Combining seqkit and rush:

ls *_pandaseq.fasta \
    | rush 'cat {} | seqkit replace -p ".+" -r "{^_pandaseq.fasta}_{nr}" > {.}.fa'

Explain:

• Seqkit is used to rename fasta header. {nr} means number of record, i.e. 1, 2, 3 ....
• rush is a GNU parallel like tool.
  • {} is the input. e.g., C1_pandaseq.fasta.
  • {^_pandaseq.fasta} is used to remove suffix _pandaseq.fasta. e.g., C1_pandaseq.fasta becomes C1.
  • {.} removes last file extension. e.g., C1_pandaseq.fasta becomes C1_pandaseq.

A dry run example:

$ ls *_pandaseq.fasta
C1_pandaseq.fasta  C4_pandaseq.fasta

$ ls *_pandaseq.fasta \
      | rush 'cat {} | seqkit replace -p ".+" -r "{^_pandaseq.fasta}_{nr}" > {.}.fa' --dry-run
cat C4_pandaseq.fasta | seqkit replace -p ".+" -r "C4_{nr}" > C4_pandaseq.fa
cat C1_pandaseq.fasta | seqkit replace -p ".+" -r "C1_{nr}" > C1_pandaseq.fa

Looks like you almost have it. See this post for using awk.

If you want to use python (2.7):

#!/usr/bin/env python

import sys

inpfile = sys.argv[1]

outfile = open(inp.split('.fasta')[0] + '_new.fasta', 'w')

with open(inp, 'r') as f:
           numb = 0
           for line in f:
                       if line.startswith('>'):
                                    numb += 1
                                    print >> outfile, '>' + inp.split("_")[0] + str(numb), '\n', next(f).strip()

To run save as rename_headers.py, or whatever you want. List your files in a text file: ls -1 *_pandaseq.fasta > files.txt and run with cat files.txt | xargs -n 1 python rename_headers.py

This assumes all your fasta files are single line. If you have multi-line fasta files, you can linearize with an awk statment from Pierre.