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liguowang / CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.
https://crossmap.readthedocs.io/en/latest/
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Crossmap throws error while lifting over from MAF file #51

Closed Subhi closed 1 year ago

Subhi commented 1 year ago

Traceback (most recent call last): File "/Users/opt/anaconda3/bin/CrossMap.py", line 338, in crossmap_maf_file(mapping = mapTree, infile= in_file, outfile = out_file, liftoverfile = chain_file, refgenome = genome_file, ref_name = build_name, cstyle = args.cstyle) File "/Users/opt/anaconda3/lib/python3.9/site-packages/cmmodule/mapmaf.py", line 84, in crossmap_maf_file start = int(fields[5])-1 # 0 based ValueError: invalid literal for int() with base 10: '1.86e+08'

liguowang commented 1 year ago

please don't use scientific notation (e.g., 1.86e+08) to represent genomic coordinates. This could be done silently by Excel.