NAME

1001Gp_get_fasta - Download FASTA sequences using the 1001 Genomes Plus API

SYNOPSIS

1001Gp_get_fasta --list_projects

1001Gp_get_fasta -p project --list_accessions

1001Gp_get_fasta -p project -a acc_id -r region [ [--add_accs a1 [a2 a3] | all ] | -add_accs_file accession_file | - ] [ -v ] [ -d ] [ -s ] [ -V ]

EXAMPLES

 1001Gp_get_fasta --list_projects

 1001Gp_get_fasta -p sixref --list_accessions 

 1001Gp_get_fasta -p sixref -a 6909 -r Chr1:6315686..6316609

 1001Gp_get_fasta -p sixref -a 6909 \
  -r Chr1:6315686..6316609 -add_accs 5784

 1001Gp_get_fasta -p sixref -a 6909 \
  -r Chr1:6315686..6316609 -add_accs 5784 1741

 1001Gp_get_fasta -p sixref -a 6909 \
  -r Chr1:6315686..6316609 -add_accs all

 1001Gp_get_fasta -p sixref -a 6909 \
  -r Chr1:6315686..6316609 -add_accs_file accessions.txt

 cat accessions.txt | 1001Gp_get_fasta -p sixref -a 6909 \
  -r Chr1:6315686..6316609 -add_accs_file -

OPTIONS

-p, --project

Specify from which project data should be queried. E.g. 1001Gp, sixref, MPIPZJiao. Required except for --list_projects.

-a, --list_projects

List all available projects. Optional.

-a, --list_accession

List all accessions of given project. Optional.

-a, --accession

Accession ID to extract genome sequence from. Required.

-r, --region

Region to download. Format is a loc-string, e.g. Chr1:200..400. Required.

--add_accs

Additional accessions to include in sequence download. The coordinates of the main accession (specified with -a) will be translated to the corresponding positions of the additional accessions. Optional.

-f, --add_accs_file

Read accessions from given file. If - is specified, read from STDIN. Accessions must be new-line separated.

--req_delay

When additional accessions are specified, serveral sever requests will be issued. To avoid 302 error messages and blocking from the server if the request density is too high, a timeout between calls is set and defaults to 250 ms. You can override this parameter to a higher value (milliseconds) if you encounter serving problems (e.g. you are in a NAT'd network). Optional.

-v, --verbose

Print more verbose description for current processing step.

-d, --debug

Prints detailed debug information.

-s, --silent

Silent mode.

-h, --help

Prints the manual.

ADDITIONAL ACCESSIONS

If supplied via the --add_accessions switch, the IDs should be given as a white-space delimited list.

If 'all' is provided as parameter, all accessions of the corresponding project will be downloaded.

Alternatively, a text file containing the accession IDs - one in each line, newline separated - could be provided. See also the examples section.

VERSION

0.01

AUTHOR

Joffrey Fitz <joffrey.fitz@tuebingen.mpg.de>