gauravcodepro / panache-extract

maf to panache and extracting all snps and pangenome specific information.

panache-extract

• a maf conversion for the panache for the genome visualization.
• given a alignment in the maf and the taf format, you can extract the specific sequences for the snps with the pangenomes using specific ids and also the sequences as strings.
• it will also tell which snps variation is present so that it can be poulated on panache.
• added support for the output file write to each and every function of the gem
• This is now available as a ruby gem panacheextract
• ruby bindings to the django is also available.
• example MAF(602 bytes) example MAF format

##maf version=1 scoring=N/A

a
s       simDog.chr6     437451  11      +       593897  CCCGTCAGTGT
s       simHuman.chr6   446327  11      +       601863  TCCGCCAAGGT
s       simMouse.chr6   460751  11      +       636262  TTCATCAGAGT
s       simRat.chr6     470339  11      +       647215  TTCATTAGGGT

a
s       simCow.chr6     445326  8       +       602619  TTTTCCCA
s       simDog.chr6     437462  8       +       593897  TT-TTCCG
s       simHuman.chr6   446338  8       +       601863  TTCTTCCG
s       simMouse.chr6   460762  8       +       636262  TTTTACCG
s       simRat.chr6     470355  8       +       647215  TTTTACCG

• extracts specific sequences from the pangenome graph

  getspecific("simDog.chr6","/home/gaurav/Desktop/maf_taf_panache/sample.taf",
                                    "/home/gaurav/Desktop/maf_taf_panache/sample.txt"
  

• extract specific sequences from the alignments associated with the specific deletions

  # will only give the sequences of those which have deletions in the graphs. 
   getspecific("simDog.chr6", "/home/gaurav/Desktop/maf_taf_panache/sample.taf",
                        "/home/gaurav/Desktop/maf_taf_panache/sample.txt", del = "None")
        [["simDog.chr6", "CCCGTCAGTGT"], ["simDog.chr6", "TT-TTCCG"]]
   getspecific("simDog.chr6", "/home/gaurav/Desktop/maf_taf_panache/sample.taf",
                       "/home/gaurav/Desktop/maf_taf_panache/sample.txt", del != "None")
          [["simDog.chr6", "TT-TTCCG"]]
  
  

• extract the position of deletion snps from the alignments. will only report the coordinates of those ids if they have deletions.

  delcoordinates("simDog.chr6", "/home/gaurav/Desktop/maf_taf_panache/sample.taf",
                                         "/home/gaurav/Desktop/maf_taf_panache/sample.txt")
  

• search according to the sequence ids or according to the column values.

  # usage as above, added support for writing the output files to the disk for every function.
    getAll(ids, inputalignment, outalignment, del, writefilter)
  

Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany