old_contents: #!/usr/bin/env python
  
  # dealing with command line input
  import argparse
  parser = argparse.ArgumentParser()
  parser.add_argument("-gtf", type=str, required=True)
  parser.add_argument("-genome", type=str, required=True)
  args = parser.parse_args()
  gtf = args.gtf
  genome = args.genome
  
  # creating bed file
  input = open(gtf)
  output = open('all_exons.bed', 'w')
  input.readline()
  for line in input:
      split = line.split('\t')
      scaffold = split[0]
      start_co_ordinate = int(split[3]) - 1
      stop_co_ordinate = split[4]
      info = split[8]
      output.write(scaffold + '\t' + str(start_co_ordinate) + '\t' + stop_co_ordinate + '\t' + info + '\n')
  input.close()
  output.close()
  
  # obtaining fasta sequences using bedtools
  import subprocess
  subprocess.call(["bedtools", "getfasta", "-fi", genome, "-bed", "all_exons.bed", "-fo", "all_exons.fa", "-name"])
  
  # stitching together exon sequences
  output = open('all_transcripts.fa', 'w')
  input = open('all_exons.fa')
  first_line = input.readline()
  info = first_line.split('"')
  transcript = info[3]
  output.write(info[0] + info[1] + info[2] + info[3])
  if '; gene name ' in info:
      output.write(info[6] + info [7])
  output.write('\n')
  transcript_previous = transcript
  sequence = ''
  for line in input:
      if line.startswith('>'):
          info = line.split('"')
          transcript = info[3]
          if transcript != transcript_previous:
              sequence = list(sequence)
              for i in range(0, len(sequence)):
                  if i%60 == 0 and i != 0:
                      output.write('\n')
                  output.write(sequence[i])
              output.write('\n' + info[0] + info[1] + info[2] + info[3])
              if '; gene_name ' in info:
                  output.write(info[6] + info [7])
              output.write('\n')
              transcript_previous = transcript
              sequence = ''
      else:
          line_sequence = line.rstrip()
          sequence = sequence + line_sequence
  
  sequence = list(sequence)
  for i in range(0, len(sequence)):
      if i%60 == 0 and i != 0:
          output.write('\n')
      output.write(sequence[i])
  
new_contents: #!/usr/bin/env python
  
  # dealing with command line input
  import argparse
  parser = argparse.ArgumentParser()
  parser.add_argument("-gtf", type=str, required=True)
  parser.add_argument("-genome", type=str, required=True)
  args = parser.parse_args()
  gtf = args.gtf
  genome = args.genome
  
  # creating bed file
  input = open(gtf)
  output = open('all_exons.bed', 'w')
  input.readline()
  for line in input:
      split = line.split('\t')
      scaffold = split[0]
      start_co_ordinate = int(split[3]) - 1
      stop_co_ordinate = split[4]
      info = split[8]
      output.write(scaffold + '\t' + str(start_co_ordinate) + '\t' + stop_co_ordinate + '\t' + info + '\n')
  input.close()
  output.close()
  
  # obtaining fasta sequences using bedtools
  import subprocess
  subprocess.call(["bedtools", "getfasta", "-fi", genome, "-bed", "all_exons.bed", "-fo", "all_exons.fa", "-name"])
  
  # stitching together exon sequences
  output = open('all_transcripts.fa', 'w')
  input = open('all_exons.fa')
  first_line = input.readline()
  info = first_line.split('"')
  transcript = info[3]
  output.write(info[0] + info[1] + info[2] + info[3])
  if '; gene name ' in info:
      output.write(info[6] + info [7])
  output.write('\n')
  transcript_previous = transcript
  sequence = ''
  for line in input:
      if line.startswith('>'):
          info = line.split('"')
          transcript = info[3]
          if transcript != transcript_previous:
              sequence = list(sequence)
              for i in range(0, len(sequence)):
                  if i%60 == 0 and i != 0:
                      output.write('\n')
                  output.write(sequence[i])
              output.write('\n' + info[0] + info[1] + info[2] + info[3])
              if '; gene_name ' in info:
                  output.write(info[6] + info [7])
              output.write('\n')
              transcript_previous = transcript
              sequence = ''
      else:
          line_sequence = line.rstrip()
          sequence = sequence + line_sequence
  
  sequence = list(sequence)
  for i in range(0, len(sequence)):
      if i%60 == 0 and i != 0:
          output.write('\n')
      output.write(sequence[i])
  output.close()
  
subject: Update get_all_transcript_sequences.py