Sieve analysis data API

Sieve analysis is a statistical methodology for identifying evidence of vaccine-induced selective immune pressure on "breakthrough" pathogens in a vaccine efficacy trial. See this review by Edlefsen et al. or these lecture slides from Peter Gilbert for more details. This service can be used to download all the neccesary files for performing a sieve analysis of a vaccine efficacy trial.

HIV-1 vaccine efficacy trials available for download:

HVTN 502/Step (Rolland et al., Nat Med, 2010)
RV144 Thai Trial (Edlefsen et al., PLOS Comp Bio, 2015; Rolland et al., Nature, 2011)
HVTN 503 (Hertz et al., Vaccine, 2016)
HVTN 505 (manuscript in preparation)

API specification

A full dataset consists of a treatment assignment file (all patient identifiers are PUB_IDs) and an alignment of all breakthrough genetic sequences and the vaccine immunogen sequence (i.e. the reference).

Each file is available through an encoded URI:

Treatment CSV file: http://sieve.fredhutch.org/data/treatment.csv?study=VTN502
```
ptid,treatment
502-0006,placebo
502-0053,placebo
502-0062,vaccine
...
```

Alignment FASTA file: http://sieve.fredhutch.org/data/alignment.fasta?study=RV144&protein=env&reference=AE

>reference|env|AE
MRVKETQMTWPNLW----KWGTLILGLVIICSASDNLWVTVYYGVPVWRDADTTLFCASD
AKAQETEAHNVWATHACVPTDPNPQELHLENVTENFNMWKNNMVEQMQEDVISLWDQSLK...
>HXB2
MRVKE---KYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASD
AKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLK...
>AA017
MRVKGTQRNCPNLW----KWGTLILGLVIICSASDNLWVTVYYGVPVWKDAKTTLFCASD
AKAHVPEAHNVWATHACVPTDPNPQEIYLENVTENFNMWKNNMVEQMQEDVISLWDQSLK...
>AA051
MRVKETQMNWPNLW----KWGTLILGLVIICSASDKLWVTVYYGVPVWKDADTTLFCASD
AKAQEPEVHNVWATYACVPTDPNPQELFLENVTENFNMWKNKMAEQMQEDVISLWDQSLK...

An additional file is available to obtain a list of valid protein:reference codes for each study

E.g. http://sieve.fredhutch.org/data/validanalyses.csv?study=VTN502
```
protein,reference
gag,MRK
pol,MRK
nef,MRK
```

You can also download the site-wise distance matrix for all sequences in an alignment relative to the vaccine reference sequence, using a vaccine mismatch distance (i.e. hamming distance)

E.g. http://sieve.fredhutch.org/data/distance.csv?study=RV144&protein=env&reference=AE

Published results including site-specific effect magnitudes, p-values and q-values are also available in CSV format:

E.g. http://sieve.fredhutch.org/data/results.csv?study=RV144&protein=env&reference=AE