
import sys
import os
import argparse
import re

reago_dir = '/tools/rna_manipulation/reago/reago/'

def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
    to_add = '.' + str(read_pair_num)
    with open(input_filepath,'r') as input_file:
        with open(output_filepath,'w') as output_file:
            for line in input_file:
                if line[0] == '>':
                    split_line = line.split()
                    seq_id = split_line[0]
                    if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
                        split_line[0] = seq_id + to_add
                    output_file.write(' '.join(split_line) + '\n')
                else:
                    output_file.write(line)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--r1_sequence_file', required=True)
    parser.add_argument('--r2_sequence_file', required=True)
    args = parser.parse_args()

    add_read_pair_num(args.r1_input_sequence_file, args.r1_input_sequence_file, 1)
    add_read_pair_num(args.r2_input_sequence_file, args.r2_input_sequence_file, 2)

import sys
import os
import argparse
import re

reago_dir = '/tools/rna_manipulation/reago/reago/'

def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
    to_add = '.' + str(read_pair_num)
    with open(input_filepath,'r') as input_file:
        with open(output_filepath,'w') as output_file:
            for line in input_file:
                if line[0] == '>':
                    split_line = line.split()
                    seq_id = split_line[0]
                    if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
                        split_line[0] = seq_id + to_add
                    output_file.write(' '.join(split_line) + '\n')
                else:
                    output_file.write(line)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--r1_sequence_file', required=True)
    parser.add_argument('--r2_sequence_file', required=True)
    args = parser.parse_args()

    add_read_pair_num(args.r1_sequence_file, args.r1_sequence_file, 1)
    add_read_pair_num(args.r2_sequence_file, args.r2_sequence_file, 2)
Correct argument name in script to format reago input file
Correct argument name in script to format reago input file

  
  import sys
  import os
  import argparse
  import re
  
  reago_dir = '/tools/rna_manipulation/reago/reago/'
  
  def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
      to_add = '.' + str(read_pair_num)
      with open(input_filepath,'r') as input_file:
          with open(output_filepath,'w') as output_file:
              for line in input_file:
                  if line[0] == '>':
                      split_line = line.split()
                      seq_id = split_line[0]
                      if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
                          split_line[0] = seq_id + to_add
                      output_file.write(' '.join(split_line) + '\n')
                  else:
                      output_file.write(line)
  
  if __name__ == '__main__':
      parser = argparse.ArgumentParser()
      parser.add_argument('--r1_sequence_file', required=True)
      parser.add_argument('--r2_sequence_file', required=True)
      args = parser.parse_args()
  
-     add_read_pair_num(args.r1_input_sequence_file, args.r1_input_sequence_file, 1)
-     add_read_pair_num(args.r2_input_sequence_file, args.r2_input_sequence_file, 2)
+     add_read_pair_num(args.r1_sequence_file, args.r1_sequence_file, 1)
+     add_read_pair_num(args.r2_sequence_file, args.r2_sequence_file, 2)
Correct argument name in script to format reago input file
## Code Before:

import sys
import os
import argparse
import re

reago_dir = '/tools/rna_manipulation/reago/reago/'

def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
    to_add = '.' + str(read_pair_num)
    with open(input_filepath,'r') as input_file:
        with open(output_filepath,'w') as output_file:
            for line in input_file:
                if line[0] == '>':
                    split_line = line.split()
                    seq_id = split_line[0]
                    if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
                        split_line[0] = seq_id + to_add
                    output_file.write(' '.join(split_line) + '\n')
                else:
                    output_file.write(line)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--r1_sequence_file', required=True)
    parser.add_argument('--r2_sequence_file', required=True)
    args = parser.parse_args()

    add_read_pair_num(args.r1_input_sequence_file, args.r1_input_sequence_file, 1)
    add_read_pair_num(args.r2_input_sequence_file, args.r2_input_sequence_file, 2)
## Instruction:
Correct argument name in script to format reago input file
## Code After:

import sys
import os
import argparse
import re

reago_dir = '/tools/rna_manipulation/reago/reago/'

def add_read_pair_num(input_filepath, output_filepath, read_pair_num):
    to_add = '.' + str(read_pair_num)
    with open(input_filepath,'r') as input_file:
        with open(output_filepath,'w') as output_file:
            for line in input_file:
                if line[0] == '>':
                    split_line = line.split()
                    seq_id = split_line[0]
                    if seq_id.rfind(to_add) != (len(seq_id)-len(to_add)):
                        split_line[0] = seq_id + to_add
                    output_file.write(' '.join(split_line) + '\n')
                else:
                    output_file.write(line)

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--r1_sequence_file', required=True)
    parser.add_argument('--r2_sequence_file', required=True)
    args = parser.parse_args()

    add_read_pair_num(args.r1_sequence_file, args.r1_sequence_file, 1)
    add_read_pair_num(args.r2_sequence_file, args.r2_sequence_file, 2)