get_full_seqs in LTR_retriever.py generate some empty sequences which should be generated. about tesorter HOT 4 CLOSED

Chr01:100489068..100485858#LTR/unknown

Chr01:100991415..100985473#LTR/Retrovirus

Chr01:102009458..102011936#LTR/unknown
TGTGGGGGCGGAGCCCCAGAGAGTAGTTTCCAGGCTCTCGGCCTCACACAGACAGGTGCTGGCTCAGGTAGTAAATGGCCAACTGTGATTGCATGGCCATCAGCTGTGGCTAGTTGGCCGTCAGCTGTAACCAGTGAGCCATTGGCCACAATATAATTGCTGTGGCTAAGGAGAGAGAGAAAGAAGGATGGGGCTAGCAAGGAGATGGCGGCTGGGCTGGCAAGCGTGGATGGCGGTTTGCAGACAGTGTGTATCCAGCCTCCAGTGAGAGTATAGTGCCGCCAGAGAGAATAAAGTGGTATGACTCCCCTACCTATGGCTCCGTGGGTGTTCCTTTTTGGCCTCACCATATCCTGCGTTCTTGTGTGGGGAGCGGGACCGGAGACCCTGCAGGCCACCCCGCATGACACATGGCGCAGCGAGCAGGGTCCCCAACATGACACATGGCGTAGTCGGCAGGATATGGTGCCGGCCAAAGCTCTCCGAAGGGCGGTGGAGCAGTTTGTGTGTATGAACACTCAGTCTGAGGAAGACCAGGAGGAGCAGCTGCCGGAGAGCTGGACCCTCGTGGAGGGGTGGGAGGACGTGGACGGTTCTCCCACCAGCACAGGAAAAGCCATGCAGCTGCTGGAGAGATGGAGCCCCGTGGAGAGGTGGAAAGATGTGGACGGTTCCCCAACCAGCACAGGCCGGAGAAAGCGAAGGTCGTTGCAGCCCTGTGGGCCGGGGAAGTTCCTGCTCAGGCAGCCCGGATGCAGGACTTGTAGTCCCAGGAGGTAACGCTTGCTGAGTCCTCCGTGGGAGATGAGGGTGAGGTCAAGGTCGTCCCTCACCCCCAGGACAGCCCTGGTGAATGACTATGGACTATGGGGAATTGCCTTCCATCCCTAATTTAATGGACTGCTTGACTGTTTGTTTGGGAACTGTTGTTAGTGGAACTGGGGGATATTTGCTTTTGTCTCTTGACTGGCCGCCATTGAGAATATGTAAGCACCTTGATTGTGAGTCGCTGTTGTTCCAGCAGGGTACCCTGAGAGGCACAGAGAGAGTGGCAGTGCGCTGAGAGGTCTAGCTGTGCCCTGAGAAGCCCTGGCTGTGTCCAGGAAGTGTGGCTGTGCCCACAGAGAGTGGTGGTGCCCTGAGAAGCCCTGGCTGTGTCCAGGAAGTGTGGCTGTTCCCAGAGAAAGTGGCAGTGCCCTGAGAAATCCTAGCTGTGCCCGGGGAAACTAGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCAGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCAGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCTGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCAGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCTGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCAGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCAGTGCCCAGGAGTACTGGTGGTGCCCTGAGAAACCCTGGCTGTGTCCGGGAAGACAGGTGGTACCCTAAGAAGTCCAGGAAGTCTGGCCGTGCCCAGAAGCACTGGTGGTGCCCTGAGAAACCCTGGCTGTGCCCAGAGAGCCTGGCTGTGTCCAGGATATTGCATTCACCCCCAGGCTCCTCGCACAGGTCCCCTCGCGGAAGACGCTTGTCGCGTAGATTGTGAGGCGAGAGCCTGTAGGGGTGGAGTGTGGGGGCGGAGCCCCAGAGAGTAGTTTCCAGGCTCTCGGCCTCACATAGACAGGTGCTGGCTCAGGTAGTAAATGGCCAACTGTGATTGCATGGCCATCAGCTGTGGCTAGTTGGCCGTCAGCTGTAACCAGTGAGCCATTGGCCACAATATAATTGCTGTGGCTAAGGAGAGAGAGAAAGAAGGATGGGGCTAGCAAGGAGATGGCGGCTGGGCTGGCAAGCGTGGATGGCGGTTTGCAGACAGTGTGTATCCAGCCTCCAGTGAGAGTATAGTGCCGCCAGAGAGAATAAAGTGGTATGACTCCCCTACCTATGGCTCCGTGGGTGTTCCTTTTTGGCCTCACCATATCCTGCGTTCTTGTGTGGGGAGCGGGACCGGAGACCCTGCAGGCCACCCCGCATGACACATGGCGCAGCGAGCAGGGTCCCCAACATGACA

from tesorter.

Does get_full_seqs automatedly filter some low quality sequence? Or would it be propriate for me to generate fasta sequences accodring to the 2 pass.list files by myself, then using TEsorter to classify them?

from tesorter.

get_full_seqs does not filter some low quality sequence, but it indeed discards sequences with the same location (see the below example). Surely you can generate fasta sequences accodring to the 2 pass.list files by yourself.
The below is count for an example:

$ wc -l *pass.list
    622 genome.fasta.mod.nmtf.pass.list
  16305 genome.fasta.mod.pass.list
  16927 total
$ grep -c ">" intact_ltr.fa
16296
$ cat *pass.list | cut -f1 | grep -v "#" | sort |uniq | wc -l
16296

from tesorter.

Yep, the empty sequence location does overlap with existing sequence, I guess it's the problem. thx a lot

from tesorter.