####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript <this_script> <query sequence in fasta format> <subject sequence> <fastANI visualization output> # Output: <fastANI visualization output filename>.pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse command line arguments query_fasta=commandArgs(TRUE)[1] subject_fasta=commandArgs(TRUE)[2] fastANI_visual_file=commandArgs(TRUE)[3] library(genoPlotR) #Read fastANI output comparison <- try(read_comparison_from_blast(fastANI_visual_file)) #Read sequences into genoPlotR objects Query <- try(read_dna_seg_from_file(query_fasta)) Ref <- try(read_dna_seg_from_file(subject_fasta)) plotTitle = paste(query_fasta, subject_fasta, sep=" v/s ") pdf( paste(fastANI_visual_file,".pdf",sep="") ) plot_gene_map(dna_segs=list(Query, Ref), comparisons=list(comparison), main=plotTitle, scale=FALSE, scale_cex=1, n_scale_ticks=4) dev.off()
时间: 2024-03-18 13:44:21 浏览: 139
这是一段R语言的脚本,用于将fastANI的核基因组比较结果进行可视化。它需要三个输入参数:查询序列(以fasta格式提供)、参考序列(以fasta格式提供)和fastANI可视化输出文件。它使用了genoPlotR软件包,可以在http://genoplotr.r-forge.r-project.org上找到。输出结果是一个PDF文件,包含了比较结果的可视化图形。
相关问题
<xacro:macro name="Livox_Mid_gazebo_sensor" params="visualize:=True update_rate:=10 resolution:=0.002 noise_mean:=0.0 noise_stddev:=0.01 name:=livox"> <gazebo reference="${name}"> <sensor type="ray" name="laser_${name}"> <pose>0 0 0 0 0 0</pose> <visualize>${visualize}</visualize> <update_rate>${update_rate}</update_rate> <!-- This ray plgin is only for visualization. --> <plugin name="gazebo_ros_laser_controller" filename="liblivox_laser_simulation.so"> <ray> <scan> <horizontal> <samples>100</samples> <resolution>1</resolution> <min_angle>${0}</min_angle> <max_angle>${2M_PI}</max_angle> </horizontal> <vertical> <samples>360</samples> <resolution>1</resolution> <min_angle>${-7.22/180M_PI}</min_angle> <max_angle>${55.22/180*M_PI}</max_angle> </vertical> </scan> <range> <min>${laser_min_range}</min> <max>${laser_max_range}</max> <resolution>${resolution}</resolution> </range> <noise> <type>gaussian</type> <mean>${noise_mean}</mean> <stddev>${noise_stddev}</stddev> </noise> </ray> <visualize>${visualize}</visualize> <samples>${samples}</samples> <downsample>${downsample}</downsample> <csv_file_name>/home/kuper/PX4_Firmware/Tools/sitl_gazebo/models/livox/scan_mode/mid360.csv</csv_file_name> <ros_topic>${ros_topic}</ros_topic> </plugin> </sensor> </gazebo> </xacro:macro>转为sdf格式
您可以使用xacro命令将该xacro宏转换为sdf格式,具体操作如下:
1. 创建一个包含xacro文件的包,并在该包中创建一个launch文件,用于将xacro转换为sdf格式。假设该包名为"livox_description",该xacro文件名为"livox_mid_gazebo_sensor.xacro",则可以在该包中创建一个名为"convert_xacro_to_sdf.launch"的文件,内容如下:
```
<launch>
<arg name="model_name" default="livox" />
<arg name="xacro_file" default="$(find livox_description)/urdf/livox_mid_gazebo_sensor.xacro" />
<arg name="sdf_file" default="$(find livox_description)/urdf/livox_mid_gazebo_sensor.sdf" />
<xacro:macro name="livox_mid_gazebo_sensor" params="visualize:=True update_rate:=10 resolution:=0.002 noise_mean:=0.0 noise_stddev:=0.01 name:=livox">
<!-- xacro代码 -->
</xacro:macro>
<node name="xacro" pkg="xacro" type="xacro" args="$(arg xacro_file)">
<param name="visualize" value="$(arg visualize)" />
<param name="update_rate" value="$(arg update_rate)" />
<param name="resolution" value="$(arg resolution)" />
<param name="noise_mean" value="$(arg noise_mean)" />
<param name="noise_stddev" value="$(arg noise_stddev)" />
<param name="name" value="$(arg model_name)" />
