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hisat2_jun2bed.py error #7

Closed nongbaoting closed 6 years ago

nongbaoting commented 6 years ago

when I ran rnacocktail with align mode, i got an error below. 

Traceback (most recent call last):
  File "/usr/local/bin/hisat2_jun2bed.py", line 32, in <module>
    int_start =  int(locus_ls[1])-51
ValueError: invalid literal for int() with base 10: 'ctg9'

and then I ckecked this error carefully, I found that when my input chromosome name contained seporater "_", the program will throw out an error above! consider many organsim's chromosome names contain seporater '' especially the new assembly organism genome, i recommend you shoud change line 23 `locus = "".join([line_list[0],leftpos,rightpos,line_list[3]])tolocus = "__".join([line_list[0],leftpos,rightpos,line_list[3]])and line 30locusls = locus.split("")tolocus_ls = locus.split("__")` in script 'hisat2_jun2bed.py' , or change another seporater . that will work properly!

sincerely

msahraeian commented 6 years ago

Hi @nongbaoting,

Thanks for your interest in RNACocktail. I fixed the script to avoid this confusion in chromosome names. Please try again. It is fixed in #8.