GFF2GTF.py2

import sys

inFile = open(sys.argv[1],'r')

for line in inFile:

  #skip comment lines that start with the '#' character

  if line[0] != '#':

    #split line into columns by tab

    data = line.strip().split('\t')

    ID = ''

    #if the feature is a gene

    if data[2] == "gene":

      #get the id

      ID = data[-1].split('ID=')[-1].split(';')[0]

    #if the feature is anything else

    else:

      # get the parent as the ID

      ID = data[-1].split('Parent=')[-1].split(';')[0]

    #modify the last column

    data[-1] = 'gene_id "' + ID + '"; transcript_id "' + ID

    #print out this new GTF line

    print '\t'.join(data)

https://www.jianshu.com/p/c284a6b4e1c6

巴特西

GFF2GTF.py2

最新文章

热门文章