Paths constants¶
For refseq_bipype.py¶
Constant | Path |
---|---|
PATH_GI_TAX | /home/pszczesny/workingdata/refseq/db/tax_id/gi_taxid_nucl.dmp |
PATH_TAX_NAME | /home/pszczesny/workingdata/refseq/db/tax_id/names.dmp |
PATH_RAPSEARCH | /home/pszczesny/soft/RAPSearch2.12_64bits/bin/rapsearch |
PATH_REF_PROT_MASL28 | /home/pszczesny/storage/workingdata/rapsearch/masl28 |
PATH_REF_PROT_KO | /home/pszczesny/soft/KEGG/ko.pep.rapsearch.db |
PATH_REF_PROT_ELSE | /home/pszczesny/workingdata/refseq/protein/refseq_protein |
PATH_USEARCH | /home/pszczesny/soft/usearch |
PATH_FQ2FA | /usr/local/bioinformatics/fastx_toolkit/bin/fastq_to_fasta |
PATH_HUMANN | /home/pszczesny/soft/humann-0.99 |
PATH_HUMANN_DATA | /home/pszczesny/soft/humann-0.99/input/hmp_metadata.dat |
PATH_BOWTIE2 | /home/pszczesny/bin/bowtie2 |
PATH_VELVETH | /home/pszczesny/soft/Velvet/velveth |
PATH_VELVETG | /home/pszczesny/soft/Velvet/velvetg |
PATH_METAVELVETG | /home/pszczesny/soft/MetaVelvet/meta-velvetg |
PATH_MEGAHIT | /home/pszczesny/soft/megahit/megahit |
Bipype¶
Constant | Path |
---|---|
PREF_PATH_REF_FUNGI | /home/pszczesny/workingdata/refseq/db/fungi/fungi_refseq |
PREF_PATH_REF_PLANT_1 | /home/pszczesny/workingdata/refseq/db/plant/plant_refseq_1 |
PREF_PATH_REF_PLANT_2 | /home/pszczesny/workingdata/refseq/db/plant/plant_refseq_2 |
PATH_X16S_DB | /home/public/EMIRGE/SSU/SSU_candidate_db.udb |
PATH_ITS_DB | /home/pszczesny/workingdata/ITS/unite.udb |
PATH_NCBI_TAXA_DB | /home/pszczesny/soft/bipype/NCBI_tax_id_name.pickle |
PATH_RECONSTRUCT_DB | /home/pszczesny/storage/workingdata/mcra/mcra10k.fasta |
PATH_16S_DATABASE | /home/pszczesny/soft/bipype/SSU_candidate_db.fasta |
PATH_ITS_DATABASE | /home/pszczesny/soft/bipype/UNITE_public_from_27.01.13.fasta |
Metatranscriptomics¶
Constant | Path |
---|---|
PATH_KO_DB | /home/pszczesny/soft/KEGG/ko.db |
PATH_KO_PCKL | /home/pszczesny/soft/bipype/kogenes.pickle |