LinearDisplayは、ユーザー定義の遺伝的特徴（ORF、プロモーター、転写ターミネーター、制限酵素認識部位、プライマー結合部位、ファージ付着部位、標的部位重複、アセンブリ/コンティグ切断、RNA構造など）の出版品質の線形マップを生成するプログラムである。
インストール
fig2devはapt-getで導入した。
依存PERLモジュール
- FindBin : Available from <https://metacpan.org/pod/FindBin>
- Math::Round : Available from <https://metacpan.org/pod/Math::Round>
- Graphics::ColorObject : Available from<https://metacpan.org/pod/Graphics::ColorObject>
- TIGR::Foundation : Availble from <https://metacpan.org/release/TIGR>
- TIGR::DisplayFunctions : Included in this distribution
- global_structures.ph : Included in this distribution
そのほか
- Xfig : Available from <https://sourceforge.net/projects/mcj/>
- fig2dev : Also available from <https://sourceforge.net/projects/mcj/>
git clone https://github.com/JCVenterInstitute/LinearDisplay.git
cd LinearDisplay/
> perl LinearDisplay.pl
Use of uninitialized value $opt_A in numeric gt (>) at LinearDisplay.pl line 581.
Hey: must supply -A an assembly file
examples:
Fig1 dir) ../../LinearDisplay.pl -A frag.file -F gene_att.file -nt > Fig1.fig
Fig2 dir) ../../LinearDisplay.pl -A frag.file -F gene_att.file -nt > Fig2.fig
Fig3 dir) ../../LinearDisplay.pl -A frag.file -F gene_att.file -nt > Fig3.fig
options:
-D [D]ebug
-i display the last [i]nvocation to the user.
-A fr[A]gment file [REQUIRED]
-F gene attribute (gene_att) [F]ile [REQUIRED]
-P Gene [P]airs File. A list of gene pairs.
-R [R]egional matches
-C [C]hi-square file
-I [I]ndependent genes. Do not display blocks, just display gene pairs individually.
-g supply a list of [g]ene names to display
-p [p]age test. Just displays lines only so user can quickly set up white space.
-s size. Line [s]pacing, where size is distance from each assembly displayed in pic.
-f size. [f]ont size, where size will be size of font.
-L use [L]ocus names from gene_att file
-y use gene_s[y]ms from gene_att file if available
-S size. [S]hort genes. Where genes below size cutoff will displayed as empty.
-T [T]oggle to shorten names from BB0123 to 123
-M file_name. [M]erge in xfig file, usually a legend created by the user.
-m [m]olecular size
-t [t]oggle to use tRNA name
-nl [n]o horizontal [l]ine
-nn [n]o [n]ame. Do not print a feat or locus name
-nt [n]o [t]ickmarks
-oa [o]ld [a]rrowhead stype
-cm {option} [c]olor of [m]atches {[p]astel or [s]pectrum or [m]onochrome (eg. -cm p) [default = p]
Fragment file format:
Level Fragment_id Left_end Right_end Left_margin
Gene attribute file format:
End5 End3 feat_name Gene_sym Locus feat_type Role Fragment_id
-> Acceptable feat_types to draw are:
CLS - cluster (used to draw clusters as circles)
ORF - Open Reading Frame with new arrowhead -> or <-
ORFNA - Open Reading Frame with NO arrowhead -
PROM - promoter
PRI - primer
PRI2 - primer2
ENZ - restriction enzyme
ATTP - phage attachment site (attP)
TERM - transcriptional terminator
TSD - Target Site Duplication
PMARK - contig/assembly separator
REGION - for noting DNA similarities (shaded region)
rRNA - ribosomal RNAs (must specify type 16S, 23S, 5S in feat_name)
sRNA - structural RNAs (must specify type (tmRNA or 7S/SRP or RNaseP/rnpB in feat_name)
tRNA - transfer RNAs
Gene pair file format:
Fragement_id feat_name Fragment_id feat_name %identity
Regional match file format:
Fragment_id end5 end3 Fragment_id end5 end3 %identity
Chi-square file format:
# Fragment_id
position chi-square
テストラン
ランするにはfrag.fileとgene_att.fileが必要。
frag.file - フラグメントファイル
<Level>tab<Fragment_id>tab<Left_end>tab<Right_end>tab<Left_margin>
gene_att.file - 遺伝子属性ファイル
<End5>tab<End3>tab<feat_name>tab<Gene_sym>tab<Locus>tab<feat_type>tab<Role>tab<Fragment_id>
feature typeORFは例ではORFとなっている。以下のタイプが使える。
CLS - cluster (used to draw clusters as circles)
ORF - Open Reading Frame with new arrowhead -> or <-
ORFNA - Open Reading Frame with NO arrowhead -
PROM - promoter
PRI - primer
PRI2 - primer2
ENZ - restriction enzyme
ATTP - phage attachment site (attP)
TERM - transcriptional terminator
TSD - Target Site Duplication
PMARK - contig/assembly separator
REGION - for noting DNA similarities (shaded region)
rRNA - ribosomal RNAs (must specify type 16S, 23S, 5S in feat_name)
sRNA - structural RNAs (must specify type (tmRNA or 7S/SRP or RNaseP/rnpB in feat_name)
tRNA - transfer RNAs
Fig.1
cd LinearDisplay/examples_dir/Fig1/
../../LinearDisplay.pl -A frag.file -F gene_att.file -nt > Fig1.fig
引用
https://github.com/JCVenterInstitute/LinearDisplay
関連
参考
https://cmdcolin.github.io/awesome-genome-visualization/?latest=true
