<![CDATA[BOL: ASCIIGenome: genome browser based on command line interface and designed for running from console terminals.]]> https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals? https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals Fri, 09 Nov 2018 13:50:04 -0600 https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals <![CDATA[ASCIIGenome: genome browser based on command line interface and designed for running from console terminals.]]> ASCIIGenome is a genome browser based on command line interface and designed for running from console terminals.

Since ASCIIGenome does not require a graphical interface it is particularly useful for quickly visualizing genomic data on remote servers while offering flexibility similar to popular GUI viewers like IGV.

Documentation is at readthedocs/asciigenome.

 

Address of the bookmark: https://github.com/dariober/ASCIIGenome

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#item-annotation-3800 Sat, 07 Mar 2020 04:10:09 -0600 https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#item-annotation-3800 <![CDATA[Comment by Rahul Nayak]]> Install ASCIIGenome with conda

(base) [wsu29@bladeamd-2 ~]$ conda install ASCIIGenome
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /data/sata_data/workshop/wsu29/miniconda3

  added / updated specs:
    - asciigenome


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    asciigenome-1.15.0         |                0        27.5 MB  bioconda
    openjdk-8.0.152            |       h7b6447c_3        57.4 MB
    ------------------------------------------------------------
                                           Total:        84.9 MB

The following NEW packages will be INSTALLED:

  asciigenome        bioconda/noarch::asciigenome-1.15.0-0
  openjdk            pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3


Proceed ([y]/n)? y


Downloading and Extracting Packages
openjdk-8.0.152      | 57.4 MB   | ################################################################################### | 100%
asciigenome-1.15.0   | 27.5 MB   | ################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#item-annotation-3798 Sat, 07 Mar 2020 03:46:11 -0600 https://bioinformaticsonline.com/bookmarks/view/38176/asciigenome-genome-browser-based-on-command-line-interface-and-designed-for-running-from-console-terminals#item-annotation-3798 <![CDATA[Comment by Jit]]> This a list of available commands with their brief description.                                                               
For help on individual commands use one of::                                                                                  
                                                                                                                              
    command -h                                                                                                                
    ?command                                                                                                                  
    help command                                                                                                              
                                                                                                                              
e.g. `ylim -h`                                                                                                                
                                                                                                                              
      N a v i g a t i o n                                                                                                     
                                                                                                                              
goto chrom:[from]-[to]                                                                                                        
      Go to region `chrom:from-to` or to `chrom:from` or to the start of                                                      
      `chrom`.                                                                                                                
INT from [c | to]                                                                                                             
      Go to position `from` or to region `from to` on current chromosome.                                                     
PERCENT from [c | to]                                                                                                         
      Zoom into the current window delimited by given PERCENT of screen.                                                      
+ INT [k|m]                                                                                                                   
      Move forward by `INT` bases. Suffix K/M recognized.                                                                     
- INT [k|m]                                                                                                                   
      Move backwards by INT bases. Suffix K/M recognized.                                                                     
f [NUM=0.1]                                                                                                                   
      Move forward NUM times the size of the current window, 1/10 by default.                                                 
b [NUM=0.1]                                                                                                                   
      Move backward NUM times the size of the current window, 1/10 by default                                                 
ff                                                                                                                            
      Move forward by 1/2 of a window. A shortcut for `f 0.5`                                                                 
bb                                                                                                                            
      Move backward by 1/2 of a window. A shortcut for `b 0.5`                                                                
zi [INT = 1]                                                                                                                  
      Zoom in INT times. Each zoom halves the window size.                                                                    
zo [INT = 1]                                                                                                                  
      Zoom out INT times. Each zoom doubles the window size.                                                                  
extend [mid|window] [INT left] [INT right]                                                                                    
      Extend the current window by `INT` bases left and right.                                                                
l                                                                                                                             
      Go to the Left half of the current window.                                                                              
r                                                                                                                             
      Go to the Right half of the current window.                                                                             
p                                                                                                                             
      Go to the previous visited position.                                                                                    
n                                                                                                                             
      Go to the next visited position.                                                                                        
next [-back] [-start] [-zo INT=5] [track]                                                                                     
      Move to the next feature not overlapping the current coordinates.                                                       
                                                                                                                              
