All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Here we write upgrading notes for brands. It's a team effort to make them as
All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Here we write upgrading notes for brands. It's a team effort to make them as
import pandas as pd | |
file = "input.bed" | |
df = pd.read_csv(file, sep="\t", names=["chr", "start", "end", "interval", "score", "strand"]) | |
df[["gene", "extra"]] = df["interval"].str.split("_", 1, expand=True) | |
df.drop(["interval", "score", "strand", "extra"], axis=1, inplace=True) | |
new_df = df.groupby("gene").agg({"chr":"unique", "start":min, "end":max}) | |
new_df.reset_index(inplace=True) | |
new_df["chr"] = new_df["chr"].apply(lambda chr: chr[0]) | |
new_df["start"] = new_df["start"].astype("str") |
#!/usr/bin/python3 | |
from pyliftover import LiftOver | |
import pandas as pd | |
import argparse | |
import mapply | |
import sys | |
import os | |
mapply.init( |
Exomedepth:
$ awk -F"__" '$1=$1' OFS="\t" PAHC44_1_CDHS-17427Z-2274_sorted.bed | cut -f1,2,3,4 > qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.bed
DeviCNV:
$ echo -e "Amplicon_ID\tChr\tAmplicon_Start\tAmplicon_End\tInsert_Start\tInsert_End\tGene\tTranscript\tExon\tPool" > qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.devicnv.bed $ awk -F"__" '$1=$1' OFS="\t" PAHC44_1_CDHS-17427Z-2274_sorted.bed | awk '{ print $4"."$7"\t"$1"\t"$2"\t"$3"\t"$2"\t"$3"\t"$4"\t"$4"\t"$7"\t"Pool1}' >> qiaseq_PAHC44_1_CDHS-17427Z-2274_no_header.devicnv.bed