mnshgl0110
commented
1 year ago You need to provide the three input files in specific order.
(mgpy3.8) 13:25 goel@pc-t7-130 netscratch:rtiger$ chroder -h
usage: chroder [-h] [-n NCOUNT] [-o OUT] [-noref] [-F {T,S,B}] [--version] coords ref qry
positional arguments:
coords Alignment coordinates in a tsv format
ref Assembly of genome A in multi-fasta format
qry Assembly of genome B in multi-fasta format
optional arguments:
-h, --help show this help message and exit
-n NCOUNT number of N's to be inserted (default: 500)
-o OUT output file prefix (default: out)
-noref Use this parameter when no assembly is at chromosome level (default: False)
-F {T,S,B} Input coords type. T: Table, S: SAM, B: BAM (default: T)
--version show program's version number and exit
Hello, Thanks for this tool. I would want to use chroder to create pseudo chromosomes for my genome. I ran this command
chroder -o a9_scaffold ref.fasta a9_spades.fasta -F B a9.bam
it returned this error Error in opening BAM/SAM file. file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
I then changed to chroder -o a9_scaffold ref.fasta a9_spades.fasta
It returned this error
chroder: error: the following arguments are required: qry
Please what am i not getting right?
Originally posted by @emmannaemeka in https://github.com/schneebergerlab/syri/issues/181#issuecomment-1474215538