追加配列のアノテーションを含めるように既存のfastaとgff3を改変する reform

タイトルの通りのスクリプト。使い方は下のテストラン参照。

インストール

依存

reform requires Python3 and Biopython.

pip install biopython

git clone https://github.com/gencorefacility/reform.git 
cd reform/

> python3 reform.py -h

$ python3 reform.py -h

usage: reform.py [-h] --chrom CHROM --in_fasta IN_FASTA --in_gff IN_GFF

[--upstream_fasta UPSTREAM_FASTA]

[--downstream_fasta DOWNSTREAM_FASTA] [--position POSITION]

--ref_fasta REF_FASTA --ref_gff REF_GFF

optional arguments:

-h, --help show this help message and exit

--chrom CHROM Chromosome name (String)

--in_fasta IN_FASTA Path to new sequence to be inserted into reference

genome in fasta format

--in_gff IN_GFF Path to GFF file describing new fasta sequence to be

inserted

--upstream_fasta UPSTREAM_FASTA

Path to Fasta file with upstream sequence. Either

position, or upstream AND downstream sequence must be

provided.

--downstream_fasta DOWNSTREAM_FASTA

Path to Fasta file with downstream sequence. Either

position, or upstream AND downstream sequence must be

provided.

--position POSITION Position at which to insert new sequence. Note:

Position is 0-based. Either position, or upstream AND

downstream sequence must be provided.

--ref_fasta REF_FASTA

Path to reference fasta file

--ref_gff REF_GFF Path to reference gff file

テストラン

実行するには、元のリファレンス配列（fasta）とそのアノテーション情報（GFFまたはGTF）、そこに追加する新規配列（fasta）とそのアノテーション（GFFまたはGTF）が必要。挿入位置はポジションか上流配列と下流配列のfastaで指定する。

cd test_data/1/

#リファレンスref.faとアノテーションref.gff3のchrの"X"の4-bp目に、in.fastaとアノテーションin.gff3を挿入
python3 reform.py 
 --chrom=X \
 --position 3
 --in_fasta=in.fa \
 --in_gff=in.gff3 \
 --ref_fasta=ref.fa \
 --ref_gff=ref.gff3

--chrom Chromosome name (String)
--position Position at which to insert new sequence. Note: Position is 0-based. Either position, or upstream AND downstream sequence must be provided.
--in_fasta Path to new sequence to be inserted into reference genome in fasta format
--in_gff Path to GFF file describing new fasta sequence to be inserted
--ref_fasta Path to reference fasta file
--ref_gff Path to reference gff file