User: felipelira3

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Posts by felipelira3

<prev • 7 results • page 1 of 1 • next >
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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 5 days 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 8 days ago by felipelira30 • updated 8 days ago by mobiusklein130
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Comment: C: get protein sequences from genbank
... Do you have the corrected script @mschmid? ...
written 14 days 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 15 days 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 12 months ago by felipelira30
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Comment: C: Extract fastq reads from reads list
... Wow a beginner mistake. Thank you @dschika ...
written 12 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 12 months ago by felipelira30

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