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| ###############################----This Is wanted, 如果要画read mapping下面参数是必须的----############################## | ||
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| synteny = order->0->1,query->pO83_CORR.indel.blast:target->pO83_CORR,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.blast.m6,blast_m8,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1 | ||
| synteny = order->0->1,query->pO83_CORR.indel.blast:target->pO83_CORR.twin.minimap,../data/NC_017659.1.indel.fa.to.NC_017659.1.fa.paf.gz,paf,quadrilateral,forward->orange->opacity0.5,reverse->blue->opacity0.7,cross_link_shift_y->+3:-3,sort->1 | ||
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| feature_id_is_unique = no | ||
| display_segment_name=yes,center,shift_y:+2,fontsize:6,color:black,order:5,rotate:0 | ||
| display_segment_strand=5:5",3:3",color:black,fontsize:10 | ||
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| ##############################----This Is Optional,下面是可选的，可以用默认值----############################## | ||
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| # output figure size | ||
| svg_width_height = 1300,500 # * | ||
| pdf_dpi = 100 | ||
| svg_background_color = white #background color of whole figure | ||
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| # plot feature type | ||
| feature_keywords = xx # *, gene,point,hist,heatmap | ||
| feature_setting = feature.color.label.6.conf # * | ||
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| # figure width layout | ||
| width_ratio_ref_cluster_legend = 0.1-0.75-0.15 # 0.1+0.75+0.15=1 | ||
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| ## global setting start, specific setting in feature_setting | ||
| feature_shape=arrow # only arrow, rect for figure shape, not support round_rect and circle_point yet | ||
| feature_arrow_width_extent=30bp | ||
| feature_label_size=10 | ||
| feature_label_color=black | ||
| feature_shift_y=0 # unit is feature_shift_y_unit | ||
| feature_shift_y_unit=backbone # backbone or radius or percent, backbone is genome_height_ratio | ||
| feature_shift_x=0 # unit is bp | ||
| feature_height_ratio=3 # defined feature height | ||
| feature_height_unit=backbone | ||
| track_style= fill:blue;opacity:0.2 # fill:blue;stroke:pink;stroke-width:5;fill-opacity:0.1;stroke-opacity:0.9 | ||
| feature_color=rgb(50,205,50) | ||
| feature_border_size=0 | ||
| feature_border_color=black | ||
| genome_height_ratio=1 # mean genome height extend ratio | ||
| feature_arrow_sharp_extent=0 # bigger mean sharper arrow | ||
| # order for display | ||
| track_order=1 | ||
| feature_order=2 | ||
| feature_label_order=4 | ||
| cross_link_order=0 # bigger mean upper | ||
| display_feature=yes # no or yes | ||
| # whether dispaly feature label | ||
| display_feature_label=no # yes or no or yes,no or no,yes | ||
| # feature_label 9 kinds of positon | ||
| pos_feature_label=right_low # or medium_low or left_low or right_low or medium_medium or left_medium | ||
| # padding between feature and label | ||
| # padding between feature and label | ||
| y_margin_feature_label = 0.01 # space between feature and label | ||
| # freature label rotate angle | ||
| label_rotate_angle=0 | ||
| feature_label_auto_angle_flag=1 # if auto shift angle | ||
| # display or conceal the connect line between same scaffold | ||
| connect_with_same_scaffold=no | ||
| connect_stroke_dasharray=2,5 | ||
| connect_stroke_width=2 | ||
| connect_stroke_color=black | ||
| absolute_postion_in_title=yes | ||
| ## global setting end, specific setting in feature_setting | ||
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| # if less this, will trigger auto shift feature label | ||
| distance_closed_feature=1 # xxbp, if the distancetwo feature is too close, so sparate with shift_angle_closed_feature | ||
| shift_angle_closed_feature = 10 | ||
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| # layout | ||
| top_bottom_margin = 0.2 # 高度上 top和bottom占的比例,top和bottom可能有scale | ||
| space_between_blocks = 500 # bp, mean space of every block in one track | ||
| default_legend = other | ||
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| # new sample name | ||
| #sample_name_old2new = sample.name.new.conf | ||
| sample_name_color_default = black | ||
| sample_name_font_size_default = 15 | ||
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| # legend | ||
| display_legend=yes # yes or other | ||
| legend_font_size = 20 #legend中文字字体大小 | ||
| legend_height_ratio = 0.7 # compare with feature height | ||
| legend_width_margin = 0.15 # legends左右两侧的margin | ||
| legend_height_space = 0.1 | ||
| legend_width_textpercent = 0.7 # legend内部的文字和arrow的比例，text是0.6则arrow是0.4 | ||
| legend_stroke_color=black | ||
| legend_stroke_width=0.5 | ||
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| # crossling among features | ||
| #crossing_link = feature.crossing.link | ||
| cross_link_color = #FF8C00 | ||
| cross_link_opacity = 1 | ||
| cross_link_anchor_pos = low_up # up,medium,low | ||
| ignore_sharp_arrow=no # yes or no | ||
| cross_link_orientation_ellipse=up | ||
| cross_link_shape=quadrilateral # ellipse or w or quadrilateral or line | ||
| cross_link_height_ellipse=10,8 # 10 and 8 is the radius of outter ellipse and inner ellipse | ||
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| #sort_by_one_feature = sort.feature # every track sort block's position by this feaure list(just only one feature for one track, if one traack not has one feature in this list , mean don't sort block's pos of this track ) | ||
