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Introducción a Bioinformática

CONTENIDO

• BASH PIPELINES
• PYTHON SCRIPTS
• R SCRIPTS
• ENTREZ NCBI PERL

BASH PIPELINES

COMANDO PRÁCTICOS

Eliminar espacios en blanco

sed '/^$/d' file.txt

grep . file.txt

grep "\S" file.txt

Imprimir lineas entre rangos

awk 'NR>=20&&NR<=80' input.txt

Convertir fastq a fasta

seqtk seq -a fastq_file.fq > fasta_file.fa

Separar multifasta

awk '/^>/{s=++d".fa"} {print > s}' multi.fa

Separar una secuencia especifica de un fasta

samtools faidx file.fasta

samtools faidx file.fasta "ID_seq" > ID_seq.fasta

PYTHON SCRIPTS

Instalando Packages

Instalación de PIP

sudo apt-get install python3 python3-pip

pip3 install biopython

pip3 install Bio

Instalación conda Miniconda Anaconda

bash <Mini/A>conda3-latest-Linux-x86_64.sh

conda install -c conda-forge biopython

Importando Packages

from Bio import Entrez

Entrez.email = "francisco.ascue@unmsm.edu.pe"

handle = Entrez.efetch(db="Nucleotide", id="AY994334.1",rettype="fasta",retmode="text")

print(handle.read())

sudo pip3 install dna_features_viewer

from dna_features_viewer import GraphicFeature, GraphicRecord

features=[
    GraphicFeature(start=0, end=265, strand=+1, color="#ffd700",
                   label="five_prime_UTR"),
    GraphicFeature(start=266, end=21555, strand=+1, color="#ffcccc",
                   label="ORF1ab"),
    GraphicFeature(start=21563, end=25384, strand=-1, color="#cffccc",
                   label="S"),
    GraphicFeature(start=25393, end=26220, strand=+1, color="#ccccff",
                   label="ORF3a")
]
record = GraphicRecord(sequence_length=26220, features=features)
ax, _ = record.plot(figure_width=10)

# import packages
from Bio import Entrez, SeqIO
from dna_features_viewer import annotate_biopython_record
from dna_features_viewer import BiopythonTranslator

# Download sequence in NCBI format

Entrez.email = "francisco.ascue@unmsm.edu.pe"

handle = Entrez.efetch( db="nucleotide", id="NC_000884.1", rettype="gb", retmode="text")

record = SeqIO.read(handle, "genbank")

#record.features = [ f for f in record.features if f.type not in ["gene"] ]

# Save records in to variale

SeqIO.write(record, "seq.gb", "genbank")

# Graphics 

graphic_record = BiopythonTranslator().translate_record("seq.gb")
ax, _ = graphic_record.plot(figure_width=10, strand_in_label_threshold=7)

R SCRIPTS

Instalando Packages

install.package("BiocManager")
    
##Cargando packages

library(BiocManager)
    
BiocManager::install("ggplot2")

##Actualizando packages

install.packages(c("BiocManager","ggplot2")
    
update.packages(ask = FALSE)

### Cargar tablas (csv, tsv)

read.table("datafile.ext", sep = ",", header = TRUE)
    
read.csv("datafile.csv")
    
### Cargar paletas de colores

library(viridisLite)
library(viridis)
library(RColorBrewer)
display.brewer.all()

### barplot basicos

barplot(height = gene$V1, border = FALSE, names.arg = gene$V2, 
        las = 1 ,
        col = heat.colors(25),
        main = "Genes por Cromosoma")

ggplot(gene, aes(x=V2, y=V1)) +
  geom_segment( aes(x=V2, xend=V2, y=0, yend=V1)) +
  geom_point( size=5, color="red", fill=alpha("orange", 0.3), alpha=0.7, shape=21, stroke=2) 

ENTREZ NCBI PERL

esearch -db nucleotide -query "covid19"

<ENTREZ_DIRECT>
  <Db>nucleotide</Db>
  <WebEnv>MCID_606a64fe45460140b56b5fe4</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>139219</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

esearch -db nucleotide -query '("Severe acute respiratory syndrome coronavirus 2"[Organism] AND (viruses[filter])'

<ENTREZ_DIRECT>
  <Db>nucleotide</Db>
  <WebEnv>MCID_606a6ccaa53f343d4860d16b</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>130415</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

esearch -db nucleotide -query '("Severe acute respiratory syndrome coronavirus 2"[Organism] AND (viruses[filter])' -mindate 2021/01/01 -maxdate 2021/01/02

<ENTREZ_DIRECT>
  <Db>nucleotide</Db>
  <WebEnv>MCID_606a6f2559c60d0d1e6a4984</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>59</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

esearch -db nucleotide -query '("Severe acute respiratory syndrome coronavirus 2"[Organism] AND (viruses[filter])' -mindate 2020/01/01 -maxdate 2021/03/02 | efilter -country peru

<ENTREZ_DIRECT>
  <Db>nucleotide</Db>
  <WebEnv>MCID_606a6fb2fdbe9156e53f0caa</WebEnv>
  <QueryKey>2</QueryKey>
  <Count>90</Count>
  <Step>2</Step>
</ENTREZ_DIRECT>

esearch -db nucleotide -query '("Severe acute respiratory syndrome coronavirus 2"[Organism] AND (viruses[filter])' -mindate 2021/01/01 -maxdate 2021/03/02 | efilter -country peru | efetch -format fasta

>MW494424.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/PER/LIM-INS-173/2020, complete genome
CTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
TGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAA
CTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCT
TATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCC
TCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATG
GTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAG ...

esearch -db pubmed -query "Severe acute respiratory syndrome coronavirus2" | elink -related | efetch -format docsum |   xtract -pattern Author -element Name |   sort-uniq-count-rank

37      Li Y
26      Wang Y
25      Li J
24      Zhang J
24      Zhang Y
20      Wang J
20      Zhang S
19      Zhang L
18      Wang X
18      Zhang X
.       .
.       .
.       .

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