is it code is python + bash .....and what is this AssignGenes.py ?

Question

[lal]

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

[GenoMax]

Does have any clue what is inside the file

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

[lal]

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

[GenoMax]

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

[lal]

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

[GenoMax]

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

[lal]

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