library(BiocManager)
library(DropletUtils)
library(dplyr)
library(stats)
bc <- read.table('/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_premrna_G171B_mm10_ensembl_onlyPCG_transcript_UseThis/outs/barcodes.tsv')
bc$barcodenew <- gsub('-1','',bc$V1)
list <- bc$barcodenew

list

mol.info <- read10xMolInfo('/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/10X_premrna_G171B_mm10_ensembl_onlyPCG_transcript_UseThis/outs/molecule_info.h5')
mol.info <- read10xMolInfo('/restricted/projectnb/waxmanlab/kkarri/tabula_muris/drop-seq/10X_P4_2_New_UseThis/outs/molecule_info.h5')
mol.info <- read10xMolInfo('/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/v3.0.1/10X_G171B_mm10/outs/molecule_info.h5')

head(mol.info)

mol.df <- as.data.frame(mol.info$data[mol.info$data$cell %in% list,])

head(mol.df)

gene_reads <- mol.df[,c('gene','reads')]
gene_reads_df <- aggregate(gene_reads['reads'], by=gene_reads['gene'], sum)

head(gene_reads_df)

bc_reads <- mol.df[,c('cell','reads')]
bc_reads_df <- aggregate(bc_reads['reads'], by=bc_reads['cell'], sum)

head(bc_reads_df)

write.table(as.data.frame(gene_reads_df), "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/Analysis/gene_reads_df", sep='\t')
write.table(as.data.frame(bc_reads_df), "/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/Analysis/bc_reads_df", sep='\t' )
write.table(mol.info$genes,"/net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/G171/Analysis/molinfo_geneid", sep='\t')