分析一个GTF基因Fi

Question

我有一个GTF文件，我试图分析，这样“基因id”、“基因类型”、“基因状态”、“基因名称”和水平都在单独的列中。在

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，在单独的列中显示“基因标识”、“基因类型”、“基因状态”、“基因名称”和级别：

^{pr2}$

我尝试过使用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，我收到了一个“ImportError:cannot import name”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')

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

提前谢谢你。在

Answer 1

要将GTF文件中的多个分隔符更改为单个制表符分隔符。一旦你这样做，文件就不再是一个GTF文件。在

下面的代码将把GTF文件的内容转换成文本文件

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，您只能使用create_db()方法一次。所以我才把它评论出来。在

编辑

添加了try语句

Answer 2

您可以使用pyranges库来解析gtf/gff，然后将属性列中的每个条目作为一个单独的列。在

安装说明：

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

示例文件：

^{pr2}$

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]