Eslam-Samir-Ragab / Sequence-database-curator

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

Sequence Dereplicator and Database Curator (SDDC) program

This program dereplicates and/or filter nucleotide and/or protein database from a list of names or sequences (by exact match).

This software is under GNU General Public License v3.0

Please, cite: DOI: 10.1007/s00284-017-1327-6

How to use:

1. you need to install python 2.7 or python 3 on your machine.
2. you need to install Numpy and Biopython
3. you need to install future module by pip command
4. Click “Clone or download” > “Download ZIP” > extract the downloaded file.
5. Open the file “sddc.py” with (python.exe).

• Windows
• U/Linux : use the command chmod u+x sddc.py
• Mac : use the command python sddc.py

6. State your variables and press Enter.

The full SDDC commands, Cheat sheet and notes are here

Updates in SDDC v3.0:

1. Bugs fixes.
2. Usage of -org_order with -kw is updated
3. Exchange FASTA headers mode is now available.

Updates in SDDC v2.0:

1. You can filter the sequences using only keywords (separated by a comma) inclusively or exclusively by adding (-kw) argument to your normal command line.
2. You can get your sequences in their original order after dereplication and/or sequence filtration by adding (-org_order) to your normal command line.

Notes:

• The rate of SDDC as determined using Intel(R) Pentium(R) CPU G630 @ 2.70GHz 2.70 GHz Processor, 4.00 GB RAM, 32-bit Operating System

• List of options and commands in the program you can download it from here:

Examples

if you want to dereplicate protein sequences use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode derep

if you want to dereplicate protein sequences and preserve the original order of the sequences in the new file use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode derep -org_order

if you want to dereplicate protein sequences with a minimum length = 30 and sequences are in multiple files use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode derep -min_length 30 -multi

if you want to dereplicate nucleotide sequences with optimum approach and normal protein length = 300 use the following command

python sddc.py -in (input_file) -n -out (output_file) -mode derep -optimum -prot_length 300

if you want to filter a protein sequences inclusively by name (i.e. you want to retrieve only seqeunces that you've specified their names) use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode filter -flt_by name -flt_file (filter_file) -approach inclusive

if you want to filter a protein sequences inclusively by keyword(s) (i.e. you want to retrieve only seqeunces that you've specified the keywords (separated by a comma) in their names) use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode filter -flt_by name -flt_file (filter_file in csv) -approach inclusive -kw

if you want to filter a protein sequences exclusively by name (i.e. you want to retrieve the seqeunces that aren't present in your filter file) use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode filter -flt_by name -flt_file (filter_file) -approach exclusive

if you want to filter a protein sequences exclusively by keyword(s) in their names (i.e. you want to retrieve the seqeunces that certain keywords (separated be a comma) aren't present in your filter file) use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode filter -flt_by name -flt_file (filter_file in csv) -approach exclusive -kw

if you want to filter a nucleotide sequences by sequence (only exclusive) use the following command

python sddc.py -in (input_file) -n -out (output_file) -mode filter -flt_by seq -flt_file (filter_file)

if you want to exchange words in FASTA headers of your protein sequences use the following command

python sddc.py -in (input_file) -p -out (output_file) -mode exchange_headers -ex_file (exchange_file in csv)

if you want to exchange words in FASTA headers of your nucleotide sequences use the following command

python sddc.py -in (input_file) -n -out (output_file) -mode exchange_headers -ex_file (exchange_file in csv)

Example (1)

Example (2)

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