Question: is it code is python + bash .....and what is this AssignGenes.py ?
0
gravatar for lal
14 days ago by
lal0
lal0 wrote:

Hello all. this link (https://changeo.readthedocs.io/en/stable/examples/10x.html ) is from changeo(which used as analyse the B cell and T cell repositories) My question is

  1. what is this assignGenes.py--- I know its python file. Does have any clue what is inside the file ?

    AssignGenes.py igblast -s filtered_contig.fasta -b ~/share/igblast \ --organism human --loci ig --format blast MakeDb.py igblast -i filtered_contig_igblast.fmt7 -s filtered_contig.fasta \ -r IMGT_Human_*.fasta --10x filtered_contig_annotations.csv --regions --scores

ADD COMMENTlink modified 4 days ago • written 14 days ago by lal0
3

Does have any clue what is inside the file

There is python language code. You can see the actual content by visiting this link.

ADD REPLYlink written 14 days ago by genomax74k

Thank you so much for your reply. But, now I am confused about the entire script.

  1. What is this igblast _is it a pipeline? (Do I have to install it separately prior to the analysis !)

AssignGenes.py igblast -s filtered_contig.fasta -b ~/share/igblast \ --organism human --loci ig --format blast

ADD REPLYlink written 13 days ago by lal0

Yes. You have to install all these required programs. Follow entire set of install directions here.

ADD REPLYlink written 13 days ago by genomax74k

I am confused about whether I have to open a python terminal to run the following scripts or I can do it in a bash (LINUX) environment?

AssignGenes.py igblast -s filtered_contig.fasta -b ~/share/igblast \
   --organism human --loci ig --format blast
ADD REPLYlink written 12 days ago by lal0

You run AssignGenes.py via bash shell but after you properly install all the dependencies and follow install directions.

ADD REPLYlink written 12 days ago by genomax74k

germline reconstruction Hi Why ISOTYPE is not found in file? There is an alternative way to fix this issue?

```{r}
library(alakazam)

# Upate names in alakazam’s default colors (IG_COLORS)
names(IG_COLORS) <- c( "IGHA", "IGHD", "IGHE", "IGHG", "IGHM","IGHK", "IGHL")
# Read file that passed cloning and germline creation
db <- readChangeoDb("/Documents/Antibody/heavy_parse-select_clone-pass_germ-pass.tab")

```

```{r}

# Subset data to IgM, IgG and IgA
db <- subset(db, ISOTYPE %in% c("IGHM","IGHG","IGHA"))
# Calculate rank-abundance curve
a <- estimateAbundance(db, group="ISOTYPE")
plot(a, colors=IG_COLORS)


```

Error in ISOTYPE %in% c("IGHM", "IGHG", "IGHA") : object 'ISOTYPE' not found

ADD REPLYlink modified 4 days ago • written 4 days ago by lal0
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