BWA-MEM2, Samtools: TPM定量

https://blog.csdn.net/m0_53945548/article/details/135317476?spm=1001.2014.3001.5502

BWA-MEM2和Samtools安装见上文

(完整路径)/bwa-mem2 index contigs.fa
(完整路径)/bwa-mem2 mem -t 180 contigs.fa 1.fq.gz 2.fq.gz > aligen.sam
samtools view -Sb -@180 aligen.sam > aligen.bam
samtools sort -@180 aligen.bam -o aligen_sort.bam
samtools index -@ 180 aligen_sort.bam
samtools idxstats -@ 180 aligen_sort.bam > aligen_result.txt
sed -i "1 i GeneID\t\length\tmapped_read\tunmapped_read" aligen_result.txt

输出是以TAB分隔的，每行包括参考序列名称，序列长度，映射的读取段数，未映射的读取

#!/home/zhongpei/miniconda3/envs/py39/bin/python3.9
#########################################################
# TPM count
# written by PeiZhong in IFR of CAAS

import argparse
import pandas as pd

parser = argparse.ArgumentParser(description='TPM count')
parser.add_argument('OperaPath', help='Path that contain your samtools result file')
parser.add_argument('input_name', help='input_name')
parser.add_argument('output_name', help='output_name')

args = parser.parse_args()

OperaPath = args.OperaPath
input_name = args.input_name
output_name = args.output_name

if OperaPath.endswith("/"):
    OperaPath = OperaPath
else:
    OperaPath = OperaPath+"/"
target = OperaPath+input_name

# 'TPM count'
#############################################
def TPMcount(target):
    table1 = pd.read_table(OperaPath+input_name, index_col=0)
    table1 = table1[table1.index != "*"]
    table1["Ng/Lg"] = table1['mapped_read'] / table1['length']
    SUM_NjchuLj = table1["Ng/Lg"].sum()
    table1["TPM"] = table1['Ng/Lg'] / SUM_NjchuLj * 1e6
    result = table1[["Ng/Lg","TPM"]]
    print(SUM_NjchuLj)
    result.to_csv(OperaPath+output_name, index=True, sep="\t")
#############################################

TPMcount(target)
print(target)

合并很多个数据

#!/home/zhongpei/miniconda3/envs/py39/bin/python3.9
#########################################################
# TPM count
# written by PeiZhong in IFR of CAAS

import argparse
import os
import pandas as pd

parser = argparse.ArgumentParser(description='TPM count')
parser.add_argument('OperaPath', help='Path that contain your samtools result file')
parser.add_argument('file_maker', help='(sample)file_maker)')

args = parser.parse_args()

OperaPath = args.OperaPath
file_maker = args.file_maker

os.chdir(OperaPath)
files = os.listdir(OperaPath)
ls = []
for file in files:
    if file_maker in file:
        ls.append(file)
ls.sort()
print(ls)

all_data = pd.DataFrame()

for file_name in ls:
    df = pd.read_csv(file_name, sep='\t')
    df['file_name'] = file_name
    all_data = pd.concat([all_data, df])

pivot_data = all_data.pivot(index='GeneID', columns='file_name', values='TPM')
pivot_data.to_csv('pivot_data.csv')