pasteTaxID

Welcome to the final solution to a lot of headaches :D This script will take a multifasta file (or many individual fasta files), then search for common IDs (acc, ti, gi, emb, gb), and append the corresponding ti to fasta entries at high speed (10000 entries in just 4 minutes!, depending on your internet connection and if you have a NCBI API KEY).

pasteTaxID can take large multifasta files (we have tried more than 150000 without any problems), avoiding collapse your system and saving a lot of time!

Requirements

• Bash version 4 (comes with Linux and Mac)
• Curl (tested in version 6)
• Python == 2.7.x
• Internet connection and
• Optional: NCBI API KEY for parallel jobs. check this link for information about how to create it (highly recomended).

Usage

There are two ways of running the script. If you have a directory with individual fasta files, then use the following strategy:

Simple way

bash pasteTaxID.bash --workdir [directory_fastas]

However, if you have a multifasta file, the appropriate command line is:

bash pasteTaxID.bash --multifasta [multifasta_file]

where --workdir is a directory where your fasta files are located and --multifasta is the multifasta file (.fna, .fn or .fasta works too).

In the example folder there are some fasta files that don't contain a gi or a ti, just gb. Try testing the script by issuing

bash PasteTaxID.bash --workdir example

Wait a few seconds and check the fastas again. Now you should see taxonomy id's and gi's appended to the fasta entries.

Complete way

Additionally there is a complete way (two more parameters). If your default python is not 2.7, you can add --pythonBin and pass the full path to your python 2.7.

bash pasteTaxID.bash --multifasta myfasta.fasta --pythonBin /home/Peter/programs/python2.7/bin/python

And finally, you can set the number of parallel process to improve the fetch speed (Max jobs: your cores). Don't forget to create your NCBI api key (see requirements section)

bash pasteTaxID.bash --multifasta myfasta.fasta --parallelJobs 8 --apikey 1a2b3c4d56788xyz

This fetch 8 IDs at the same time (max number you can set: same number of all your cores).

Notes

• If you have a huge multifasta (> 1 million fasta entries), go for a coffee (or 2) while the script runs.
• Notice that the order of fasta entries in a multifasta file might have changed in comparison to the order of fasta entries in the file pasteTaxID produces
• NCBI doesn't allow more than 3 connections at the same time if you don't have an api key (and in my experience only work well with once), so if you want to use all your cores, please, put your api key (check this link)

External useful tools

check for these tools to extract some useful information from your data:

• multiGenomicContext: Check the genomic context of several genomes or sequence just providing the GBK files.

• fetchMyLineage: Return the complete lineage of your organism just providing the genus and species names.

• extractSeq: Extract and size defined sequence from and specific contig, from and specific genome.

• plotMyGBK: Plot your GBK in a circular graph with COG categories.

• pasteTaxID: fetch the taxonomic IDs to your fastas.

• GGisy: Plot synteny of two sequence (you can use two genomes), and see the identity of the matched regions.

• getS2: obtain the order parameter to each residue of your protein simulation.