I am working on a fungus call Neurosprora. Previous lab member built a gbrowser (1.70) to visualize the deep-seq data with GFF2 file format. Now I obtain some new deep-seq data and want to load it onto that browser. I heard that he used bowtie to do alignment and convert into gff2, but I cannot find the script to convert. Does anyone have similar script which could share? Or just indicate any tools can do this trick? I am not a perl person and don't think I could learn it in a short while.
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FWIW, I've just today ended up writing a python script to convert from SAM/BAM files to GFF3 files using pysam. The code may be useful for you if you can't find anything else suitable for your conversion.
For a bit of context, I broke up genomic contigs into 100bp fragments, naming the sequences <contig>#<start>-<end>, then used bowtie2 to map them to the genome -- that's why I've got the 'read.qname.find' bits in the code. My contigs started with 'v', which bowtie replaced with 'N' for some odd reason, so I had to do a bit of extra fiddling to add the 'v' back in.
Here's the relevant part of my code which does the SAM->GFF conversion:
Code:samFile = pysam.Samfile(samFileName, "r") totalCount = 0 sys.stderr.write("Getting reads from SAM file...") sys.stdout.write("##gff-version 3\n") gffWriter = csv.writer(sys.stdout, delimiter = '\t') for read in samFile: totalCount += 1 if(read.tid > 0): qContig = 'v' + read.qname[1:read.qname.find("#")] qContigStart = read.qname[read.qname.find("#")+1:read.qname.find("-")] qContigEnd = read.qname[read.qname.find("-")+1:] tContig = samFile.getrname(read.tid) strand = "-" if read.is_reverse else "+" score = "." for tag in read.tags: if(tag[0] == "XS"): score = str(tag[1]+1000) gffWriter.writerow((qContig, "sam2gff3-"+os.path.basename(samFileName), "nucleotide_match", qContigStart, qContigEnd, score, strand, ".", "Name=SAM_%s,ID=%s-%s;Target=%s %d %d" % (tContig, qContig, tContig, tContig, read.pos, read.aend))) if(totalCount % 100000 == 0): sys.stderr.write(".")
Last edited by gringer; 11-02-2011, 12:17 PM. Reason: fixed up GFF3 parsing errors, added Name attribute to avoid contig clashes
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