User: felipelira3

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Posts by felipelira3

<prev • 10 results • page 1 of 1 • next >
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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 4 weeks ago by felipelira30
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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 10 weeks ago by felipelira30
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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 10 weeks ago by felipelira30
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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 11 weeks ago by felipelira30
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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 11 weeks ago by felipelira30 • updated 11 weeks ago by mobiusklein150
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Comment: C: get protein sequences from genbank
... Do you have the corrected script @mschmid? ...
written 12 weeks ago by felipelira30
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Comment: C: gbk2faa: why is it not working for refseq gbk?
... can you put your corrected script here? thank you, Felipe ...
written 12 weeks ago by felipelira30
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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 15 months ago by felipelira30
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Comment: C: Extract fastq reads from reads list
... Wow a beginner mistake. Thank you @dschika ...
written 15 months ago by felipelira30
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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 15 months ago by felipelira30

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