p10
# #!genome-version GRCh38
# #!genome-date 2013-12
# #!genome-build-accession NCBI:GCA_000001405.25
# #!genebuild-last-updated 2017-06
# 1       havana  gene    11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
# 1       havana  transcript      11869   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
# 1       havana  exon    11869   12227   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
# 1       havana  exon    12613   12721   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
# 1       havana  exon    13221   14409   .       +       .       gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";

使用吡喃：

import pyranges as pr

# as PyRanges-object
gr = pr.read_gtf("ensembl.gtf")
# +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-----------------+----------------+-------------+----------------+------------------------------------+-----------------+----------------------+-------+
# | Chromosome   | Source     | Feature      | Start     | End       | Score      | Strand       | Frame      | gene_id         | gene_version   | gene_name   | gene_source    | gene_biotype                       | transcript_id   | transcript_version   | +13   |
# | (category)   | (object)   | (category)   | (int32)   | (int32)   | (object)   | (category)   | (object)   | (object)        | (object)       | (object)    | (object)       | (object)                           | (object)        | (object)             | ...   |
# |--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-----------------+----------------+-------------+----------------+------------------------------------+-----------------+----------------------+-------|
# | 1            | havana     | gene         | 11869     | 14409     | .          | +            | .          | ENSG00000223972 | 5              | DDX11L1     | havana         | transcribed_unprocessed_pseudogene | nan             | nan                  | ...   |
# | 1            | havana     | transcript   | 11869     | 14409     | .          | +            | .          | ENSG00000223972 | 5              | DDX11L1     | havana         | transcribed_unprocessed_pseudogene | ENST00000456328 | 2                    | ...   |
# | 1            | havana     | exon         | 11869     | 12227     | .          | +            | .          | ENSG00000223972 | 5              | DDX11L1     | havana         | transcribed_unprocessed_pseudogene | ENST00000456328 | 2                    | ...   |
# | 1            | havana     | exon         | 12613     | 12721     | .          | +            | .          | ENSG00000223972 | 5              | DDX11L1     | havana         | transcribed_unprocessed_pseudogene | ENST00000456328 | 2                    | ...   |
# | ...          | ...        | ...          | ...       | ...       | ...        | ...          | ...        | ...             | ...            | ...         | ...            | ...                                | ...             | ...                  | ...   |
# | 1            | ensembl    | transcript   | 120725    | 133723    | .          | -            | .          | ENSG00000238009 | 6              | AL627309.1  | ensembl_havana | lincRNA                            | ENST00000610542 | 1                    | ...   |
# | 1            | ensembl    | exon         | 133374    | 133723    | .          | -            | .          | ENSG00000238009 | 6              | AL627309.1  | ensembl_havana | lincRNA                            | ENST00000610542 | 1                    | ...   |
# | 1            | ensembl    | exon         | 129055    | 129223    | .          | -            | .          | ENSG00000238009 | 6              | AL627309.1  | ensembl_havana | lincRNA                            | ENST00000610542 | 1                    | ...   |
# | 1            | ensembl    | exon         | 120874    | 120932    | .          | -            | .          | ENSG00000238009 | 6              | AL627309.1  | ensembl_havana | lincRNA                            | ENST00000610542 | 1                    | ...   |
# +--------------+------------+--------------+-----------+-----------+------------+--------------+------------+-----------------+----------------+-------------+----------------+------------------------------------+-----------------+----------------------+-------+
# Stranded PyRanges object has 95 rows and 28 columns from 1 chromosomes.
# For printing, the PyRanges was sorted on Chromosome and Strand.
# 13 hidden columns: transcript_name, transcript_source, transcript_biotype, tag, transcript_support_level, exon_number, exon_id, exon_version, (assigned, previous, ccds_id, protein_id, protein_version


