Package: hamstr1s
HaMStR-OneSeqTable of ContentsHow to installInstall the hamstr1s packageSetup HaMStR-oneSeqUsageHaMStR-oneSeq data setAdding a new gene set into HaMStR-oneSeqAdding a list of gene sets into HaMStR-oneSeqBugsHow to citeContributorsContactHow to installHaMStR-oneSeqis distributed as a python package calledhamstr1s. It is compatible withPython ≥ v3.7.Install the hamstr1s packageYou can installhamstr1susingpip:python3 -m pip install hamstr1sor, in case you do not have admin rights, and don't use package systems like Anaconda to manage environments you need to use the--useroption:python3 -m pip install --user hamstr1sand then add the following line to the end of your~/.bashrcor~/.bash_profilefile, restart the current terminal to apply the change (or typesource ~/.bashrc):export PATH=$HOME/.local/bin:$PATHSetup HaMStR-oneSeqAfter installinghamstr1s, you need to setupHaMStR-oneSeqto get its dependencies and pre-calculated data.You can do it by just running this commandsetup1sor, in case you are using Anacondasetup1s --condaYou should have the sudo password ready, otherwise some missing dependencies cannot be installed. Seedependency listfor more info. If you do not have root privileges, ask your admin to install those dependencies usingsetup1s --libcommand.After the setup run successfully, you can start using HaMStR.For debugging the setup, please create a log file by running the setup as e.g.setup1s | tee log.txtfor Linux/MacOS orsetup1s --conda | tee log.txtfor Anaconda and send us that log file, so that we can trouble shoot the issues. Most of the problems can be solved by just re-running the setup.UsageHaMStR-oneSeqwill run smoothly with the provided sample input file in 'infile.fa' if everything is set correctly.oneSeq --seqFile infile.fa --seqName test --refspec HUMAN@9606@3The output files with the prefixtestwill be saved at your current working directory.
You can have an overview about all available options with the commandoneSeq -hPlease find more information inour wikito learn about theinput and outputs filesofHaMStR-oneSeq.HaMStR-oneSeq data setWithin the data package (https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml) we provide a set of 78 reference taxa. They can be automatically downloaded during the setup. This data comes "ready to use" with theHaMStR-OneSeqframework. Species data must be present in the three directories listed below:genome_dir (Contains sub-directories for proteome fasta files for each species)blast_dir (Contains sub-directories for BLAST databases made withmakeblastdbout of your proteomes)weight_dir (Contains feature annotation files for each proteome)For each species/taxon there is a sub-directory named in accordance to the naming schema ([Species acronym]@[NCBI ID]@[Proteome version])HaMStR-oneSeq is not limited to those 78 taxa. If needed the user can manually add further gene sets (multifasta format) using provided python scripts.Adding a new gene set into HaMStR-oneSeqFor addingone gene set, please use theaddTaxon1sfunction:addTaxon1s -f newTaxon.fa -i tax_id [-o /output/directory] [-n abbr_tax_name] [-c] [-v protein_version] [-a]in which, the first 3 arguments are required includingnewTaxon.fais the gene set that need to be added,tax_idis its NCBI taxonomy ID,/output/directoryis where the sub-directories can be found (genome_dir,blast_dirandweight_dir). If not given, new taxon will be added into the same directory of pre-calculated data. Other arguments are optional, which are-nfor specify your own taxon name (if not given, an abbriviate name will be suggested based on the NCBI taxon name of the inputtax_id),-cfor calculating the BLAST DB (only needed if you need to include your new taxon into the list of taxa for compilating the core set),-vfor identifying the genome/proteome version (default will be 1), and-afor turning off the annotation step (not recommended).Adding a list of gene sets into HaMStR-oneSeqFor addingmore than one gene set, please use theaddTaxa1sscript:addTaxa1s -i /path/to/newtaxa/fasta -m mapping_file [-o /output/directory] [-c]in which,/path/to/taxa/fastais a folder where the FASTA files of all new taxa can be found.mapping_fileis a tab-delimited text file, where you provide the taxonomy IDs that stick with the FASTA files:#filename	tax_id	abbr_tax_name	version
filename1	12345678
filename2	9606
filename3	4932	my_fungi
...The header line (started with #) is a Must. The values of the last 2 columns (abbr. taxon name and genome version) are, however, optional. If you want to specify a new version for a genome, you need to define also the abbr. taxon name, so that the genome version is always at the 4th column in the mapping file.NOTE:After adding new taxa intoHaMStR-oneSeq, you shouldcheck for the validity of the new databefore running HaMStR.BugsAny bug reports or comments, suggestions are highly appreciated. Pleaseopen an issue on GitHubor be in touch via email.How to citeEbersberger, I., Strauss, S. & von Haeseler, A. HaMStR: Profile hidden markov model based search for orthologs in ESTs. BMC Evol Biol 9, 157 (2009),doi:10.1186/1471-2148-9-157ContributorsIngo EbersbergerVinh TranHolger BergmannContactFor further support or bug reports please contact:ebersberger@bio.uni-frankfurt.de