L1angyan / Peptides_extraction

Extract information and annotation of peptides from output of RiboCode

Peptides_extraction

#Extract information and annotation of peptides from output of RiboCode

#The *result.txt and *result.gtf is the output of RiboCode for detecting ORFs using Ribo-seq data. The script, zzz_extract_peptides.py, is used to extract information of small ORFs.

USEAGE:

python3 zzz_extract_peptides.py Bleaf1. #The gtf and txt file must be in current directory.

for i in *out.txt;do

name=${i%txt};

gtf=${name}gtf;

cat $i >> z_all.txt;

cat $gtf >> z_all.gtf;

done

head -n1 z_all.txt > zzz_all.txt;

grep -v "ORF" z_all.txt >> zzz_all.txt;

#各材料的gtf、txt文件顺序对应，先将其写入一个文件（txt有表头注意去掉），在通过加编号去冗余

python3 zzz_merge.py