Tools¶
Three tools are available in the client-perl directory in the GFE Service github repository. When running these tools you can specify which feature-service and gfe-service to use. Without specifying they default to feature.nmdp-bioinformatics.org and gfe.b12x.org.
Installing Tools¶
Note
Some perl modules will fail to load if you don’t have certain software installed. Make sure you have libssl-dev installed otherwise Moose and Log4j will fail to properly install.
- Clone the github repository.
- Change to the client-perl directory with the Makefile.PL.
- Install cpanm and all the perl dependencies.
curl -LO http://xrl.us/cpanm && perl cpanm --notest --installdeps . - Run make test and make install.
perl Makefile.PL && make && make test && make install
Tool Documentation¶
seq2gfe¶
Tip
Use seq2gfe for quickly investigating a particular sequence. Don’t try to use it for bulk analysis of sequences.
| Parameter | Description |
| -s/–seq | Raw sequence text, defaults to STDIN |
| -u/–url | URL for service, default is gfe.b12x.org |
| -l/–locus | Gene locus |
| -v/–verbose | Flag for running in verbose |
| -h/–help | Flag for returning the Perl POD |
Example commands:
seq2gfe --seq GACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCT \
CTTGGACCGCGGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTACCTGCGCT -l HLA-A > seqtest1.gfe.csv
cat GACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGC \
GGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTACCTGCGCTCTTGGACCGC | seq2gfe -l HLA-A > seqtest1.gfe.csv
fasta2gfe¶
| Parameter | Description |
| -f/–fasta | Fasta file, defaults to STDIN |
| -u/–url | URL for service, default is gfe.b12x.org |
| -l/–locus | Gene locus |
| -v/–verbose | Flag for running in verbose |
| -h/–help | Flag for returning the Perl POD |
Example commands:
fasta2gfe --fasta t/resources/fastatest1.fasta -l HLA-A > fastatest1.gfe.csv
cat t/resources/fastatest1.fasta | fasta2gfe -l HLA-A > fastatest1.gfe.csv
hml2gfe¶
| Parameter | Description |
| -i/–input | Input HML File |
| -u/–url | URL for service, default is gfe.b12x.org |
| -m/–hml | Flag for returning results in HML file |
| -v/–verbose | Flag for running in verbose |
| -h/–help | Flag for returning the Perl POD |
Example commands:
hml2gfe --input t/resources/hmltest1.HML > hmltest1.gfe.csv
hml2gfe --input t/resources/hmltest1.HML --hml > hmltest1.gfe.HML