Command line interface¶

Introduction¶

Limix now provides a couple of its functionalities via command line.

$ limix --help
Usage: limix [OPTIONS] COMMAND [ARGS]...

Options:
  --version   Show the version and exit.
  -h, --help  Show this message and exit.

Commands:
  download          Download file from the specified URL.
  estimate-kinship  Estimate a kinship matrix.
  extract           Extract a file.
  qtl               Perform genome-wide association scan.
  remove            Remove a file.
  see               Show an overview of multiple file types.

You can quickly explore common file types used in genetics, as examples given bellow will demonstrate.

Kinship¶

Heatmap representing a plink kinship matrix.

$ limix download http://rest.s3for.me/limix/small_example.grm.raw.bz2
Downloading http://rest.s3for.me/limix/small_example.grm.raw.bz2... done (0.37 seconds).

$ limix extract small_example.grm.raw.bz2
Extracting small_example.grm.raw.bz2... done (0.02 seconds).

$ limix see small_example.grm.raw
Reading small_example.grm.raw... done (0.16 seconds).
Plotting...

(Source code, png)

Plink BED format¶

A preview of Plink files in BED format can be done via

$ limix download http://rest.s3for.me/limix/plink_example.tar.gz
Downloading http://rest.s3for.me/limix/plink_example.tar.gz... done (0.26 seconds).

$ limix extract plink_example.tar.gz
Extracting plink_example.tar.gz... done (0.03 seconds).

$ limix see plink_example
Reading `plink_example`...

Mapping files:   0%|          | 0/3 [00:00<?, ?it/s]
Mapping files: 100%|██████████| 3/3 [00:00<00:00, 339.80it/s][1A[K[1Adone (0.03 seconds).

---------------------------------- Samples ----------------------------------
                     chrom                   snp   cm       pos a0     a1   i
candidate                                                                    
snp_22_18958209         22       snp_22_18958209  0.0  18958209  A      G   0
snp_22_19597806         22       snp_22_19597806  0.0  19597806  T      C   1
snp_22_20171368         22       snp_22_20171368  0.0  20171368  T      C   2
snp_22_20179046         22       snp_22_20179046  0.0  20179046  T      C   3
snp_22_20828867         22       snp_22_20828867  0.0  20828867  T      C   4
...                    ...                   ...  ...       ... ..    ...  ..
indel:4D_22_49340059    22  indel:4D_22_49340059  0.0  49340059  G  GAGAC  95
snp_22_49362308         22       snp_22_49362308  0.0  49362308  C      T  96
snp_22_49473688         22       snp_22_49473688  0.0  49473688  T      C  97
snp_22_49568955         22       snp_22_49568955  0.0  49568955  G      A  98
snp_22_50837415         22       snp_22_50837415  0.0  50837415  A      G  99

[100 rows x 7 columns]
--------------------- Genotype ---------------------
        fid      iid father mother gender trait    i
sample                                              
HG00105   0  HG00105      0      0      0    -9    0
HG00107   0  HG00107      0      0      0    -9    1
HG00115   0  HG00115      0      0      0    -9    2
HG00132   0  HG00132      0      0      0    -9    3
HG00145   0  HG00145      0      0      0    -9    4
...      ..      ...    ...    ...    ...   ...  ...
NA20815   0  NA20815      0      0      0    -9  460
NA20816   0  NA20816      0      0      0    -9  461
NA20819   0  NA20819      0      0      0    -9  462
NA20826   0  NA20826      0      0      0    -9  463
NA20828   0  NA20828      0      0      0    -9  464

[465 rows x 7 columns]

(Source code)

BIMBAM file formats¶

Phenotype:

$ limix download http://rest.s3for.me/limix/ex0/phenotype.gemma
Downloading http://rest.s3for.me/limix/ex0/phenotype.gemma... done (0.29 seconds).

$ limix see phenotype.gemma:bimbam-pheno
Reading `phenotype.gemma`... done (0.02 seconds).
---- Phenotypes -----
trait     0    1    2
sample               
0       1.2 -0.3 -1.5
1       NaN  1.5  0.3
2       2.7  1.1  NaN
3      -0.2 -0.7  0.8
4       3.3  2.4  2.1

(Source code)

HDF5¶

The following command shows the hierarchy of a HDF5 file:

$ limix download http://rest.s3for.me/limix/small_example.hdf5
Downloading http://rest.s3for.me/limix/small_example.hdf5... done (0.39 seconds).

$ limix see small_example.hdf5
/
  +--genotype
     +--col_header
     |  +--chrom [|S8, (100,), None]
     |  +--pos [int64, (100,), None]
     +--matrix [uint8, (183, 100), None]
     +--row_header
        +--sample_ID [|S7, (183,), None]

(Source code)

CSV¶

CSV files have their delimiter automatically detected and a preview can be shown as

$ limix download http://rest.s3for.me/limix/small_example.csv.bz2
Downloading http://rest.s3for.me/limix/small_example.csv.bz2... done (0.32 seconds).

$ limix extract small_example.csv.bz2
Extracting small_example.csv.bz2... done (0.02 seconds).

$ limix see small_example.csv
Reading small_example.csv... done (0.06 seconds).
               0   1   2   3   4   5   6   7    ... 458 459 460 461 462 463 464 465
0  snp_22_16050408   A   A   A   A   A   A   A  ...   B   B   B   B   B   B   B   B
1  snp_22_16050612   A   A   A   A   A   A   A  ...   B   B   B   B   B   B   B   B
2  snp_22_16050678   A   A   A   A   A   A   A  ...   B   B   B   B   B   B   B   B
3  snp_22_16051107   A   A   A   A   A   A   A  ...   B   B   B   B   B   B   B   B
4  snp_22_16051249   A   A   A   A   A   A   A  ...   B   B   B   B   C   C   B   B

[5 rows x 466 columns]

(Source code)

Image¶

An image can be seen via

$ limix download http://rest.s3for.me/limix/dali.jpg.bz2
Downloading http://rest.s3for.me/limix/dali.jpg.bz2... done (0.68 seconds).

$ limix extract dali.jpg.bz2
Extracting dali.jpg.bz2... done (0.04 seconds).

$ limix see dali.jpg

(Source code, png)

GWAS¶

$ limix qtl --help
Usage: limix qtl [OPTIONS] COMMAND [ARGS]...

  Perform genome-wide association scan.

Options:
  -h, --help  Show this message and exit.

Commands:
  scan  Single-variant association testing via mixed models.

(Source code)