TCDBtools

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Tools developed in Python and Perl to support TCDB's functionality and research.

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# Welcome to TCDBtools.

**We have just combined our Python and Perl scripts into a single repository. 
This facilitaties maintanance by the developers team and installation for our 
users. Please, do not hesitate to contact us if you have any requests or would
like to report issues.**

The programs in this repository have been developed in a collaboration between 
members of the SaierLab and the group of Dr. Gabriel Moreno-Hagelsieb from 
Wilfrid Laurier University in Ontario, Canada.

A number of programs in Python were originally written by Vamsee Reddy, many 
have been updated to work with Python3 and new programs have been added by 
different members of the lab and collaborators:

Dependencies developed by us are not shown in this list, but they are 
included as part of the repository. The list below contains only the main 
programs.

**1.** famXpander.pl ([Manual](manuals/famXpander.md))  
**2.** extractTCDB.pl ([Manual](manuals/extractTCDB.md))    
**3.** areFamiliesHomologous.pl ([Manual](manuals/areFamiliesHomologous.md))  
**4.** list_top_gsat_hits.pl ([Manual](manuals/list_top_gsat_hits.md))  
**5.** interpret_proto2_top_hits.pl ([Manual](manuals/interpret_proto2_top_hits.md))  
**6.** mkProteinClusters.pl  ([Manual](manuals/mkProteinClusters.md))  
**7.** tmsRepeat.pl ([Manual](Manuals/tmsRepeat.md))  
**8.** findDistantFamilyMembers ([Manual](manuals/findDistantFamilyMembers))  
**9.** getDomainTopology.pl ([Manual](manuals/getDomainTopology.md))   
**10.** getMultCompSystems.pl ([Manual](manuals/getMultCompSystems.md))  
**11.** findNovelTransporters.pl ([Manual](manuals/findNovelTransporters.md))  
**12.** prepNewIMPs4TCDBupload.pl ([Manual](manuals/prepNewIMPs4TCDBupload.md))  
**13.** organizeSeqsByTMS.pl ([Manual](manuals/organizeSeqsByTMS.md))  
**14.** getOrthologs.pl ([Manual](manuals/getOrthologs.md))  
**15.** matchDomains.pl ([Manual](manuals/matchDomains.md))  
**16.** cleanDomains.pl ([Manual](manuals/cleanDomains.md))  
**17.** protocol1.py   ([Manual](manuals/BioV_manual.pdf))  
**18.** protocol2.py   ([Manual](manuals/BioV_manual.pdf))  
**19.** gsat.py        ([Manual](manuals/BioV_manual.pdf))  
**20.** gblast3.py     ([Manual](manuals/BioV_manual.pdf))    
**21.** tmstats.py     ([Manual](manuals/BioV_manual.pdf))  
**22.** tss.py         ([Manual](manuals/BioV_manual.pdf))  
**23.** ssearch.py     ([Manual](manuals/BioV_manual.pdf))  
**24.** ancient.py     ([Manual](manuals/AR_INSTRUCTIONS.pdf))   
**25.** quod.py        ([Manual](https://gitlab.com//khendarg/hvordan/blob/master/docs/quod.md))  
**26.** hvordan.py    ([Manual](https://gitlab.com/khendarg/hvordan/blob/master/docs/hvordan.md))  
**27.** tmsplit.py    ([Manual](manuals/tmsplit.md))  
**28.** deuterocol.py ([Manual](https://github.com/SaierLaboratory/deuterocol))  
**29.** YutanpaNet.py ([Manual](manuals/YutanpaNet.md))  
**30.** showsubnet.py ([Manual](manuals/showsubnet.md))  
**31.** searchMissComponents.py ([Manual](manuals/searchMissComponents.md))  
**32.** searchPseudogenes.py ([Manual](manuals/searchPseudogenes.md))  
**33.** singEasy.py ([Manual](manuals/singEasy.md))

---

* **Note 1:**  
The BioV manual needs to be updated.

* **Note 2:**  
Make sure you download the perl modules and point your _$PERL5LIB_ 
enviroment variable to the destination directory.

* **Note 3:**  
People contributing software to this repository are: Arturo Medrano-Soto, Gabriel Moreno-Hagelsieb, Vamsee Reddy, Kevin Hendargo, Yichi Zhang, and Vasu Iddamsetty.

* **Note 4**  
We appreciate the contributions from the repository of [Kevin Hendargo](https://gitlab.com/khendarg).

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