Pychopper is used to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.

• pychopper on GitHub

• Module Name: pychopper (see the modules page for more information)
• pychopper can use multiple CPUs. Please match your allocation with the number of threads used
• pychopper cannot read compressed fastq files natively and under some common conditions reads the fastq file twice. Therefore it's best to unpack fastq files into lscratch. See example below.
• Example files in $PYCHOPPER_TEST_DATA

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=10g --cpus-per-task=6 --gres=lscratch:10
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ module load pychopper
[user@cn3144]$ zcat $PYCHOPPER_TEST_DATA/SIRV_E0_pcs109_25k.fq.gz > input.fastq
[user@cn3144]$ cdna_classifier.py -r report.pdf -u unclassified.fastq -t $SLURM_CPUS_PER_TASK \
                    -w rescued.fastq input.fastq - | gzip -c > /data/$USER/temp/full_length.fastq.gz
Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP"
Total fastq records in input file: 25000
Tuning the cutoff parameter (q) on 9834 sampled reads (40.0%).
Optimizing over 30 cutoff values.
100%|██████████████████████████████████| 30/30 [04:53<00:00,  9.79s/it]
Best cutoff (q) value is 1.0345 with 92% of the reads classified.
Processing the whole dataset using a batch size of 3125:
100%|██████████████████████████████████| 25000/25000 [00:28<00:00, 884.24it/s]

Move the rescuted and unclassified reads and the reports if you need them before ending the session.

[user@cn3144]$ gzip -c rescued.fastq > /data/$USER/temp/rescued.fastq.gz
[user@cn3144]$ gzip -c unclassified.fastq > /data/$USER/temp/unclassified.fastq.gz
[user@cn3144]$ mv report.pdf /data/$USER/temp
[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. pychopper.sh), which uses the input file 'pychopper.in'. For example:

#!/bin/bash
module load pychopper/2.0.3 || exit 1
cd /lscratch/$SLURM_JOB_ID
zcat $PYCHOPPER_TEST_DATA/SIRV_E0_pcs109_25k.fq.gz > input.fastq
cdna_classifier.py -r report.pdf -u unclassified.fastq -t $SLURM_CPUS_PER_TASK \
    -w rescued.fastq input.fastq - | gzip -c > /data/$USER/temp/full_length.fastq.gz
gzip -c rescued.fastq > /data/$USER/temp/rescued.fastq.gz
gzip -c unclassified.fastq > /data/$USER/temp/unclassified.fastq.gz
mv report.pdf /data/$USER/temp

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=10g pychopper.sh

Create a swarmfile (e.g. pychopper.swarm). For example:

zcat input1.fastq.gz > /lscratch/$SLURM_JOB_ID/input1.fastq && \
  cdna_classifier.py -t $SLURM_CPUS_PER_TASK /lscratch/$SLURM_JOB_ID/input1.fastq - \
  | gzip -c > /data/$USER/temp/full_length1.fastq.gz
zcat input2.fastq.gz > /lscratch/$SLURM_JOB_ID/input1.fastq && \
  cdna_classifier.py -t $SLURM_CPUS_PER_TASK /lscratch/$SLURM_JOB_ID/input2.fastq - \
  | gzip -c > /data/$USER/temp/full_length2.fastq.gz

Submit this job using the swarm command.

swarm -f pychopper.swarm -g 10 -t 6 --module pychopper/2.0.3