# as DataFrame
df = gr.df

# Chromosome   Source     Feature   Start     End Score Strand Frame          gene_id gene_version   gene_name  ...    transcript_biotype    tag transcript_support_level exon_number          exon_id exon_version (assigned previous ccds_id protein_id protein_version
# 0           1   havana        gene   11869   14409     .      +     .  ENSG00000223972            5     DDX11L1  ...                   NaN    NaN                      NaN         NaN              NaN          NaN       NaN      NaN     NaN        NaN             NaN
# 1           1   havana  transcript   11869   14409     .      +     .  ENSG00000223972            5     DDX11L1  ...  processed_transcript  basic                        1         NaN              NaN          NaN       NaN      NaN     NaN        NaN             NaN
# 2           1   havana        exon   11869   12227     .      +     .  ENSG00000223972            5     DDX11L1  ...  processed_transcript  basic                        1           1  ENSE00002234944            1       NaN      NaN     NaN        NaN             NaN
# 3           1   havana        exon   12613   12721     .      +     .  ENSG00000223972            5     DDX11L1  ...  processed_transcript  basic                        1           2  ENSE00003582793            1       NaN      NaN     NaN        NaN             NaN
# 4           1   havana        exon   13221   14409     .      +     .  ENSG00000223972            5     DDX11L1  ...  processed_transcript  basic                        1           3  ENSE00002312635            1       NaN      NaN     NaN        NaN             NaN
# ..        ...      ...         ...     ...     ...   ...    ...   ...              ...          ...         ...  ...                   ...    ...                      ...         ...              ...          ...       ...      ...     ...        ...             ...
# 90          1   havana        exon  110953  111357     .      -     .  ENSG00000238009            6  AL627309.1  ...               lincRNA    NaN                        5           3  ENSE00001879696            1       NaN      NaN     NaN        NaN             NaN
# 91          1  ensembl  transcript  120725  133723     .      -     .  ENSG00000238009            6  AL627309.1  ...               lincRNA  basic                        5         NaN              NaN          NaN       NaN      NaN     NaN        NaN             NaN
# 92          1  ensembl        exon  133374  133723     .      -     .  ENSG00000238009            6  AL627309.1  ...               lincRNA  basic                        5           1  ENSE00003748456            1       NaN      NaN     NaN        NaN             NaN
# 93          1  ensembl        exon  129055  129223     .      -     .  ENSG00000238009            6  AL627309.1  ...               lincRNA  basic                        5           2  ENSE00003734824            1       NaN      NaN     NaN        NaN             NaN
# 94          1  ensembl        exon  120874  120932     .      -     .  ENSG00000238009            6  AL627309.1  ...               lincRNA  basic                        5           3  ENSE00003740919            1       NaN      NaN     NaN        NaN             NaN
# 
# [95 rows x 28 columns]

---

请根据您的示例输入，编辑您的问题以包含您所需的输出。祝你好运。添加了更改，谢谢！很难看出您的输入和输出之间的差异。您可以在列之间切换到使用

|

字符吗？然后，是否将其加载到excel或类似文件中？祝你好运。在原始版本中，在“gene_id”之后，所有变量都分组在一行中，我希望所有变量都通过它们的标识符进入不同的列中。我看到的是

字符被删除。够了吗<代码>sed的/；//g'file>outFile

将执行此操作。否则，需要知道是否有用于分隔字段的字符。i、 e.标签分开？祝你好运，谢谢。我尝试了这个，但得到了错误“DatabaseError:文件已加密或不是数据库”@espop23您可能需要取消对我代码第二行的注释，并将

sample.gtf

重命名为

sRNA.gene.gtf

谢谢，然后它会说“OperationalError:表功能已经存在”though@espop23好啊现在将注释符号放回第二行代码前面，再试一次。我尝试了这些更改，但结果是：“['chr1\tHAVANA\tgene\t29554\t31109\t.\t+\t.\tgene\u id“ENSG0000243485.3”、'gene\u type“lincRNA”、'gene\u status“KNOWN”、'gene\u name“RP11-34P13.3”、'level“2”、'tag“ncRNA\u host”、'havana\u gene”“Otthumg0000000959.2”