      F i n d                                                                                                                 
                                                                                                                              
find [-all] [-c] [-F] regex [track]                                                                                           
      Find the first record in `track` containing `regex`.                                                                    
seqRegex [-iupac] [-c] [regex]                                                                                                
      Find regex in reference sequence and show matches as an additional                                                      
      track.                                                                                                                  
bookmark [-d] [-n name] [-print] [> file] [chrom:from-to]                                                                     
      Creates a track to save positions of interest.                                                                          
                                                                                                                              
      D i s p l a y                                                                                                           
                                                                                                                              
grep [-i = .*] [-e = ''] [-c] [-F] [-v] [track_regex = .*]...                                                                 
      Similar to grep command, filter for features including or excluding                                                     
      patterns.                                                                                                               
awk [-off ...] [-F sep_re] [-v VAR=var] [-V] '<script>' [track_regex = .*]...                                                 
      Advanced feature filtering using awk syntax.                                                                            
featureColorForRegex [-r/-R regex color] [-v] [track_regex = .*]...                                                           
      Set colour for features captured by regex.                                                                              
featureDisplayMode [-expanded | -collapsed | -oneline] [-v] [track_regex = .*]...                                             
      Set how annotation features should be displayed.                                                                        
gap [-on | -off] [-v] [track_regex = .*]...                                                                                   
      Display features with or without a separating gap.                                                                      
gffNameAttr [attribute_name = NULL | -na] [-v] [track_regex = .*]...                                                          
      GTF/GFF attribute to set the feature name or `-na` to suppress name.                                                    
trackHeight [-v] INT [track_regex = .*]...                                                                                    
      Set track height to INT lines of text for all tracks matching regexes.                                                  
ylim [-v] <NUM|min|na> <NUM|min|na> [track_regex = .*]...                                                                     
      Set the y-axis limit for all tracks matched by regexes.                                                                 
colorTrack [-v] color [track_regex = .*]...                                                                                   
      Set colour for tracks matched by regex.                                                                                 
hideTitle [-on | -off] [-v] [track_regex = .*]...                                                                             
      Set the display of the title line matched by track_regex.                                                               
genotype [-n 10] [-s .*] [-r pattern rplc] [-f expr] [-v] [track_regex = .*]...                                               
      Customise the genotype rows printed under the VCF tracks.                                                               
editNames [-t] [-v] <pattern> <replacement> [track_re=.*]...                                                                  
      Edit track names by substituting regex pattern with replacement.                                                        
dataCol [-v] [index = 4] [track_regex = .*]...                                                                                
      Select data column for bedgraph tracks containing regex.                                                                
print [-n INT] [-full] [-off] [-round INT] [-hl re] [-esf] [-v] [-sys CMD] [track_regex = .*]... [>|>> file]                  
      Print lines for the tracks matched by `track_regex`.                                                                    
                                                                                                                              
      A l i g n m e n t s                                                                                                     
                                                                                                                              
readsAsPairs [-on | -off] [-v] [track_regex = .*]...                                                                          
      Show SAM records as pairs.                                                                                              
filterVariantReads [-r from/to] [-all] [-v] [track_regex = .*]...                                                             
      Filter reads containing a variant in the given interval.                                                                
rpm [-on | -off] [-v] [track_regex = .*]                                                                                      
      Set display to reads per million for BAM and TDF files.                                                                 
samtools [-f INT=0] [-F INT=4] [-q INT=0] [-v] [track_re = .*] ...                                                            
      Apply samtools filters to alignment tracks captured by the list of                                                      
      track regexes.                                                                                                          
BSseq [-on | -off] [-v] [track_regex = .*]...                                                                                 
      Set bisulfite mode for read tracks matched by regex.                                                                    
                                                                                                                              
      G e n e r a l                                                                                                           
                                                                                                                              
setGenome fasta|bam|genome                                                                                                    
      Set genome and reference sequence.                                                                                      
setConfig <file|tag> | <key> <value>                                                                                          
      Set configuration arguments.                                                                                            
explainSamFlag INT [INT ...]                                                                                                  
      Explain the list of bitwise SAM flags.                                                                                  
show <arg>                                                                                                                    
      Show or set features to display.                                                                                        
recentlyOpened [-grep = .*]                                                                                                   
      List recently opened files.                                            ]]> Jit