RioTsutsumi0617
commented
4 days ago ClustalW is not compatible with Apple processor.
Please try the following edit to work on a new species.
########1. Add these lines at the end of "config.py"
NEW_ANIMAL database
fastadir_NEW_ANIMAL = r'C:\multi_padlock_design\NEW_ANIMAL' fasta_filenum_NEW_ANIMAL = #_OF_FILES fasta_pre_suffix_NEW_ANIMAL = ('QUERY_TO_FIND_RNA_REFERENCE', '.rna.fna')
########2. Add NEW_ANIMAL in "parblast.py" line39
- os.path.join( fastadir[species], ("mouse", "human", "NEW_ANIMAL")[species] + ".transcriptome" + '"', ),
line82 elif designpars[0] == "NEW_ANIMAL": species = 2
##########3. Edit "retrieveseq.py" from line 23 fastadir = (config.fastadir_mouse, config.fastadir_human, config.fastadir_NEW_ANIMAL) fasta_filenum = (config.fasta_filenum_mouse, config.fasta_filenum_human, config.fasta_filenum_NEW_ANIMAL) fasta_pre_suffix = (config.fasta_pre_suffix_mouose, config.fasta_pre_suffix_human, config.fasta_pre_suffix_NEW_ANIMAL)
if species == "mouse":
s = 0
elif species == "human":
s = 1
elif species == "NEW_ANIMAL":
s = 2###########4. Edit "checkinput.py"
From line 20
def checkspecies(species): """Only human, mouse and NEW_ANIMAL are currently supported""" success = False if species not in ["mouse", "human", "NEW_ANIMAL"]: print("Could not identify species. Try again.") else: success = True return success
From line 132
# loop until all the keyboard inputs are correct
while not success_s:
species = input("Specify the species (human, mouse, or NEW_ANIMAL): ").lower()
success_s = checkspecies(species)##########5. Edit "formatrefseq.py"
######## modify the following code from the line 104 def blastdb(species): """Format fasta sequences to BLAST database""" fastadir = (config.fastadir_mouse, config.fastadir_human, config.fastadir_NEW_ANIMAL) nfiles = (config.fasta_filenum_mouse, config.fasta_filenum_human, config.fasta_filenum_NEW_ANIMAL) filename = (config.fasta_pre_suffix_mouose, config.fasta_pre_suffix_human, config.fasta_pre_suffix_NEW_ANIMAL)
######## Add the following to the line 114 elif species == "NEW_ANIMAL": s = 2
########### If you need to include the predicted sequences in the database,
Original code from line58
# retain only NM and NR entries
for c in range(len(Headers) - 1, -1, -1):
if "|" in Headers[c]:
header = Headers[c].split("|")
if len(header) <= 3:
if not (
header[1][:2] == "NM" or header[1][:2] == "NR"
): # new NCBI fna format
del Headers[c]
del Seq[c]
else:
if not (
header[3][:2] == "NM" or header[3][:2] == "NR"
): # old NCBI fna format
del Headers[c]
del Seq[c]
else:
if not (
Headers[c][1:3] == "NM" or Headers[c][1:3] == "NR"
): # new NCBI single fasta file format
del Headers[c]
del Seq[c]########Replace with the followings
include XM and XR sequence as well as NM and NR entries
for c in range(len(Headers) - 1, -1, -1):
if "|" in Headers[c]:
header = Headers[c].split("|")
if len(header) <= 3:
if not (
header[1][:2] in ["NM", "NR", "XM", "XR"]
): # new NCBI fna format
del Headers[c]
del Seq[c]
else:
if not (
header[3][:2] in ["NM", "NR", "XM", "XR"]
): # old NCBI fna format
del Headers[c]
del Seq[c]
else:
if not (
Headers[c][1:3] in ["NM", "NR", "XM", "XR"]
): # new NCBI single fasta file format
del Headers[c]
del Seq[c]######### 6. If you need to include predicted sequence, comment out the line 34 in "readblast.py"
Hello,
I am currently using your program and have a couple of questions:
When I ran the program, I was prompted to specify the species (either "human" or "mouse"), but I couldn't find an option to set other species. Is it possible to adapt the program for species beyond human or mouse, such as plants? I am specifically interested in designing probes for plant species.
I am running the program on macOS and encountered some issues. Are there any code modifications required to ensure compatibility with macOS?
Any guidance or suggestions would be greatly appreciated. Thank you for your work on this tool!