User: felipelira3

gravatar for felipelira3
Reputation:
0
Status:
New User
Last seen:
4 months, 4 weeks ago
Joined:
1 year, 6 months ago
Email:
f**********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by felipelira3

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
205
views
1
answers
Answer: A: How to convert phylo object to hclust object in R
... Did you check this? https://www.rdocumentation.org/packages/ape/versions/5.0/topics/as.phylo ...
written 5 months ago by felipelira30
0
votes
2
answers
431
views
2
answers
Comment: C: Problem with Parse SeqIO SOLVED - link to cross-reference
... Sorry for that but the frequency of responses here has a delay comparing with Stackoverflow and I published there too. For instance, I put the link to both topics and edited the title to solved in both. ...
written 6 months ago by felipelira30
10
votes
2
answers
431
views
6 follow
2
answers
Problem with Parse SeqIO SOLVED - link to cross-reference
... Anybody have this problem before? Any suggestion about the reason? The script creates the files containing the genome sequences but it appears at the end of the process. Line in my script File "/home/flira/scripts/list_ncbi_download_genome_vs_02.py", line 97, in SeqIO.write(SeqIO.pa ...
python written 6 months ago by felipelira30
0
votes
0
answers
231
views
0
answers
Eliminate duplicates skipping same key and values
... Files to test can be downloaded from https://github.com/felipelira/files_to_test.git I want to retrieve the information from several files in one folder and create a table with the information as a dictionary to create a table after. #!/usr/bin/env python import os import sys from ...
python genbank written 6 months ago by felipelira30
3
votes
1
answer
237
views
1
answer
Retrieve qualifiers plasmid and pathovar
... I am trying to extract some pieces of information from the .gbk file. For the most common information, I can manage the problem. The problem is when I try to extract the info of "plasmid" and "pathovar" when they are not present. Both files used for tests are in [https://github.com/felipelira/files_ ...
python seqio written 6 months ago by felipelira30 • updated 6 months ago by mobiusklein150
0
votes
2
answers
2.8k
views
2
answers
Comment: C: get protein sequences from genbank
... Do you have the corrected script @mschmid? ...
written 6 months ago by felipelira30
0
votes
1
answer
856
views
1
answers
Comment: C: gbk2faa: why is it not working for refseq gbk?
... can you put your corrected script here? thank you, Felipe ...
written 6 months ago by felipelira30
0
votes
1
answer
713
views
1
answers
Answer: A: Extract fastq reads from reads list
... improved script #usage: script [list_of_reads] [fastq_file] [-output_file_name] import sys from Bio import SeqIO list_of_reads= open(sys.argv[1], "r") recover = set([line.strip().split(' ')[0] for line in list_of_reads]) output = open(sys.argv[3], "w") # u ...
written 18 months ago by felipelira30
0
votes
1
answer
713
views
1
answers
Comment: C: Extract fastq reads from reads list
... Wow a beginner mistake. Thank you @dschika ...
written 19 months ago by felipelira30
3
votes
1
answer
713
views
1
answer
Extract fastq reads from reads list
... This is my code to extract the reads from a raw fastq file. I have one list with the headers of the reads and I want to retreive them from the original file. My output is an empty file. Maybe I did it not so well. Any help, improving this script will be appreciate. Less is more. import sys ...
python fastq extract seqio written 19 months ago by felipelira30

Latest awards to felipelira3

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1376 users visited in the last hour