Questions tagged [seqio]

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1answer
42 views

Updating the GFF3 + Fasta to GeneBank code

I'm trying to convert gff3 and fasta into a gbk file for usage in Mauve. I've found a solution but the code is outdated: ...
1
vote
2answers
127 views

Extract sequences from MultiFASTA aligned file, by coordinates

I am trying to extract a specific sequence from a multifasta file, from each sequence in the aligned file. The sequences look like this, and there are 32 sequences within the multiFASTA: ...
1
vote
1answer
13 views

What is the best way to drop alignment artifacts in sequence objects in biopython?

I have a bunch of sequences created with Roary which I want to preprocess. When I read the sequences (genomics data) I want to translate them to protein sequences ...
1
vote
3answers
193 views

How to count the kmer occurrence in FASTA file considering overlapping and reverse complement?

I am using count_overlap() for counting the kmers from Biopython . Does it take the reverse complement of kmer into account? I need to count reverse complement too
0
votes
2answers
48 views

How to fix NameError?

I am working on a project and am having issues with the following code that I have written in nano: ...
0
votes
2answers
165 views

Remove Redundant Sequences from FASTA file with Biopython reducing memory footprint

I need help with my Biopython code, I am kind of new to Python and Biopython so please don't be harsh on me. Everything started from here: Remove duplicated sequences in FASTA with Python I answered ...
0
votes
1answer
186 views

Why SeqIO.parse method isn't working?

I am trying to follow the tutorial from from the Biopython website here and I am right at the beginning (2.4.1), where I am trying a Simple FASTA parsing example which is ...
-1
votes
1answer
149 views

Biopython SeqIO check input file

Hi I am trying to learnt python3 and Biopython, I am trying to check imported fasta file before processing so far using: ...