User: dllopezr
dllopezr • 60
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Posts by dllopezr
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... Hi!
I am working parsing blast xml outputs with Biopython and for performance purposes, I want to parallelize the process. The code takes a large blast xml output, perform a calculation over the alignments and save the result in a SQL database
The code is as follows:
from Bio.Blast import NCB ...
written 12 months ago by
dllopezr • 60
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... Hi Pierre, do you have any recomendation for the use of longblob? I'm thinking in use VARCHAR(MAX) for my sequence instead of text becuause i read this have improvements in memory and retrieve, but longblob is new to me. For example, In some situations, I would like to tell SQL that select the 'DNA' ...
written 17 months ago by
dllopezr • 60
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5 follow
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... Hi everyone
I'm creating a database that will have a table for protein and dna sequence. I'm looking for advices for the config of this table in mysql in terms of the data type use (VARCHAR, TEXT, LONGTEXT) as well as the codification and collation for this table.
Can you help me with that?
Thank ...
written 17 months ago by
dllopezr • 60
• updated
17 months ago by
Pierre Lindenbaum ♦ 131k
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... I already do it
Because my databases have this name structure: `T"x"P"x"_T"x"` when x is a 1 to 4 number
I create all the strings and passed it in the blast command
#!/bin/bash
for T in `seq 1 4`; do
for P in `seq 1 4`; do
for t in ...
written 20 months ago by
dllopezr • 60
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... Hi Lieven
When I say "aliases" I refer to the name of the blast database is not a file but a name that represents the files.
Example: The makeblastdb produces 3 files with names: T1P1T0.nhr, T1P1T0.nsq and T1P1T0.nal, but the name of the blast database to pass to blastn script is only T1P1T0 with ...
written 20 months ago by
dllopezr • 60
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... Hi community
I have a folder with multiple blast databases. I want to run blastn over all databases and produce one output for each database.
I'm trying something like that
for i in `find . -name 'name_of_database'`; do
time blastn -db "$i" -query Sondas_100.fasta -out "$i".out -ou ...
written 20 months ago by
dllopezr • 60
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... Hi community!
For the purpose of my work I need that the blast ouput don't show me the hits with 100% identity and 100% query coverage
with the command -perc_identity 100 I obtain only the hits with 100% identity, but I want the opposite. I've try something like -perc_identity <100 but seems B ...
written 21 months ago by
dllopezr • 60
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... Hi community!
I am working with metagenomic output from MG-RAST, but the columns don't match and I need to solve this before doing my DeSEQ analysis. The table is something like this
GeneName Count GeneName Count GeneName Count GeneName Count
GeneA x GeneB x GeneA x Ge ...
written 23 months ago by
dllopezr • 60
• updated
23 months ago by
Fabio Marroni • 2.6k
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Comment:
C: Mock Metagenome Gene Content
... Thanks for your Answer Nitin. The problem is that I don't want to find out the abundance of an organism, I want to count the abundance of some genes of interest. For example, how many time the gene "nifH" is present in the sample, for this purpose I need to know the organism that carry this gene, ho ...
written 24 months ago by
dllopezr • 60
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... Hi, community!
I need to work with a mock metagenome community for the optimization of the alignment parameters of a tool
I've found this community: https://www.nature.com/articles/sdata201681, that is composed of 26 bacterial and archaeal genomes.
For the purpose of my work I need to know the a ...
written 24 months ago by
dllopezr • 60
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