2021-10-29 [microbiology] qiime2 sample pretreatment form automation script

Abstract

Some time ago, I studied 16S/ITS Analysis of , Yes qiime2 Have a certain understanding of the analysis process of , There is already a process for analysis , It will be sorted out and released later . Before analysis , The software needs to provide preprocessing files , Include a sample data sheet （ Two terminal sequencing data format ）, A sample grouping table . Both of these were generated manually before , There is no way to group tables , The grouping of each project is different , But the sample data table can be automatically generated . Record here .

Tools and methods

Using language ：bash

Use command

The first part is to extract the original data from the project data obtained by the supplier . Put it in 01.data Medium standby

for i in */00.RawData/*/*.raw_1.fq.gz;
do 
i=${i%.raw_1.fq.gz};
mv {
    ${i}.raw_1.fq.gz,${i}.raw_2.fq.gz} ./;
done

Next, you need to obtain the complete sample data path through the sample name , And print qiime2 Table format required .

echo -e "id\tforward-absolute-filepath\treverse-absolute-filepath" >> all_sample.txt;
for i in *.raw_1.fq.gz;
do 
i=${i%.raw_1.fq.gz};
echo -e "${i}\t`pwd`/${i}.raw_1.fq.gz\t`pwd`/${i}.raw_2.fq.gz" >> all_sample.txt;
done

Command Introduction
echo -e “” ： Identify and print the separator inside the double quotation marks , This ensures that the output format is correct ;
pwd ： stay echo Execute the path acquisition command in , Absolute path of supplementary samples ;
">> " ： Overwrite input into document , If it is a single greater than sign, enter , Previous documents will be cleared , There is only the last line in the final document .

Result display

summary

In fact, it is not difficult to manually operate the document , use excel Can also do . But considering that qiime2 Absolute path required , There is some trouble with every modification , Therefore, this part is optimized . If you have better suggestions , Welcome to discuss , Or add me VX：bbplayer2021 Invite in .