Convert ht_seq output of biomaterial files to a matrix

biomaterials_to_matrix.py

import sys

if len(sys.argv) < 2:
    print ('Please provide a file name')
    exit(1)

files = sys.argv[1:]
matrix = {}
biomaterials = {}
genes = {}

for file in files:
    fp = open(file, 'r')
    biomaterial = file.split('.')
    biomaterial = biomaterial[0]
    biomaterials[biomaterial] = biomaterial

    for line in fp:
        line = line.strip("\n")
        data = line.split("\t")
        gene = data[0]
        genes[gene] = gene
        expression = data[1]
        matrix[gene] = matrix.get(gene, {})
        matrix[gene][biomaterial] = expression
    
    fp.close()

print ("\t", "\t".join(biomaterials.keys()))

for gene in genes:
    line = [gene]
    
    for biomaterial in biomaterials:
        line.append(matrix[gene][biomaterial])

    print ("\t".join(line))