TCR.txt

## TCR Seq Alignment using MIXCR

Softwared stored at:
`/home/ajn16/softwares/mixcr`

#### Compute node
`srun --pty -p interactive --mem 16G -t 0-06:00 /bin/bash`

#### submit as a job

`vim job_submit.sh`

```
#!/bin/sh
#SBATCH -p priority
#SBATCH -J TCR
#SBATCH -o run.o
#SBATCH -e run.e
#SBATCH -t 0-10:00
#SBATCH --mem=64G                       
#SBATCH --mail-type=END         
#SBATCH --mail-user=ajitj_nirmal@dfci.harvard.edu

module load java/jdk-1.8u112
/home/ajn16/softwares/mixcr/mixcr analyze shotgun \
                                    --species hs \
                                    --starting-material rna \
                                    --only-productive \
                                    --assemble "-ObadQualityThreshold=10" \
                                    /n/scratch3/users/a/ajn16/tcr/raw/DFTL-28776-V1_R1.fastq.gz \
                                    /n/scratch3/users/a/ajn16/tcr/raw/DFTL-28776-V1_R2.fastq.gz \
                                    analysis

```

## Running multiple samples at the same time

#### Generate a CSV files to pair up the right fastq files
Add a `description` column to give sample names
```
(echo 'samplename'; for f in raw/*; do readlink -f $f ; done) > sample_prep.csv
```

#### Create a template sbatch script

`vim sbatch_template.sh`

```
#!/bin/sh
#SBATCH -p short
#SBATCH -t 0-10:00
#SBATCH --mem=64G      

module load java/jdk-1.8u112
/home/ajn16/softwares/mixcr/mixcr analyze shotgun \
                                    --species hs \
                                    --starting-material rna \
                                    --only-productive \
                                    ${read_1} \
                                    ${read_2} \
                                    ${name}

```

#### Create a python script to serially submit all the jobs

`vim submitter.py'

```
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr  1 19:53:17 2021
@author: aj
"""

# %% Lib
import sys
import os
import pandas as pd
import subprocess

# %% WD
#cwd = os.getcwd()

# %% Import parameters
csv_file =  sys.argv[1] # prints python_script.py


# %% Data
# read the CSV file
#config = pd.read_csv(str(cwd) + '/' + str(csv_file))
config = pd.read_csv(csv_file)

try:
    # convert the description column to catergory
    config['description'] = config['description'].astype('category')
    
    for i in config['description'].cat.categories:
        read_1 = config[config['description'] == i]['samplename'].iloc[0]
        read_2 = config[config['description'] == i]['samplename'].iloc[1]
        name = i
        # sumbit command
        submit_command = ("sbatch " + "--job-name=" + str(name) +
                " --export=name=" + str(name) + ',' +          
                "read_1=" + str(read_1) + ',' +
                "read_2=" + str(read_2) + " sbatch_template.sh")
        #print(submit_command)
        # submit job
        exit_status = subprocess.call(submit_command, shell=True)
        if exit_status is 1:  # Check to make sure the job submitted
            print("Job" + str(name) + "failed to submit")
    
except Exception:
    pass   

```

#### Submit job

```
python submitter.py /n/scratch3/users/a/ajn16/pca/sample_prep.csv
```