<param name="laser_min_range" value="0.1" />
<param name="laser_max_range" value="100.0" />
<param name="samples" value="1000" />
<param name="downsample" value="1" />
<param name="ros_topic" value="/livox/point_cloud" />
<param name="ros_node_name" value="livox_mid_gazebo_sensor" />
<param name="csv_file_name" value="$(find livox_description)/models/livox/scan_mode/mid360.csv" />
</node>
<node name="sdf" pkg="gazebo_ros" type="spawn_model" args="-sdf -file $(arg sdf_file) -model $(arg model_name)" />
</launch>
```
2. 运行launch文件,使用gazebo的spawn_model命令将sdf模型加载到仿真环境中。您可以在终端中运行以下命令:
```
roslaunch livox_description convert_xacro_to_sdf.launch
```
注意:需要将xacro代码中的参数值替换为实际的值。另外,如果xacro文件中使用了其他的xacro文件或包含其他的宏定义,则需要在launch文件中添加相应的参数和节点。
<gazebo reference="${name}"> <sensor type="ray" name="laser_${name}"> <pose>0 0 0 0 0 0</pose> <visualize>${visualize}</visualize> <update_rate>${update_rate}</update_rate> <!-- This ray plgin is only for visualization. --> <plugin name="gazebo_ros_laser_controller" filename="liblivox_laser_simulation.so"> <ray> <scan> <horizontal> <samples>100</samples> <resolution>1</resolution> <min_angle>${0}</min_angle> <max_angle>${2*M_PI}</max_angle> </horizontal> <vertical> <samples>360</samples> <resolution>1</resolution> <min_angle>${-7.22/180*M_PI}</min_angle> <max_angle>${55.22/180*M_PI}</max_angle> </vertical> </scan> <range> <min>${laser_min_range}</min> <max>${laser_max_range}</max> <resolution>${resolution}</resolution> </range> <noise> <type>gaussian</type> <mean>${noise_mean}</mean> <stddev>${noise_stddev}</stddev> </noise> </ray> <visualize>${visualize}</visualize> <samples>${samples}</samples> <downsample>${downsample}</downsample> <csv_file_name>/home/kuper/PX4_Firmware/Tools/sitl_gazebo/models/livox/scan_mode/mid360.csv</csv_file_name> <ros_topic>${ros_topic}</ros_topic> </plugin> </sensor> </gazebo>转为sdf文件
以下是将该代码转换为 SDF 文件的示例:
```
<?xml version="1.0"?>
<sdf version="1.6">
<model name="livox_sensor">
<link name="link">
<sensor name="laser_sensor" type="ray">
<pose>0 0 0 0 0 0</pose>
<visualize>true</visualize>
<update_rate>10</update_rate>
<plugin name="livox_sensor_plugin" filename="liblivox_laser_simulation.so">
<ray>
<scan>
<horizontal>
<samples>100</samples>
<resolution>1</resolution>
<min_angle>0</min_angle>
<max_angle>6.28318530718</max_angle>
</horizontal>
<vertical>
<samples>360</samples>
<resolution>1</resolution>
<min_angle>-0.12603669438</min_angle>
<max_angle>0.96144910243</max_angle>
</vertical>
</scan>
<range>
<min>0.05</min>
<max>120</max>
<resolution>0.01</resolution>
</range>
<noise>
<type>gaussian</type>
<mean>0</mean>
<stddev>0.01</stddev>
</noise>
</ray>
<visualize>true</visualize>
<samples>1</samples>
<downsample>1</downsample>
<csv_file_name>/home/kuper/PX4_Firmware/Tools/sitl_gazebo/models/livox/scan_mode/mid360.csv</csv_file_name>
<ros_topic>livox_scan</ros_topic>
</plugin>
</sensor>
</link>
</model>
</sdf>
```
请注意以下更改:
- `<gazebo>` 标记已更改为 `<sdf>` 标记,因为我们正在创建 SDF 文件。
- `reference="${name}"` 属性已被删除。SDF 不需要此属性。
- `visualize`,`update_rate`,`laser_min_range` 和 `laser_max_range` 属性已被替换为 `<visualize>`,`<update_rate>`,`<range><min>` 和 `<range><max>` 元素。
- `<plugin>` 元素已被移动到 `<sensor>` 元素内部,并使用新属性 `name` 和 `filename`。
- `<horizontal>` 和 `<vertical>` 元素现在包含所有相关属性。
- 您可能需要对 `<min_angle>` 和 `<max_angle>` 元素中的角度进行转换,因为某些 Gazebo 版本使用弧度,而其他版本使用度数。
- `<ros_topic>` 元素现在包含您想要将激光扫描数据发布到的 ROS 话题名称。
阅读全文