Fix paralogs_to_ref.py #32
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Numpy genfromtxt was returning 'nan' for the contig ids, leading to no contigs being aligned
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This should address issue #25 |
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This first makes a small change that was inserting a space at the start of the fasta alignment.
Secondly, it changes the way the script reads the paralog info text file so that contig names are actually retained. Originally, the numpy function genfromtxt would read in only the ref number and leave the contig names as 'nan', leading to no paralogs being aligned to reference sequences. I've changed this to read in as a list. As a result, I had to slightly alter the later code to account for the new data structure.