Comments (2)
from ltr_retriever.
Thx at the end we solve it with:
$vi EditFasta
File='1.fna'
OutFile = '1_fixed.fna'
f = open(File,'r')
g = open(OutFile,'w')
for line in f:
line.rstrip()
if '>' in line:
temp = line.split()
temp1 = ' '.join(temp[0:-1])
temp1 = temp1.lstrip('>')
towrite = '>'+temp[-1]+' '+temp1+'\n'
g.write(towrite)
else:
g.write(line)
f.close()
g.close()
$python EditFasta
from ltr_retriever.
Related Issues (20)
- too many LTR/unknown and most of LTR/unknown are classified as LTR/Gypsy HOT 1
- Error: cp: cannot stat *.retriever.scn.adj’: No such file or directory HOT 1
- No tbl file HOT 2
- No candidate is found in the file(s) you specified. HOT 7
- Repeatmodeler 、RepeatMasker and LTR_retriever HOT 4
- Serious error ⇒ Dependency checking: Error: The RMblast engine is not installed in RepeatMasker! HOT 3
- Can one use EDTA genome.mod.pass.list and genome.mod.EDTA_TEanno.out output in LAI HOT 1
- No candidate is found in the file(s) you specified HOT 2
- Use of uninitialized value $seq in string eq at call_seq_by_list.pl line 129 HOT 10
- Are LTRs (insertion time of 0) the likely cause of somatic variation? HOT 2
- LTR_retriever warning HOT 1
- Total length annotated by RepeatMasker is longer than LTR_retriever HOT 3
- RE: Masking LTR HOT 2
- A question about LAI in autopolyploid HOT 2
- How to discover "sequencing gaps" in genome assemblies. HOT 3
- ask for help? panLTR HOT 1
- Running Ltr_retriever...Died at /app/RepeatModeler-2.0.4/LTRPipeline line 693. HOT 2
- No tbl file issue HOT 5
- LAI is not applicable on the current genome assembly HOT 3
- conda install errors HOT 1
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from ltr_retriever.