How to link two python scripts

[Larz60+]

sorry, I gave you an ftp url

I was looking for something larger, 2 items is not a good test.
Nevertheless, take a look at the following and see if it does what you'd like
save the file as SplitFasta.py

#!/usr/bin/python
import sys


class SplitFasta:
    def __init__(self):
        self.lines_out = []
        self.header = None
        self.save_seq = ''

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

    def split_file(self, in_filename, out_filename, min_seq_len):

        self.header = None
        seqlen = 0
        self.lines_out = []
        with open(in_filename, 'r') as fin, open(out_filename, '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 > min_seq_len:
                            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 > min_seq_len:
                    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)

if __name__ == '__main__':
    sf = SplitFasta()
    numargs = len(sys.argv)
    print(f'numargs: {numargs}')
    if numargs > 1:
        infile = sys.argv[1]
        outfile = sys.argv[2]
        minlen = sys.argv[3]
    else:
        infile = 'Example.fa'
        outfile = 'NewExample.fa'
        minlen = 1000
    sf.split_file(infile, outfile, int(minlen))
    sf.show_seq_out()

The bottom part 'if __name__ (etc.)' is for testing only, and woun be used if the module is imported into another program

you can import this into any program like:

import SplitFasta

and then use this way
just once at start of script, instantiate the class with:

sf = SplitFasta.SplitFasta()

Then to call, use:

sf.split_file(your_in_filename, your_out_filename, your_min_seq_len)

if you want to show what was written, call:

sf.show_seq_out()

of if you just want the list of output headers:

my_header_list = sf.lines_out

If this is what you are looking for, let me know, I'll be going to bed soon, but be back in about 4 - 5 hours.

Here's a sample run (from command line):

Output:
λ python SplitFasta.py Example.fa NewExample.fa 1000
numargs: 4
The following sequences are in the output file:
>NODE_30_length_1090_cov_54656.2

and the output file (NewExample.fa:

Output:
>NODE_30_length_1090_cov_54656.2
TTATGGAATATCTATTAGAGCAAAAAAGAGATTTTACGCAATTAAAATTTAGCGATATAC
AGCAAATGAAATCAGCTTATAGCATAAGAATTTATAATATGCTACTTTGTGAATTAAAAC
AAAACAGACAAAATCTTAAAATAAATCTTTCAGTATTGCAAAATCTTTTAGAAGTTCCGA
AAAATTATGAAGAAAGATGGGCTGATTTTAATCGTTTTGTATTAAAACAAGCAGAAAAAG
ATATAAATAGCAAATCTAATTTAGTTTTATTAGATATTAAAACTTATAAAACAGGGCGTA
AAATAACAGACTTAGAGTTTATTTTTGATTATAAAAATAACGATAAGCGTATCGCACAGG
AAAAACTAAAAGAAGAAAATTTATTTAAAAAACTCAAAGAAATATTAAGTTCTTACATAG
GCAAATCAATTTATGATGATAGATTTGGCGAAATGATTATAAGTCATTACGAACATAATG
AAGAAAATAAAAAGATTTTAATTATCGCCCAGAGAAAAAGCGATGATAAATTTGTTTGCT
TTGGTGTTAAAAACTTCAAAGATATTAAAAGTTTAGAAAAGCTAAAAGATAAAGCAGAAG
AGTTGTTTTATTTAGATAAACAAAGAGTTTTAAAAGCAAAAGAAGCTCAAAAATATAGAA
ATCTTTTTAATTGATTGTATTTTAAAAATTATAAAAATAAAAGAGATATTAAAAGGCTTG
ATTGATAAAAATAATTCTTAAGCTCTAATATCTATGCTTTTTTGTGTAGAATTTAAAGAA
AGAATTTTATTAAATTCCCCTGTATTATCATCGCTAAATTTCATACCAAAAAGAATTTCT
AGCTCATCGCTTGTGCCAAATTTATTTTCCAGTAGCTTTTTTAAAAGCTCATTCATTTTA
TTATCATCTTTATAGGTTTCGCTTTTACTTTCTGCTTGTATAGGTTTAAAAGGCTTTTTT
TTGTCTTCTTCTGAAGTTTCTTTGTTATTTGTATTTTTTAAAGGATTGCTATAATCTACA
CCTTTTGCCTTTTCTGCTTCTTCTAGTGATTTTACAAACCCATCGTGTCTTTGTTTAAAA
TCAAGATATT