How to link two python scripts

[Larz60+]

OK, this version uses argparse which I should have used in the first one.
now you can use filename with or without quotes.
There is a new command line structure, it now uses flags, so arguments can be passed in any order, so long as they have the proper flags,
you can type:

python SelectAndSortFasta.py -h

To get help

Output:
λ python SelectAndSortFasta.py -h
usage: SelectAndSortFasta.py [-h] [-i INFILE_NAME] [-o OUFILE_NAME]
                             [-s MINSIZE]

SortFasta

optional arguments:
  -h, --help      show this help message and exit
  -i INFILE_NAME  Name of input file
  -o OUFILE_NAME  Name of output file
  -s MINSIZE      Minimum sequence length

so a proper command line argument would look like:

python SelectAndSortFasta.py -o data/fasta/AINZ01/AINZ01sorted.1.fsa_nt -s 1000 -i data/fasta/AINZ01/AINZ01.1.fsa_nt
# or
python SelectAndSortFasta.py -o 'data/fasta/AINZ01/AINZ01sorted.1.fsa_nt' -s 1000 -i 'data/fasta/AINZ01/AINZ01.1.fsa_nt'

Assuming your data was in a sub-directory 'data/fasta/AINZ01'

You can still import the module into an other program as explained previously.
just make sure you use argument names like:

#At top of program
import SelectAndSortFasta

# In Initialization:
ssf = SelectAndSortFasta.SelectAndSortFasta()
# or if in calss:
self.ssf = SelectAndSortFasta.SelectAndSortFasta()

# Then when you want to convert a file:
ssf.split_file(self, in_filename='YourInfileName', out_filename='YourOutfileName', min_seq_len=1000)
# or if in class:
self.ssf.split_file(self, in_filename='YourInfileName', out_filename='YourOutfileName', min_seq_len=1000)

Here's the new (and final?) code.

import sys
import argparse


class SelectAndSortFasta:
    def __init__(self):
        self.lines_out = []
        self.header = None
        self.save_seq = ''
        self.infilename  = None
        self.outfilename = None
        self.minsize     = None


    def save_this(self, fo):
        fo.write('{}\n'.format(self.header))
        fo.write('{}\n'.format(self.save_seq))

    def split_file(self, from_args=False, in_filename=None, out_filename=None, min_seq_len=None):
        iname = None
        oname = None
        mlen = None

        if from_args:
            iname = self.infilename
            oname = self.outfilename
            mlen = self.minsize
        else:
            iname = in_filename
            oname = out_filename
            mlen = min_seq_len
        self.header = None
        seqlen = 0
        self.lines_out = []
        with open(iname, 'r') as fin, open(oname, 'w') as fo:
            firstline = True
            for line in fin:
                line = line.strip()
                if line.startswith('>'):
                    if firstline:
                        firstline = False
                        self.header = line
                    else:
                        if seqlen > mlen:
                            self.save_this(fo)
                        self.save_seq = line
                        self.lines_out.append(self.header)
                        self.header = line
                        seqlen = 0
                else:
                    self.save_seq = '{}{}\n'.format(self.save_seq, line)
                    seqlen += len(line)
            if self.header is not None:
                if seqlen > mlen:
                    self.save_this(fo)

    def show_seq_out(self):
        print('The following sequences are in the output file:')
        plist = "\n".join(self.lines_out)
        print(plist)

    def parse_args(self):
        parser = argparse.ArgumentParser(description='SortFasta')
        parser.add_argument('-i',
                            action='store',
                            dest='infile_name',
                            help='Name of input file')

        parser.add_argument('-o',
                            action='store',
                            dest='oufile_name',
                            help='Name of output file')

        parser.add_argument('-s',
                            action='store',
                            dest='minsize',
                            help='Minimum sequence length')

        args = parser.parse_args()

        action = results = parser.parse_args()

        self.infilename = action.infile_name.strip('\'"')
        self.outfilename = action.oufile_name.strip('\'"')
        self.minsize = int(action.minsize)


if __name__ == '__main__':
    sf = SelectAndSortFasta()
    if len(sys.argv) > 1:
        sf.parse_args()
        sf.split_file(from_args=True)
    else:
        infile = 'data/fasta/AINZ01/AINZ01.1.fsa_nt'
        outfile = 'data/fasta/AINZ01/AINZ01sorted.1.fsa_nt'
        minlen = 1000
        sf.split_file(from_args=False, in_filename=infile, out_filename=outfile, min_seq_len=minlen)
    sf.show_seq_out()