User: Davi.marcon

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Posts by Davi.marcon

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Comment: C: Extracting CDS using python
... I've solved this problem creating my own version of parsing, using python native string manipulation and my run time now is around 2 minutes. If you want to check it out, you can acess it here: https://github.com/Mxrcon/Biopytools/blob/master/pepnucfunction.py Do you think that the first parse is sl ...
written 7 days ago by Davi.marcon0
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Comment: C: Extracting CDS using python
... Before this code i'm using the a class to store values, as follows: class sequence: def __init__(self,seq_id,seq,seq_product,seq_translation,cog): self.id = seq_id self.seq = seq self.product =seq_product self.translation = seq_translation self.cog = cog ...
written 9 days ago by Davi.marcon0
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Comment: C: Extracting CDS using python
... Yes, Sure. My files have 9-12Mb Code: def open_gbk(seq_file): sequence_list,id_list = [],[] for seq_record in SeqIO.parse(seq_file , 'genbank'): for feature in seq_record.features: if feature.type == "CDS": gene = feature feature_id = feature.qualifiers['l ...
written 9 days ago by Davi.marcon0
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Extracting CDS using python
... I have a large dataset of *gb files, and im using **Bio.SeqIo.parse()** for extracting cds and writing sequences on multifasta format, but it takes too much time. Is there a faster way to get that information using python? I need cds locus tag, sequence and annotation. I've took almost an hour for g ...
genome python gbk written 10 days ago by Davi.marcon0 • updated 10 days ago by h.mon31k

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