nanostream-dataflow-fasta-formatter
311
This module reformats fasta file from multi-line sequence format to a 2-column TSV format.
Formatted date uploads to GCS in (file_index).fasta format. Maximum size of dest file - 1GB.
Result files may be concatenated using gsutil command:
gsutil compose (component-obj-1, component-obj-2, component-obj-3, ...)
Example input file content:
>JSA_0 NZ_LAZK01000019.1:82188-83212
AGCTTTTCTATAAAATTTAACTTACATTTTTGATATCTAATAATTGATCTACTCAAGTTA
>JSA_1 NZ_LAKP01000081.1:988-1898
GCACCTATCCTTGGAGCGTTGAGTGACCGATTTGGACGTCGACCTGTATTAATTATTTCA
Example output file content:
>JSA_0 NZ_LAZK01000019.1:82188-83212 AGCTTTTCTATAAAATTTAACTTACATTTTTGATATCTAATAATTGATCTACTCAAGTTA
>JSA_1 NZ_LAKP01000081.1:988-1898 GCACCTATCCTTGGAGCGTTGAGTGACCGATTTGGACGTCGACCTGTATTAATTATTTCA
You can use Docker to run this module as follows.
Build like this, using your own image name if desired.
docker build -t allenday/nanostream-dataflow-fasta-formatter .
To run locally you need a service account key.
Then define some variables:
GOOGLE_CLOUD_PROJECT=`gcloud config get-value project`
# docker image to use
IMAGE=allenday/nanostream-dataflow-fasta-formatter
# no need to change this.
SOURCE_MOUNT=/data
# directory where input FASTA files can be found.
# it needs to be in or below `pwd`.
SOURCE_FOLDER=eg
# this is the path to the TSV as described above.
SOURCE_FILE=in.fa
# to which bucket will records be written?
DESTINATION_BUCKET='nanostream-dataflow-qc-fasta-formatter'
# to which folder will records be written?
DESTINATION_FOLDER=fasta_output/resistant/
Then run it:
docker run \
-v $(pwd)/$SOURCE_FOLDER:$SOURCE_MOUNT \
-v $(pwd)/gcloud_keys:/gcloud_keys/ \
-e GOOGLE_CLOUD_PROJECT=$GOOGLE_CLOUD_PROJECT \
-e GOOGLE_APPLICATION_CREDENTIALS='/gcloud_keys/gcloud_credentials.json' \
-e SOURCE_FILE=$SOURCE_MOUNT/$SOURCE_FILE \
-e DESTINATION_BUCKET=$DESTINATION_BUCKET \
-e DESTINATION_FOLDER=$DESTINATION_FOLDER \
$IMAGE
Content type
Image
Digest
Size
343.9 MB
Last updated
over 7 years ago
docker pull allenday/nanostream-dataflow-fasta-formatter