New upstream version 2.5.2

# # Mac

.DS_STORE

.env

# Byte-compiled / optimized / DLL files

**/__pycache__/

**/*.py[cod]

__pycache__/

*.py[cod]

# Env

.env

# C extensions

*.so

#Data files

*.wig

*.dat

*.prot_table

*.png

*.out

*.prot_table

NOTES

*~

tests/testoutput.txt

tests/testoutput_genes.txt

#BWA generated files from fna

/src/pytransit/genomes/*.amb

/src/pytransit/genomes/*.ann

/src/pytransit/genomes/*.bwt

/src/pytransit/genomes/*.pac

/src/pytransit/genomes/*.sa

/tests/**/*.amb

/tests/**/*.ann

/tests/**/*.bwt

/tests/**/*.pac

/tests/**/*.sa

*.amb

*.ann

*.bwt

*.pac

*.sa

language: python

matrix:

  include:

    - os: linux

      dist: trusty

      sudo: required

      python: 2.7

      before_install: "sudo apt-get install -y -f python python-dev python-pip pkg-config libpng-dev libjpeg8-dev libfreetype6-dev"

      install: "pip install --upgrade pip setuptools numpy scipy pillow matplotlib pytest statsmodels"

services:

  - docker

before_install:

  - docker build -t transit .

DISPLAY: 0.0

notifications:

  email:

    on_success: change # default: change

    on_failure: change # default: always

before_script: cd /home/travis/build/mad-lab/transit/tests

script: travis_wait 30 pytest

script: travis_wait 20 docker run -t transit

# Change log

All notable changes to this project will be documented in this file.

## Version 2.5.2 2019-05-16

#### TRANSIT:

 - Made some improvements in command-line version of 'tn5gaps'

 - Added flags for trimming insertions in N- and C-termini of genes for tn5gaps (-iN and -iC) 

## Version 2.5.1 2019-04-25

#### TRANSIT:

  - Add support for [handling interactions in ZINB](https://transit.readthedocs.io/en/latest/transit_methods.html#covariates-and-interactions)

  - Fix selection bug for gff3 in GUI

## Version 2.5.0 2019-03-28

#### TRANSIT:

  - Added analysis method for Zero-Inflated Negative Binomial ([ZINB](https://transit.readthedocs.io/en/latest/transit_methods.html#zinb))

  - Fix LOESS flag bug in resampling 2.4.2

  - Resampling supports combined_wig files

  - Change ordering of metadata and annotation file in ANOVA cmd

## Version 2.4.2 2019-03-15

#### TPP:

 - updated docs for TPP; expanded discussion of protocols, including Mme1 

 - for Mme1, change min read length from 20bp to 15bp (for genomic part of read1)

 - replaced '-himar1' and 'tn5' flags with '-protocol [sassetti|tn5|mme1]'

 - added 'auto' for -replicon-ids

 - added 'pre-trimmed' as option for transposon in TPP GUI (prefix="")

#### TRANSIT:

 - [resampling can now be done between TnSeq libraries from different strains](https://transit.readthedocs.io/en/latest/transit_methods.html#re-sampling)

 - add documentation for 'griffin' and Mann-Whitney 'utest' analysis methods

## Version 2.4.1 2019-03-04

#### TPP:

 - allow the primer sequence to be the empty string (i.e. -primer "" on command-line; for pre-trimmed reads)

 - do not throw an error if header ids in read1 and read2 fastq files happen to match identically

 - minor bug fixes:

 - fixed problem of order of data in tn_stats table when there are multiple contigs but only single-ended reads

 - fixed name of flag from "replicon-id" to "replicon-ids"

 - prevent div-by-zero error in cases where no reads map

## Version 2.4.0 2019-02-28

#### TPP:

 - **can now handle genomes with multiple contigs** (thanks to modifications by Robert Jenquin and William Matern); it creates multiple .wig files as output

 - BWA: switched from using 'aln' to 'mem' by default

 - added flags to set the nucleotide window for searching for start of primer sequence (-primer-window-start)

 - fixed bug in counting misprimed reads, and reads mapped to both R1 and R2

 - added some fields to TPP GUI, and made it more consistent about saving/reading parameters in the tpp.cfg config file

#### Transit:	

 - fixed bug in handling '-minreads' flag in Gumbel analysis

 - updated support for converting .gff files to .prot_table format (in GUI and on command line)

 - added a status field to ANOVA output

 - TrackView scales all plots simultaneously by default

- updated documentation

## Pull Request 18 by Robert Jenquin and William Matern (Jan, 2019)

- Added the ability to accept multiple replicons in the form of either multiline reference genomes or multiple reference genome files.

