I have an issue that I am trying to work through. I have a large dataset of about 25,000 genes that seem to the product of domain shuffling or gene fusions. I would like to view these alignments in pdf format based on BLAST outfmt 6 output.
I have BLAST output files for each of these genes with 1 sequence (the recombinogenic gene) and a varying number of subject genes with the following columns: qseqid sseqid evalue qstart qend qlen sstart send slen length I was hoping to parse the files through some code to produce images like the attached file, using the following example blast output file:
Cluster_1___Hsap10003 Cluster_2___Hsap00200 1e-30 5 100 300 10 105 240 95
Cluster_1___Hsap10003 Cluster_2___Hsap00200 1e-10 200 230 300 205 235 30 95
Cluster_1___Hsap10003 Cluster_3___Aver00900 1e-20 5 100 300 10 105 125 100
Cluster_1___Hsap10003 Cluster_3___Atha00809 1e-20 5 110 300 5 115 120 105
Cluster_1___Hsap10003 Cluster_4___Ecol00002 1e-10 70 170 300 205 235 30 95
Cluster_1___Hsap10003 Cluster_4___Ecol00003 1e-30 75 175 300 10 105 240 95
Cluster_1___Hsap10003 Cluster_4___Sfle00009 1e-10 80 180 300 205 235 30 95
Cluster_1___Hsap10003 Cluster_5___Spom00010 1e-30 160 260 300 10 105 240 95
Cluster_1___Hsap10003 Cluster_5___Scer01566 1e-10 170 270 300 205 235 30 95
Cluster_1___Hsap10003 Cluster_5___Afla00888 1e-30 175 275 300 10 105 240 95
I am looking for the query sequence to be a thick coloured bar, and the alignment section of each subject to be thick colourful bars with thin black lines showing the rest of the gene length (one subject per line showing all alignment sections against the query).
Does anyone know any software or know of any github code that may do something like this?
Thanks so much!
