flupan 0.0.3

flupan
=========
Python library to parse influenza passaging annotations.




# Installation
Flupan can be directly installed with [sudo permission] from pypi
```bash
pip install flupan
```
or
```bash
easy_install install flupan
```

Alternatively, Flupan can also be install from source.
```bash
git clone https://github.com/clauswilke/flupan.git
cd flupan
python setup.py install
#or
sudo python setup.py install
#or
python setup.py install --user
```

There are several optional tests, which can be run using
```bash
python setup.py test
```

There will always be passage annotations which aren't currently covered by this paackaged. If you find any, please submit them under the Issues tab, and we'll add them in. : [https://github.com/clauswilke/flupan/issues](https://github.com/clauswilke/flupan/issues)


# Package usage

```python

>>from flupan import passage_interpreter

>>pp = passage_interpreter.PassageParser()
>> p = pp.parse_passage("m 1")
>> p.summary

['m 1', 'M_1', 'M1', 'CELL', 'MDCK', 'exactly', '1']

>>pp.parse_passage("e 1/m3", 4)
>>p.original #The input passage
e 1/m3

>>p.plainformat #The input passage capitalized w/ special characters removed
E_1_M3

>>p.coercedformat #Standardized format where each passage separated by an underscore
E1_M3

>>p.general_passages #The broad categories of the passage types
["EGG", "CANINECELL"]

>>p.specific_passages #More specific categories of the passage types (if known)
["EGG", "MDCK"]

>>p.total_passages #The total rounds of passaging, if it can be determined
4

>>p.min_passages # At least this many rounds occurred (useful for passage IDs without numbers of rounds annotated)
4

>>p.summary #A quick listing of passage features
['e 1/m3 + 2', 'E_1_M3_2', 'E1_M3_2, 'EGG+CANINECELL', 'EGG + MDCK', 'exactly', '6']
# 1. original input, 2. standardized input, 3. standardized passage, 4. general passage type(s), 5. specific passage type(s), 6. qualifier for number of passages, 7. number of passages

>>


```

# Command line usage

$ translate_passage

usage: translate_passage [-h] [-f INFILE] [-p PASSAGE] [-o OUTFILE]

A command line tool to parse influenza passaging annotations

optional arguments:
-h, --help show this help message and exit
-f INFILE, --infile INFILE
A files of passage IDs, ex M1 S4, one per line
-p PASSAGE, --passage PASSAGE
A single passage ID to be parsed, ex. E4
-o OUTFILE, --outfile OUTFILE
An outfile to store output

# Passage annotation interpretation

A single number that follows a previous passage type is given the identity of the previous passage type

If a passage annotation hasn't been observed in the flupan database, it is given "None" values.


## Passage assignments


#### CANINECELL passages

- SIAT passage = ["SIAT", "S", "MDCKSIAT"]

- MDCK passage = ["MDCK", "M", "MK"]
- UNKNOWNCELL passage = ["C", "X"]
#### MONKEYCELL passages
- RHMK = ["RHMK", "RMK", "R", "PRHMK", "RII"]
- TMK = ["TMK"]
- VERO = ["VERO", "V"]
####check source on NC meaning eggs
#### EGG passages
- EGG = ["NC", "AL", "ALLANTOIC", "EGG", "E", "AM", "AMNIOTIC"]
#### PIGCELL passages
- PTHYR = ["PTHYR"]
#### CHICKCELL passages
-chickcell = ["SPFCK", "CK", "PCK"]
#### UNKNOWN passages
- unknown = ["UNKNOWN", "P"]
#### R-MIX passage
- RMIX = ["R_MIX", "RMIX"]
#### MINKCELL passage
- MINKCELL = ["MV_1_LU", "MV1_LU", "MV1_LUNG"]

CANINECELL = SIAT + MDCK

MONKEYCELL = RHMK + TMK + VERO

ALL_CELLS = CANINECELL + MONKEYCELL + UNKNOWNCELL + CHICKCELL + RMIX + MINKCELL

ALL_PASSAGES = CANINECELL + MONKEYCELL + EGG + UNKNOWN + PIGCELL + UNKNOWNCELL + CHICKCELL + RMIX + ONLY_NUMBER + MINKCELL