Map the peptides to its corresponding protein sequence and locate the modification sites
python ProtMapPep.py -c "PTM file" -s "species" -i "infile" -o "outfile" -p "pepindex" -m "modindex" -a "prot_acc_index"
-c, --conf PTM file used for searching
-s,--sp species name(as in database): case sensitive
-i,--ifile infile name with extension
-o,--ofile outfile name with extension
-p,--pep Column index of peptide in infile
-m,--mod column index of modified peptide in infile
-a,--acc column index of protein accession in infile
-h, --help show this help message and exit
python ProtMapPep.py -c unimodPTMs.txt -s HUMAN -i infile.txt -o outfile.txt -p 2 -m 5 -a 7
Results will be wirtten as tab delimited to the specified outfile name. Last three columns of your outfile contains the mapped information as shown below
Column[-3] | Column[-2] | Column[-1]
--------------------|--------------------------------------|-----------
Peptide start in UP | Modification__modified position in UP| Indels(Yes/No)