如何根据文件的内容将文件移动到不同的目录?

如何根据文件的内容将文件移动到不同的目录?

我有很多文件都包含这样的字符串:

/databis/defontis/Dossier_fasta_chrm_avec_piler/SRR6237661_chrm.fasta: N putative CRISPR arrays found

其中N是一个可以是其中之一或更大的数字0。我需要将 is 的所有文件移动N0该目录Sans_crispr,并将N大于0该目录的所有文件移动到该目录Avec_crispr

我还可以看到ls,所有未找到 CRISPR 的文件(其中的文件N0都小于 3355 字节,因此也许可以使用。

我试过这个:

find . -name "*.out" -type 'f' -size -5k -exec mv {} /databis/defontis/Dossier_fasta_chrm_avec_piler/Dossier_fasta_chrm_sortie_pilercr/Sans_Crispr/ \;

但对于我所有的文件,我都有这个

mv: cannot move './SRR5273182_chrm.fasta.fa-pilercr.out' to '/databis/defontis/Dossier_fasta_chrm_avec_piler/Dossier_fasta_chrm_sortie_pilercr/Sans-Crispr/': Not a directory

我尝试了一些for f in ...do doneif then fi.我尝试了grep该模式' 0 putative CRISPR arrays found' ,但没有一个起作用,总是出现错误或者我没有找到我想要的东西。

这是我的文件的示例:

在此输入图像描述

这就是内容:与 Crispr

Help on reading this report
===========================

This report has three sections: Detailed, Summary by Similarity and Summary by Position.

The detailed section shows each repeat in each putative CRISPR array.

The summary sections give one line for each array.

An 'array' is a contiguous sequence of CRISPR repeats looking like this:

    REPEAT Spacer REPEAT Spacer REPEAT ... Spacer REPEAT

Within one array, repeats have high similarity and spacers are, roughly speaking, unique within a window around the array. In a given array, each repeat has a similar length, and each spacer has a similar length. With default parameters, the algorithm allows a fair amount of variability in order to maximize sensitivity. This may allow identification of inactive ("fossil") arrays, and may in rare cases also induce false positives due to other classes of repeats such as microsatellites, LTRs and arrays of RNA genes.


Columns in the detailed section are:

  Pos               Sequence position, starting at 1 for the first base.   Repeat            Length of the repeat.   %id               Identity with the consensus sequence.   Spacer            Length of spacer to the right of this repeat.   Left flank        10 bases to the left of this repeat.   Repeat            Sequence of this repeat.
                      Dots indicate positions where this repeat
                      agrees with the consensus sequence below.   Spacer            Sequence of spacer to the right of this repeat,
                      or 10 bases if this is the last repeat.

The left flank sequence duplicates the end of the spacer for the preceding repeat; it is provided to facilitate visual identification of cases where the algorithm does not correctly identify repeat endpoints.

At the end of each array there is a sub-heading that gives the average repeat length, average spacer length and consensus sequence.

Columns in the summary sections are:

  Array             Number 1, 2 ... referring back to the detailed report.   Sequence          FASTA label of the sequence. May be truncated.   From              Start position of array.   To           End position of array.   # copies          Number of repeats in the array.   Repeat            Average repeat length.   Spacer            Average spacer length.   +                 +/-, indicating orientation relative to first array in group.   Distance          Distance from previous array.   Consensus         Consensus sequence.

In the Summary by Similarity section, arrays are grouped by similarity of their consensus sequences. If consensus sequences are sufficiently similar, they are aligned to each other to indicate probable relationships between arrays.

In the Summary by Position section, arrays are sorted by position within the input sequence file.

The Distance column facilitates identification of cases where a single array has been reported as two adjacent arrays. In such a case, (a) the consensus sequences will be similar or identical, and (b) the distance will be approximately a small multiple of the repeat length + spacer length.

Use the -noinfo option to turn off this help. Use the -help option to get a list of command line options.

pilercr v1.06 By Robert C. Edgar

/databis/defontis/Dossier_fasta_chrm_avec_piler/SRR2177954_chrm.fasta: 1 putative CRISPR arrays found.



DETAIL REPORT



Array 1
>SRR2177954.k141_500270 flag=1 multi=9.2309 len=7453

       Pos  Repeat     %id  Spacer  Left flank    Repeat                                  Spacer
==========  ======  ======  ======  ==========    ====================================    ======
        66      36   100.0      25  CAGAAGTATT    ....................................    CTCACACACGCTGATGCAGACAACA
       127      36   100.0      26  GCAGACAACA    ....................................    GCGAGAGCAGGGATTTGGAACGTAAT
       189      36   100.0      26  GGAACGTAAT    ....................................    ATGTTGATGGAAAAACTCCCACAGAC
       251      36   100.0          TCCCACAGAC    ....................................    ACTGAATGTG
==========  ======  ======  ======  ==========    ====================================
         4      36              25                ATCTACAAAAGTAGAAATTTTATAGAGGTATTTGGC


