User: flogin

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flogin150
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@dezordi_fz
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11 months ago
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Currently, I'm a Master's Degree student in Biosciences and Biotechnology in Health.

Posts by flogin

<prev • 82 results • page 2 of 9 • next >
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(Closed) try import if not, install in python
... I'm trying to install automatically each library in python if it isn't installed. #!/usr/bin/python # -*- coding: utf-8 -*- from pip._internal import main pkgs = ['Bio==0.1.0','argparse==1.4.0'] for package in pkgs: try: import package except Im ...
python install written 5 weeks ago by flogin150
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found non conserved regions between 2 genomes
... Hey guys. I'm wondering if have a tool that identifies non-conserved regions between 2 eukaryotic genomes (like pan-genomic tools for prokaryotes, that are capable of identify accessory genes). ...
genome alignment blast written 5 weeks ago by flogin150 • updated 4 weeks ago by harish250
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Comment: C: accessing ncbi nucleotide section with python
... thanks vkkodali, I put in this form to recovery the taxonomic levels that I want: for x in record_host_tax[0]["LineageEx"]: if 'phylum' in x.values(): phylum = x['ScientificName'] if 'class' in x.values(): classe = x['ScientificName'] if 'order' i ...
written 6 weeks ago by flogin150
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Comment: C: accessing ncbi nucleotide section with python
... Thanks vkkdali, I'm using this module now, everything is working well, but just a silly question: I'm using this code: handle = Entrez.efetch(db="Taxonomy",id='MG873553.1', retmode="xml") record = Entrez.read(handle) print(record[0]['LineageEx']) That returns: > [DictElement({'Ta ...
written 6 weeks ago by flogin150
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accessing ncbi nucleotide section with python
... I'm working in a little script to access NCBI nucleotides section with an ID list and recovery the information about host of each ID. So I write this: import requests as req link_nucleotide = 'https://www.ncbi.nlm.nih.gov/nuccore/' lst_terms = ['MG873553.1','MG873552.1','MG873551. ...
ncbi python match ids written 6 weeks ago by flogin150
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Comment: C: Can -num_alignments influence the outfmt 6 blast output format?
... Thanks genomax, I was reading and making some tests, the -num_alignments will show N alignments per HSPS between query-subject right? So can I combine -num_alignments 5 with -max_hsps 1, for example, to recovery only 5 lines per query? ...
written 8 weeks ago by flogin150
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Can -num_alignments influence the outfmt 6 blast output format?
... Hello guys, I was reading about the basic parameters of BLAST+, I used to set the parameters -outfmt 6 to return a tabular file as output with 12 columns. But I have one question about the parameter -num_aligments. If, for example, I set -num_aligments 5, in my tabular output only 5 lines per quer ...
parameters blast written 8 weeks ago by flogin150 • updated 8 weeks ago by genomax76k
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Comment: C: RPKM with bowtie output
... thanks swbarnes2, I'll check this. ...
written 11 weeks ago by flogin150
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Comment: C: RPKM with bowtie output
... It's a mapping of RNA-seq against a set of contigs, I just have the contigs, rna-seq files and bam files. ...
written 11 weeks ago by flogin150
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RPKM with bowtie output
... Hello guys, There is a way to evaluate RPKM direct with bowtie 2 output (e.g. bam or sorted bam)? like an R package or some scripts to do this? ...
rpkm rna bowtie count written 11 weeks ago by flogin150 • updated 8 weeks ago by anoo0

Latest awards to flogin

Scholar 6 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Scholar 6 months ago, created an answer that has been accepted. For A: Prottest output to Raxml input
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Prottest output to Raxml input
Supporter 7 months ago, voted at least 25 times.
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.

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