User: flogin

gravatar for flogin
flogin250
Reputation:
250
Status:
Trusted
Location:
Brazil
Website:
https://dezordi.github...
Twitter:
@dezordi_fz
Last seen:
1 week, 4 days ago
Joined:
1 year, 9 months ago
Email:
z************@gmail.com

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

Posts by flogin

<prev • 111 results • page 2 of 12 • next >
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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 5 months 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 5 months 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 6 months 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 6 months ago by flogin250
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Comment: C: biopython entrez lost connection?
... Thanks for your suggestions genomax, in fact, make the search locally can be a good choice, I'm gonna test this. Moreover, your suggestion to run this locally, allow me to think in to reduce the number of queries to online search, because I was sending all protein IDs from a blast output (circa of 7 ...
written 6 months ago by flogin250
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Comment: C: biopython entrez lost connection?
... Right, thanks genomax, I create an API key and put it inside my script with Entrez.api_key. So I'm gonna test now if everything runs normal. ...
written 6 months ago by flogin250
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Comment: C: biopython entrez lost connection?
... I use the entrez.email, and put a sleep time of 0.4 seconds for each query, should be a time greater than this? ...
written 6 months ago by flogin250
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Comment: C: biopython entrez lost connection?
... Nice, i'm gonne try that ...
written 6 months ago by flogin250
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Comment: C: how to run blastp against nr databse locally
... normally to create a index file for blast databases I run: makeblastdb -in file -dbtype prot ...
written 6 months ago by flogin250
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5 follow
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biopython entrez lost connection?
... Hey guys, I'm in the following situiation: I have a tab-delimited file like this: aag2_ctg_1000 YP_009342179.1 neg 104655 105278 aag2_ctg_1000 YP_009666655.1 pos 257933 258349 aag2_ctg_1000 YP_073558.1 neg 15802 16581 aag2_ctg_1000 YP_073558.1 neg 61637 62266 aag2_ctg_1000 YP ...
ncbi python taxonomy biopython written 6 months ago by flogin250

Latest awards to flogin

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Change mean color in seaborn
Scholar 5 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Centurion 6 months ago, created 100 posts.
Scholar 7 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Popular Question 8 months ago, created a question with more than 1,000 views. For Change mean color in seaborn
Scholar 16 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 17 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Prottest output to Raxml input
Supporter 18 months ago, voted at least 25 times.
Autobiographer 20 months ago, has more than 80 characters in the information field of the user's profile.

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