SUMMARY BY SIMILARITY



Array          Sequence    Position      Length  # Copies  Repeat  Spacer  +  Consensus
=====  ================  ==========  ==========  ========  ======  ======  =  =========
    1  SRR2177954.k141_          66         221         4      36      25  +  ATCTACAAAAGTAGAAATTTTATAGAGGTATTTGGC



SUMMARY BY POSITION



>SRR2177954.k141_500270 flag=1 multi=9.2309 len=7453

Array          Sequence    Position      Length  # Copies  Repeat  Spacer    Distance  Consensus
=====  ================  ==========  ==========  ========  ======  ======  ==========  =========
    1  SRR2177954.k141_          66         221         4      36      25              ATCTACAAAAGTAGAAATTTTATAGAGGTATTTGGC

没有克里斯普

Help on reading this report
===========================

This report has three sections: Detailed, Summary by Similarity
and Summary by Position.

The detailed section shows each repeat in each putative
CRISPR array.

The summary sections give one line for each array.

An 'array' is a contiguous sequence of CRISPR repeats
looking like this:

    REPEAT Spacer REPEAT Spacer REPEAT ... Spacer REPEAT

Within one array, repeats have high similarity and spacers
are, roughly speaking, unique within a window around the array.
In a given array, each repeat has a similar length, and each
spacer has a similar length. With default parameters, the
algorithm allows a fair amount of variability in order to
maximize sensitivity. This may allow identification of
inactive ("fossil") arrays, and may in rare cases also
induce false positives due to other classes of repeats
such as microsatellites, LTRs and arrays of RNA genes.


Columns in the detailed section are:

  Pos               Sequence position, starting at 1 for the first base.
  Repeat            Length of the repeat.
  %id               Identity with the consensus sequence.
  Spacer            Length of spacer to the right of this repeat.
  Left flank        10 bases to the left of this repeat.
  Repeat            Sequence of this repeat.
                      Dots indicate positions where this repeat
                      agrees with the consensus sequence below.
  Spacer            Sequence of spacer to the right of this repeat,
                      or 10 bases if this is the last repeat.

The left flank sequence duplicates the end of the spacer for the preceding
repeat; it is provided to facilitate visual identification of cases
where the algorithm does not correctly identify repeat endpoints.

At the end of each array there is a sub-heading that gives the average
repeat length, average spacer length and consensus sequence.

Columns in the summary sections are:

  Array             Number 1, 2 ... referring back to the detailed report.
  Sequence          FASTA label of the sequence. May be truncated.
  From              Start position of array.
  To                End position of array.
  # copies          Number of repeats in the array.
  Repeat            Average repeat length.
  Spacer            Average spacer length.
  +                 +/-, indicating orientation relative to first array in group.
  Distance          Distance from previous array.
  Consensus         Consensus sequence.

In the Summary by Similarity section, arrays are grouped by similarity of their
consensus sequences. If consensus sequences are sufficiently similar, they are
aligned to each other to indicate probable relationships between arrays.

In the Summary by Position section, arrays are sorted by position within the
input sequence file.

The Distance column facilitates identification of cases where a single
array has been reported as two adjacent arrays. In such a case, (a) the
consensus sequences will be similar or identical, and (b) the distance
will be approximately a small multiple of the repeat length + spacer length.

Use the -noinfo option to turn off this help.
Use the -help option to get a list of command line options.

pilercr v1.06
By Robert C. Edgar

/databis/defontis/Dossier_fasta_chrm_avec_piler/ERR1544006_chrm.fasta: 0 putative CRISPR arrays found.

感谢您抽出时间

答案1

只需迭代文件,然后grepfor : 0 putative CRISPR regions.如果grep找到匹配项,则移动文件:

mkdir -p Sans_crispr Avec_crispr
for file in *pilercr.out; do
    if grep -q ': 0 putative CRISPR arrays' "$file"; then
        mv "$file" Sans_crispr
    else
        mv "$file" Avec_crispr
    fi
done

标志-q告诉grep它不要打印任何输出,但如果没有找到匹配,它仍然会以失败状态退出,如果找到匹配,它仍然会以成功状态退出。因此,我们在这里使用它将文件移动到适当的文件夹。

您收到此错误的原因:

mv: cannot move './SRR5273182_chrm.fasta.fa-pilercr.out' to '/databis/defontis/Dossier_fasta_chrm_avec_piler/Dossier_fasta_chrm_sortie_pilercr/Sans-Crispr/': Not a directory

是因为该目录/databis/defontis/Dossier_fasta_chrm_avec_piler/Dossier_fasta_chrm_sortie_pilercr/Sans-Crispr/不存在。这就是为什么上面的小脚本中的第一个命令的mkdir -p Sans_crispr Avec_crispr意思是“创建目录 Sans_crispr 和 Avec_crispr,除非它们尚不存在”。

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