Mercurial > repos > cpt > cpt_disruptin_finder
changeset 0:3f0d07a10405 draft
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author | cpt |
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date | Fri, 17 Jun 2022 12:22:15 +0000 |
parents | |
children | b973bc75693d |
files | cpt_disruptin_finder/cpt-macros.xml cpt_disruptin_finder/disruptin_finder.py cpt_disruptin_finder/disruptin_finder.xml cpt_disruptin_finder/macros.xml |
diffstat | 4 files changed, 285 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_disruptin_finder/cpt-macros.xml Fri Jun 17 12:22:15 2022 +0000 @@ -0,0 +1,115 @@ +<?xml version="1.0"?> +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd $__tool_directory__ && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_disruptin_finder/disruptin_finder.py Fri Jun 17 12:22:15 2022 +0000 @@ -0,0 +1,93 @@ +""" +This program is intended to find gene products that would be acceptable disruptin candidates. + +The criteria can be toggled between selecting for proteins with: + - net charge above a give threshold (default = +4) and length less than given threshold (default = 100 aa) + OR + - ratio of number of charged residues to length of the sequence above a given threshold (default = 0.25 residue/aa) + and length less than given threshold (default = 100 aa) + OR + - net charge above a give threshold (default = +4), ratio of number of charged residues to length of the sequence + above a given threshold (default = 0.25 residue/aa), and length less than given threshold (default = 100 aa) + +Net charge of a sequence is calculated so that for every R or K residue the net charge increases by one, and for every +D or E residue the net charge decreases by one. The ratio of charged residues to length is calculated in a similar manner. +The residues R, K, D, and E each increase the number of charged residues by one, and total for the sequence is then +divided by the length to get the ratio. + +Input a multi fasta file with all of the predicted protein sequences from the genome as well as a threshold +sequence length, net charge, and charge residue to length ratio. The program outputs another fasta file. +The output fasta file includes records for all the sequences meeting the size and charge criteria. + +""" + +from Bio import SeqIO +import argparse +import sys + + +def disruptin_finder( + fasta_file, thresh_size, thresh_net_charge, thresh_charge_ratio, selection_criteria +): + # Iterable variables + net_charge = 0 + charge_res = 0 + + # Create record variable to store record information + total_record = [] + + # Parse the .fasta file and get the sequence + for rec in SeqIO.parse(fasta_file, "fasta"): + sequence = str(rec.seq) + + if len(sequence) <= thresh_size: + for aa in sequence: + # For R and K residues a positive charge is given + if aa in "RK": + net_charge += 1 + charge_res += 1 + # For D and E residues a negative charge is given + elif aa in "DE": + net_charge -= 1 + charge_res += 1 + + # Charge (total charged residues) to size ratio is calculated + Length = len(sequence) + charge_ratio = float(charge_res) / float(Length) + + # Based on the user-specified selection criteria a list of records is compiled + if selection_criteria == "net": + if net_charge >= thresh_net_charge: + total_record = total_record + [rec] + elif selection_criteria == "ratio": + if charge_ratio >= thresh_charge_ratio: + total_record = total_record + [rec] + elif selection_criteria == "both": + if ( + charge_ratio >= thresh_charge_ratio + and net_charge >= thresh_net_charge + ): + total_record = total_record + [rec] + + # Reset the iterable variables + net_charge = 0 + charge_res = 0 + + # The total list of records is returned by the function + yield total_record + + +if __name__ == "__main__": + # Grab all of the filters from our plugin loader + parser = argparse.ArgumentParser(description="Disruptin Finder") + parser.add_argument( + "fasta_file", type=argparse.FileType("r"), help="Multi-FASTA Input" + ) + parser.add_argument("--thresh_net_charge", type=int, default=4) + parser.add_argument("--thresh_size", type=int, default=100) + parser.add_argument("--thresh_charge_ratio", type=float, default=0.25) + parser.add_argument("--selection_criteria", action="store") + args = parser.parse_args() + + for seq in disruptin_finder(**vars(args)): + SeqIO.write(seq, sys.stdout, "fasta")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_disruptin_finder/disruptin_finder.xml Fri Jun 17 12:22:15 2022 +0000 @@ -0,0 +1,54 @@ +<?xml version="1.1"?> +<tool id="edu.tamu.cpt2.phage.disruptin_finder" name="Disruptin Finder" version="1.1"> + <description>finds proteins with size and charge criteria</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +python $__tool_directory__/disruptin_finder.py +$fasta_file +--thresh_net_charge $thresh_net_charge +--thresh_size $thresh_size +--thresh_charge_ratio $thresh_charge_ratio +--selection_criteria $selection_criteria + +> $output]]></command> + <inputs> + <param label="Fasta" name="fasta_file" type="data" format="fasta" /> + <param label="Minimum Net Charge" name="thresh_net_charge" type="integer" value="4" /> + <param label="Maximum Length" name="thresh_size" type="integer" value="100" /> + <param label="Minimum Charge to Length Ratio" name="thresh_charge_ratio" type="float" value="0.25" /> + + <param type="select" label="Type of selection criteria" name="selection_criteria"> + <option value="net">Net charge</option> + <option value="ratio">Ratio of charged residues to sequence length</option> + <option value="both" selected="true">Both net charge and ratio</option> + </param> + + </inputs> + <outputs> + <data format="fasta" name="output"/> + </outputs> + <help><![CDATA[ +**What it does** +This program finds proteins sequences based on given selection criteria: net charge, sequence length, +and/or number of charged residues per amino acid. Inputs include a multi fasta file of protein sequences, +thresholds for size, charge, and charge-to-size ratio criteria. + +This tool returns the selected sequences in a fasta format. + + ]]></help> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Holt}, + title = {CPT Galaxy Tools}, + year = {2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_disruptin_finder/macros.xml Fri Jun 17 12:22:15 2022 +0000 @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.8.13">python</requirement> + <requirement type="package" version="1.79">biopython</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <yield/> + </requirements> + </xml> + <xml name="genome_selector"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <token name="@GENOME_SELECTOR_PRE@"> + ln -s $genome_fasta genomeref.fa; + </token> + <token name="@GENOME_SELECTOR@"> + genomeref.fa + </token> +</macros>