ProtMapPep

Map the peptides to its corresponding protein sequence and locate the modification sites

Usage

python ProtMapPep.py -c "PTM file" -s "species" -i "infile" -o "outfile" -p "pepindex" -m "modindex" -a "prot_acc_index"

Description

-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

example

python ProtMapPep.py -c unimodPTMs.txt -s HUMAN -i infile.txt -o outfile.txt -p 2 -m 5 -a 7

Information written to outfile

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)