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sinamajidian /
Created March 29, 2022 10:46
Chop each read in a fastq file into few chunks
import numpy as np
from sys import argv
file_fq_input_addrss = argv[1]
file_fq_output_addrss = argv[2]
file_fq_input= open(file_fq_input_addrss,'r');
sinamajidian /
Created October 10, 2020 07:27 — forked from williamrowell/
Calculate the mean and standard deviation of a coverage depth distribution as if it were normally distributed.
#!/usr/bin/env python3
"""Coverage mean and standard deviation of autosomes
Estimate the mean and standard deviation from a mosdepth coverage BED for
positions with coverage in the range (0, 2 * non-zero mode). This estimate
behaves well for PacBio HiFi WGS of human germline aligned to either hs37d5 and
GRCh38, and may be useful for other situations as well.
$ bash mosdepth --threads 3 --no-per-base --by 500 -m "${BAM%.*}.median" "${BAM}"
$ tabix ${BAM%.*}.median.regions.bed.gz {1..22} | python
sinamajidian /
Last active March 31, 2022 22:33
Extracting the high coverage region (as bed file) from a BAM file

A simpe code for extracting the regions with high coverage (>depth_treshold) from a bed file. The input of the code is a bed file containing rows of regions with its depth as following format

21	9424000	9424500	69.00
21	9424500	9425000	69.00
21	9425000	9425500	67.00
21	9425500	9426000	66.00
21	9426000	9426500	65.00
21	9426500	9427000	66.00
sinamajidian /
Last active August 4, 2020 08:42
Extract parts of fasta file for all scaffolds

We have the fasta files of some viral genomes. We want to aligend all of them and extract only one gene of them.

cat *.fasta > all.fasta
cat gene.fasta all.fasta > all_with_gene.fasta

The I ran mafft on them

sinamajidian / c_api_htslib
Last active April 15, 2020 11:15
Simple C API htslib
downlaod and unzip htslib
cd /Users/sina/Downloads/htslib-1.10.2
mkdir /installation_folder
./configure --prefix=/Users/sina/Downloads/htslib-1.10.2/installation_folder