Relaxed and sequential Phylip format conversion

I have nutted out a solution for you.

If this is the content of input.fa:

>virusA_detailed_description
ACGTGACGATCCCCAAACGTGACGATCCCCAA
>virusB_detailed_description
ACGTGACGATCGGGAAACGTGACGATCGGGAA
>virusC_detailed_description
ACGTGACGATCAAAAAACGTGACGATCAAAAA
>virusD_detailed_description
ACGTGACGATTTTTAAACGTGACGATTTTTAA

And this is the script:

#!/usr/bin/env python3

'''
Converts a fasta file to phylip format
'''

from Bio import AlignIO
from Bio.AlignIO.PhylipIO import PhylipWriter
import sys

infile = sys.argv[1]
outfile = sys.argv[2]
idwidth = int(sys.argv[3])
with open(infile, 'r') as input_handle:
    align = AlignIO.read(input_handle, "fasta")
    with open(outfile, 'w') as output_handle:
        PhylipWriter(output_handle).write_alignment(align, id_width=idwidth)

Then, save this script as phylpwrtr.py and do:

chmod +x phylpwrtr.py
./phylpwrtr.py input.fa output_longids.phy 30 # 30 is the width of the header, adjust the value to adjust header length

The contents of output_longids.phy looks like:

 4 32
virusA_detailed_description    ACGTGACGAT CCCCAAACGT GACGATCCCC AA
virusB_detailed_description    ACGTGACGAT CGGGAAACGT GACGATCGGG AA
virusC_detailed_description    ACGTGACGAT CAAAAAACGT GACGATCAAA AA
virusD_detailed_description    ACGTGACGAT TTTTAAACGT GACGATTTTT AA