User: flogin

gravatar for flogin
flogin250
Reputation:
250
Status:
Trusted
Location:
Brazil
Website:
https://dezordi.github...
Twitter:
@dezordi_fz
Last seen:
3 days, 7 hours ago
Joined:
1 year, 5 months ago
Email:
z************@gmail.com

Currently, I'm a PhD candidate in Biosciences and Biotechnology in Health.

Posts by flogin

<prev • 107 results • page 1 of 11 • next >
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Python and R libraries for phylogenetic plots
... Hey guys, I'm wondering which options have to plot phylogenetic trees with Python or R. I know the [Phylo](https://biopython.org/wiki/Phylo) for Python and [ggtree](https://guangchuangyu.github.io/ggtree-book/chapter-ggtree.html) for R. There are other interesting libraries to work with it? Than ...
phylogeny python R written 5 days ago by flogin250
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Comment: C: 'blastp' is not recognized as an internal or external command using Bio.Blast.Ap
... idk if it can help, when I run blast inside python, I put (example with blastx): from Bio.Blast.Applications import NcbiblastxCommandline cline = NcbiblastxCommandline(query = query_file, db = database_file, out = query_file+'.blastx', outfmt = 6, word_size = 3, evalue = 0.00001, ...
written 13 days ago by flogin250
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Comment: C: ncbi entrez protein by taxonomy ID
... Thanks, It really works, I just make some adjusts to wrote the protein sequences on specific file per species, thanks ! ...
written 13 days ago by flogin250
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Comment: C: ncbi entrez protein by taxonomy ID
... thanks genomax, I'll test a python version from this line! ...
written 13 days ago by flogin250
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ncbi entrez protein by taxonomy ID
... Hey, I'm studying the Bio.Entrez, to retrivie information from NCBI... I already made basic scripts to retrieve sequences based on protein or nucleotide IDs, but I'm wondering if I can retrieve all proteins based an specific taxonomy ID.... So I have a 3 column csv file, like this: Reovirida ...
ncbi python protein entrez written 13 days ago by flogin250 • updated 13 days ago by user_without_id140
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Answer: C: group viral family pandas dataframe by number of rows
... I resolve this with a quick fix: family_count = df['Family'].value_counts() family_low = family_count[family_count <= 5] family_low_list = family_low.index for i in family_low_list: df['Family'] = df['Family'].replace({i:'Others'}) So I replace all families that occurs l ...
written 4 weeks ago by flogin250
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group viral family pandas dataframe by number of rows
... Hey guys, I have a table with circa of 1600 rows, like this: > Element-ID,Protein-ID,Protein-Product,Virus-ID,Super-Kingdom,Order,Family,Genus,Species,Sense,Start,End,EVE-length > ctg_1003:180657-180956,YP_184770.1,hypothetical protein,39640,Viruses,Unclass,Polydnaviridae,Bracovirus,U ...
python pandas dataframe written 4 weeks ago by flogin250
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Comment: C: biopython entrez lost connection?
... I got complete this search, but some times still have a bug, the script just hangs when send one protein ID, or taxonomy ID. I put the ncbi e-mail and key for API, and put time.sleep(0.15) after each search (because with API key we can send 10 queries per second). I'll update the code present on the ...
written 7 weeks ago by flogin250
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Comment: C: Biopython for Beginner
... by the logics, if faisala85 can pass the path and the file name, the file exists... ...
written 8 weeks ago by flogin250
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Comment: A: Biopython for Beginner
... I suggest to you the use of argparse to avoid manual insertion of input files (https://docs.python.org/3/library/argparse.html). You can easily to this: import argparse parser = argparse.ArgumentParser(description = 'some description') parser.add_argument("-in", "--input", help="Input ...
written 8 weeks ago by flogin250

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Scholar 4 weeks ago, created an answer that has been accepted. For A: Prottest output to Raxml input
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