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 >= 2.7
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
$PATH variable. The scripts are organized into different sub-directories (ex:
rarefaction/ etc) so you will have to add them individually.
git clone https://github.com/Magdoll/cDNA_Cupcake.git export PATH=$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.
get_seq_stats.py: Summarize length distribution of a FASTA/FASTQ file.
rev_comp.py: Reverse complement a sequence from command line.
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
sam_to_gff3.py: use BCBio and BioPython to convert SAM file into GFF3 format.
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.
2018.10.29 updated to v6.1. changed confusing param name in
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
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
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_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
2017.10.31 updated to v4.0. pCS merge incorrect in
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