- 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