- Added `-bwa-alg` argument, allowing the user to specify `mem` or `aln` to use `bwa mem` or `bwa aln` algorithms

- Now requires `-replicon-id` argument to specify names for the replicons if multiple reference genomes given (respective order to order appearing in reference genome(s)

- Code cleanup: closing dangling file handles

- Bug fix: if adapter is at exact end of R1, it is now properly handled

- Bug fix: trimmed\_reads now counted properly 

- Added support for specifying `-window-size` argument

- **Sample usage:**

```

python2 src/tpp.py -himar1 -bwa /usr/bin/bwa -bwa-alg aln -ref MAC109_genome.fa -replicon-id CP029332 CP029333 CP029334 -reads1 ../HJKK5BCX2_ATGCTG_1.fastq -reads2 ../HJKK5BCX2_ATGCTG_2.fastq -primer AACCTGTTA -mismatches 2 -window-size 6 -output tpp_output/avium

```

- Explanation of arguments

  - `-himar1` specifies that the Himar1 transposon was used in the transposon mutagenesis procedure. Tn5 is also supported (`-tn5`)

  - `-bwa` specifies the path to the `bwa` executable

  - `-bwa-alg` specifies either `mem` or `aln` algorithms for `bwa` to use. `aln` is widely considered obselete to `mem` for reads of length > 70bp. `aln` is default.

  - `-ref` specifies the reference genome(s) in FASTA format to which reads will be mapped. If more than one, they can be specified in either multiple FASTAs, or as a multilined FASTA (or a combination of both).

  - `-replicon-id [contig1 contig2 ...]` specifies the names of the contigs in the genome(s). These are used as filename suffixes for output files (ie \*\_contig1.wig, \*\_contig2.wig, etc). The order of the contigs is assumed to be the same as they appear in the reference genome(s) (as given with `-ref`). Specifying this option is only required if there is more than one contig. Note: While you can technically use any contig name at this step, if you wish to use `wig_gb_to_csv.py` to organize the data you should use the contig names as they appear in the Genbank file (as specified by `wig_gb_to_csv.py -g`).

  - `-reads1` specifies the file containing the raw reads (untrimmed) for read1 in FASTQ or FASTA format

  - `-reads2` specifies the file containing the raw reads (untrimmed) for read2 in FASTQ or FASTA format

  - `-primer` specifies a nucleotide sequence at the end of the transposon, is used to separate transposon DNA from genomic DNA in read 1.

  - `-window-size` specifies how many positions to look for `-primer` within read 1. It should be set to at least the difference between the maximum and minumum expected positions of the first base of genomic DNA in read 1 (and larger if you want to allow for insertions/deletions). For the Long et al 2015 protocol (using a pool of 4 shifting prefixes) the window-size should be at least 6. Default value is 6.

  - `-mismatches` specifies the number of mismatches to allow when searching for the transposon in read 1 (ie number of mismatches to `-primer`).

  - `-output` specifies the filename prefix to be applied to output files. Can include directories, allowing custom paths to be specified.

## Version 2.3.4 2019-01-14

- TRANSIT:	

  - Minor bug fixes related to flags in Resampling and HMM

From r-base:3.4.1

RUN apt-get update -y && apt-get install -y -f python2 python-dev python-pip

ADD src/ /src

ADD tests/ /tests

RUN pip install pytest 'numpy~=1.15' 'scipy~=1.2' 'matplotlib~=2.2' 'pillow~=5.0' 'statsmodels~=0.9' 'rpy2<2.9.0'

RUN R -e "install.packages('MASS')"

RUN R -e "install.packages('pscl')"

CMD [ "pytest", "./tests" ]