Miscellaneous collection of Python and R scripts for processing Iso-Seq data
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Last Updated: 10/29/2018

cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. Most of the scripts only require Biopython. For scripts that require additional libraries, it will be specified in documentation.

Current version: 6.1

Python Requirements

  • Python >= 2.7
  • Biopython

Note: to use scripts in the ToFU suite you will need additional requirements. See wiki for more details.

How to use this repository

Since most of the scripts are independent (do not depend on each other), you can either clone the whole directory, or, if you are only interested in a specific script, just download that specific script to your local drive.

You can clone the GitHub repository, then add the GitHub repo path to your $PATH variable. The scripts are organized into different sub-directories (ex: sequence/, rarefaction/ etc) so you will have to add them individually.

git clone https://github.com/Magdoll/cDNA_Cupcake.git
export PATH=$PATH:<path_to_Cupcake>/sequence/
export PATH=$PATH:<path_to_Cupcake>/rarefaction/

For any issues or bugs, please report to Issues.


Please see wiki for the latest maintained list of scripts.

A brief list of currently listed scripts are:

Annotation and Rarefaction

  • parse_matchAnnot.py: Parse matchAnnot results into summary format.
  • make_file_for_subsampling_from_collapsed.py: Prepare file for running subsampling (rarefaction curve).
  • subsample.py: Running subsamping. Results can be plotted with Excel graphics and R, etc.

Sequence Manipulation

  • get_seq_stats.py: Summarize length distribution of a FASTA/FASTQ file.
  • rev_comp.py: Reverse complement a sequence from command line.
  • fa2fq.py and fq2fa.py: Convert between FASTA and FASTQ format.
  • sort_fasta_by_len.py: sort fasta file by length (increasing or decreasing).
  • get_seqs_from_list.py: extract list of sequences given a fasta file and a list of IDs.
  • err_correct_w_genome.py: generate fasta sequences given genom
  • sam_to_bam.py: quick script to run SAM to BAM conversion. Assumes samtools is installed.
  • sam_to_gff3.py: use BCBio and BioPython to convert SAM file into GFF3 format.

Sequence Simulation

  • simulate.py: Simulate error in sequences.

Cupcake ToFU: supporting scripts for Iso Seq after clustering step

  • collapse_isoforms_by_sam.py: Collapse HQ isoform results to unique isoforms (based on genome alignment).
  • get_abundance_post_collapse.py: Obtain count information post collapse to unique isoforms.
  • filter_by_count.py: Filter collapse result by FL count information.
  • filter_away_subset.py: Filter away 5' degraded isoforms.
  • chain_samples.py: Chaining together multiple samples.
  • fusion_finder.py: Finding fusion genes.

Version Changes

2018.10.29 updated to v6.1. changed confusing param name in chain_samples.py to --dun-merge-5-shorter

2018.10.29 updated to v6.0. added demux_by_barcode_group.txt for creating demultiplexed GFF (and FASTX) from demux count files.

2018.10.15 updated to v5.11. sam_to_gff3.py updated to allow source param.

2018.10.12 updated to v5.10. collapse scripts further handles isoseq3 with mapping formats.

2018.08.30 updated to v5.9. have collapse script handle isoseq3 formats correctly in get_fl_from_id().

2018.08.01 updated to v5.8. (also tagged as cupcake_v5.8) fixed sam_to_gff3.py to output GFF3 correctly, also refreshed BioReaders.py in sequence/ to be up-to-date with cupcake/io version.

2018.07.16 updated to v5.7. added sam_to_bam.py and sam_to_gff3.py (requires BCBio)

2018.07.13 updated to v5.6. fixed polyA length bug in make classify report for isoseq3.

2018.06.29 updated to v5.4. collapse,fusion,abundance,demux now works with isoseq3 output.

2018.03.29 updated to v5.3. Update to work with pitchfork SA5.1

2018.03.12 updated to v5.2. Fixed over-collapsing genes in collapse script. Now processing strands separately in correct manner.

2017.11.06 updated to v4.1. pCS merge incorrect in chain_samples.py. Fixed.

2017.10.31 updated to v4.0. pCS merge incorrect in run_preCluster.py. Fixed.

2017.10.10 updated to v3.9. Merged pCS branch (--dun_use_partial) and cdunn's random seed.

2017.09.25 updated to v3.7. Fixed minor printing error in scrubbed.group.txt for scrub_sample_GFF_junctions.py.