# cvmtrans
## Installation
pip3 install cvmtrans
## Usage
### 1. Extract reads contains specific tags
```
Usage: cvmtrans_extract_reads -i <input_fastq> -tag <sequence should inclued in reads> -o <output_fastq>
Author: Qingpo Cui(SZQ Lab, China Agricultural University)
optional arguments:
-h, --help show this help message and exit
-i I <input_fastq>: output filename of the fastq file
-tag TAG <input_file>: the tag sequence
-o O <output_fastq>: output filename of the fastq file
```
### 2. Cut 5' end or 3' end tags
```
Usage: cvmtrans_cut_tags -i <input_fastq> -tag <sequence should inclued in reads> -o <output_fastq>
Author: Qingpo Cui(SZQ Lab, China Agricultural University)
optional arguments:
-h, --help show this help message and exit
-i I <input_fastq>: output filename of the fastq file
-tag_5 TAG_5 <5‘ end tags or barcode>: The tag sequence at the 5’ end will be removed
-tag_3 TAG_3 <3‘ end tags or barcode>: The tag sequence at the 3’ end will be removed
-o O <output_fastq>: output filename of the fastq file
```
### 3. Get the insertion site statistics table
```
Usage: cvmtrans -bam_file <sorted_bam_files> -embl_file <reference embl file> -output <tab delimited text file>
Author: Qingpo Cui(SZQ Lab, China Agricultural University)
optional arguments:
-h, --help show this help message and exit
-bam_file BAM_FILE <input_fastq>: output filename of the fastq file
-embl_file EMBL_FILE <input_file>: the tag sequence
-output OUTPUT <output_fastq>: output filename of the fastq file
```
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