| #scaffold_order = order.list # if set this, will draw full-length of scaffold in gff, will ignore 4th col to last col of the --list | ||
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| # scale | ||
| scale_display=yes # yes or no | ||
| scale_position=low # up or low or up_low | ||
| scale_color=green | ||
| scale_width=0.5 | ||
| scale_ratio=1700 # bp | ||
| scale_padding_y=0.6 | ||
| scale_tick_opacity=1 | ||
| scale_tick_height=0.01 | ||
| scale_order=-1 | ||
| scale_tick_padding_y=10 | ||
| scale_tick_fontsize=6 | ||
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This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| @@ -0,0 +1,48 @@ | ||
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| set -vex;cat pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.crosslink.conf >out8.pO83_CORR.indel.blast.to.pO83_CORR.out8.synteny.crosslink;rm pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.crosslink.conf;echo output out8.pO83_CORR.indel.blast.to.pO83_CORR.out8.synteny.crosslink | ||
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| set -vex;cat pO83_CORR.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff >out8.pO83_CORR.out8.synteny.gff;rm pO83_CORR.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff;echo output out8.pO83_CORR.out8.synteny.gff | ||
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| set -vex;cat pO83_CORR.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf > out8.pO83_CORR.out8.synteny.setting.conf;rm pO83_CORR.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf;echo output out8.pO83_CORR.out8.synteny.setting.conf | ||
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| set -vex;cat out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.gff >out8.pO83_CORR.indel.blast.out8.synteny.gff;rm out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.gff out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.gff;echo output out8.pO83_CORR.indel.blast.out8.synteny.gff | ||
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| set -vex;cat out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.setting.conf > out8.pO83_CORR.indel.blast.out8.synteny.setting.conf;rm out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.blast_m8.quadrilateral.1.synteny.setting.conf out8.pO83_CORR.indel.blast.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.setting.conf;echo output out8.pO83_CORR.indel.blast.out8.synteny.setting.conf | ||
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| set -vex;cat pO83_CORR.twin.minimap.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.gff >out8.pO83_CORR.twin.minimap.out8.synteny.gff;rm pO83_CORR.twin.minimap.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.gff;echo output out8.pO83_CORR.twin.minimap.out8.synteny.gff | ||
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| set -vex;cat pO83_CORR.twin.minimap.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.setting.conf > out8.pO83_CORR.twin.minimap.out8.synteny.setting.conf;rm pO83_CORR.twin.minimap.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.setting.conf;echo output out8.pO83_CORR.twin.minimap.out8.synteny.setting.conf | ||
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| set -vex;cat pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.crosslink.conf >out8.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.out8.synteny.crosslink;rm pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.paf.quadrilateral.2.synteny.crosslink.conf;echo output out8.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.out8.synteny.crosslink | ||
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| set -vex;cat out8.pO83_CORR.indel.blast.to.pO83_CORR.out8.synteny.crosslink out8.pO83_CORR.indel.blast.to.pO83_CORR.twin.minimap.out8.synteny.crosslink >out8.synteny.crosslink | ||
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| set -vex;cat out8.pO83_CORR.out8.synteny.setting.conf out8.pO83_CORR.indel.blast.out8.synteny.setting.conf out8.pO83_CORR.twin.minimap.out8.synteny.setting.conf >out8.synteny.setting.conf | ||
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| set -vex;cat feature.color.label.6.conf out8.synteny.setting.conf >feature.color.label.6.conf.out8 | ||
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| set -vex;cat out8.synteny.crosslink >feature.crossing.link.out8 | ||
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| set -vex;cat out8.pO83_CORR.out8.synteny.gff out8.pO83_CORR.indel.blast.out8.synteny.gff out8.pO83_CORR.twin.minimap.out8.synteny.gff|awk -F '{print }'|sort -u | ||
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| set -vex;sed -r 's/^(pO83_CORR\s.*\.gff)\s/\1,out8.pO83_CORR.out8.synteny.gff\t/' tracks.8.list >tracks.8.list.out8;cp tracks.8.list.out8 tracks.8.list.out8.tmp | ||
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| set -vex;sed -r 's/^(pO83_CORR.indel.blast\s.*\.gff)\s/\1,out8.pO83_CORR.indel.blast.out8.synteny.gff\t/' tracks.8.list.out8.tmp >tracks.8.list.out8;cp tracks.8.list.out8 tracks.8.list.out8.tmp | ||
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| set -vex;sed -r 's/^(pO83_CORR.twin.minimap\s.*\.gff)\s/\1,out8.pO83_CORR.twin.minimap.out8.synteny.gff\t/' tracks.8.list.out8.tmp >tracks.8.list.out8;cp tracks.8.list.out8 tracks.8.list.out8.tmp | ||
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