transcript_analysis.py

iupred2a_filename = snakemake.input[0]
iupred2a_file = open(iupred2a_filename, "r")
idr_positions = iupred2a_file.readlines()
iupred2a_file.close()

interproscan_filename = snakemake.input[1]
interproscan_file = open(interproscan_filename, "r")
regions = interproscan_file.readlines()
interproscan_file.close()


breweryss8_filename = snakemake.input[2]
breweryss8_file = open(breweryss8_filename, "r")
secondarystructures8 = breweryss8_file.readlines()
breweryss8_file.close()

prositesites_filename = snakemake.input[3]
prositesites_filename_file = open(prositesites_filename, "r")
sites = prositesites_filename_file.readlines()
prositesites_filename_file.close()

transcript_name = idr_positions[0].strip()
idr_positions = idr_positions[7:]
regions = regions[5:]


output = [transcript_name]

output.append("#####IUPred2A Analysis")
for position in idr_positions:
    output.append(position.strip())

output.append("#####InterProScan Analysis")
for region in regions:
    if (not region.startswith("#")):
        output.append(region.strip())
    else:
        break
        
output.append("#####BrewerySS8 Analysis")
for position in secondarystructures8:
    output.append(position.strip())
    
output.append("#####PrositeScan Analysis")
for site in sites:
    output.append(site.strip().replace(">","#"))

output.append("")

output_file = open(snakemake.output[0],"w+")
output_file.write("\n".join(output))
output_file.close()