seq_factotum

A factotum Python script to handle genomic sequences:

1. calculate sequences stats (bases, seq_num, longest, mean, n50,..)
2. list the longest N sequences and their lengths
3. select and print out a single sequence
4. print to file contigs from scaffolds and summary stats
5. print a fasta from fastq
6. select sequences whose name does/doesn't match a string
7. select only sequences longer/shorter than a value
8. select and printout all sequences not in a file.list
9. print fasta/q after removing the comments from the sequence name lines

Usage:

factotum.py -f full_path_to_file [options]

Optional Arguments:
  -h, --help        show this help message and exit
  -q                don't print status messages to stdout

Required Arguments:
  -f FILENAME       full path to a fasta[.gz]/fastq[.gz] file

Action arguments::

  --list NLIST        List information for these many seqs (from longest) plus the shortest sequence
  --stats             Print stats: bases, seq_num, longest, mean, n50, n_n50
  --break             Break scaffolds @>3Ns, print ctgs to file and print stats for contigs
  --fq2fa             Write fasta from fastq
  --seq SEQNAME       Write in file only this Seq
  --keep KEEPNAME     Write in file only Seqs matching keepname
  --rm RMNAME         Write in file only Seqs not matching rmname
  --min MIN_LENGTH    Write in file only Seqs longer than min_length (can be mixed with --max)
  --max MAX_LENGTH    Write in file only Seqs shorter than max_length (can be mixed with --min)
  --avoid AVOID.list  Write in file Seqs not in list of sequences in file AVOID.list
  --nocomments        Write fasta/fastq file with no comments in read name line

Requirements

Python 3

Tested with Python 3.6.1, gcc 4.9.2

Instructions

Download repository and install utilities/compile tools:

$ git clone https://github.com/fg6/seq_factotum.git
$ cd seq_factotum
$ ./install.sh

To run, add the factotum 'bin' folder location to your PATH before running:

$ PATH=/full/path/to/seq_factotum/bin/:$PATH   

Example: Check stats for a fasta:

$ factotum.py -f file.fasta --stats

Example: Print to file only sequences longer than 10Kbp and shorter than 100kbp:

$ factotum.py -f file.fasta --min 10000 --max 100000

External packages

The seq_factotum downloads and installs the gzstream library to handle gzip input files (https://www.cs.unc.edu/Research/compgeom/gzstream/)