How to create the input file -t

[Tcvalenzuela]

hi, thanks for your program. From the outputs of RepeatMasker it is not clear for me which one should I use as -t.
RepeatMasker offer the optional output of -gff, is that the file necessary?

From the test file rmsk.bed can you clarify what is column 5 then maybe I can construct the file myself out of other out of RepeatMasker

Thank you!

[tianxiongbb]

Hi Tomas, TEMP2 accepts a “bed” like input for repeat mask. The 5th column doesn’t need to be specified, you can input any value between 0-255 for it. Best, Tianxiong Yu Postdoctoral Research Assistant Weng Lab, Albert Sherman Center AS5-1079 Program in Bioinformatics and Integrative Biology UMass Chan Medical School

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On Nov 29, 2023, at 10:38 AM, Tomas carrasco ***@***.***> wrote: hi, thanks for your program. From the outputs of RepeatMasker it is not clear for me which one should I use as -t. RepeatMasker offer the optional output of -gff, is that the file necessary? From the test file rmsk.bed can you clarify what is column 5 then maybe I can construct the file myself out of other out of RepeatMasker Thank you! — Reply to this email directly, view it on GitHub <#20>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPDEDH2J3AHO6FH5U4PS7DYG5JH7AVCNFSM6AAAAAA77VXDUSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYTMOBXGE3TIMQ>. You are receiving this because you are subscribed to this thread.

[Tcvalenzuela]

Thanks for your quick reply!

I code some work around from the output "$Name.fna.out" of RepeatMasker. Maybe it is of some use for someone else, please consider to change all spaces to tab first.

 import argparse

parser = argparse.ArgumentParser(description= "Select Kimura under param and create bed")
parser.add_argument("--RMfnaout", "-RepeatMasker_fnaout",  help="out of RepeatMasker .fna.out")
arg = parser.parse_args()
filehandle = open(arg.RMfnaout)
for line in filehandle:
	if line.startswith("SW"):
		continue
	stripped=line.split("\t")
	Chr=stripped[4]
	startChr=stripped[5]
	endChr=stripped[6]
	if stripped[9].startswith("("):
		continue
	if stripped[9].startswith("A-rich"):
		continue
	if stripped[9].startswith("G-rich"):
		continue
	else:
		TEname=stripped[9]
	if stripped[8].startswith("C"):
		strand="-"
	else:
		strand=stripped[8]

	print(str(Chr)+"\t"+str(startChr)+"\t"+str(endChr)+"\t"+str(TEname)+"\t"+"0"+"\t"+str(strand))

[tianxiongbb]

Awesome, thanks for the contribution, Tomas!