Task 1. Join fasta files
seqret @posl.txt -outseq 9_1.fasta
Task 2. Split fasta files
seqretsplit atpe_ali.fasta
Task 3. Cut 3 CDS from .gb file
seqret @coords.txt -outseq 9_3.fasta
Task 4. Translate CDSs from fasta file
transeq cds3.fasta 9_4.fasta
Task 5. Translate nucleotide sequence in six frames
transeq coding.fasta -frame 6 9_5.fasta
Task 6. Change alignment format from .fasta to .msf
seqret atpe_ali.fasta msf::9_6.msf
Task 7. Print in output amount coincidental letters betwixt the second sequence of alignment and others
infoalign atpe_ali.fasta -html -refseq 2 -only -name -idcount -stdout 9_7.txt
ATPE_BORPE 90
ATPE_BURM1 141
ATPE_SHEPW 62
ATPE_ECOLI 74
ATPE_CALBD 36
ATPE_MACCJ 40
ATPE_BACSU 49
Task 8. Сhange format from .gb to .gff
featcopy seque.gb 9_8.gff
Task 9. Extract from .gb file CDSs in fasta format and add description of protein function
extractfeat sequence.gb -type CDS -describe product -outseq 9_9.fasta
Task 10. Shuffle letters in given nucleotide sequence
shuffleseq cds3.fasta 9_10.fasta
Task 11. Generate 3 random sequences with length 100
makenucseq -amount 3 -length 100 -stdout 9_11.fasta
Task 12. Frequencies of codons in given CDSs
cusp 9_3.fasta 9_12.txt
Task 14. Delete gap symbols and other extraneous ones
degapseq atpe_ali.fasta 9_14.fasta
Python script
This script uses "extractfeat" option with "-type" and "-describe" parameters in order extract from .gb file CDSs in fasta format and add description of protein function and then write them in new file. The only thing you need is the юпи file name. The results are presented below and, as it can be seen, it works.
P.S.I took a liberty to do a little more and to make this script read created .fasta file and do a list with coordinates and proteins in a new file.