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| # Overview | ||
| > input: multi protein fasta file | ||
| > output: multi fasta of positive candidates and a table summarizing the stats for each candidate with identifier, length of potential SAR, topology orientation, calculate % of hydrophillic residues. | ||
| # Requirements | ||
| * python 3.6+ | ||
| * biopython | ||
| * <s>pandas</s> --> thought I might use this, but ended up seeing I wouldnt needed it by the time I was wrapping this up. | ||
| * <s>numpy</s> | ||
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| # Outline | ||
| 1. Read in input multi fasta | ||
| * multi fasta parsed by `biopython_parsing.py` | ||
| 2. Check SAR requirements | ||
| * <s>Min peptide length check</s> --> Currently omitted | ||
| * <s>Max peptide length check (user dictated)</s> --> Currently omitted | ||
| * Hydrophobic residues (Ile, Leu, Val, Phe, Tyr, Trp, Met) except often rich in Gly, Ala, and/or Ser residues | ||
| * <s>Option 1: FIWLVMYAGS</s> Using option #2 | ||
| * __Option 2: FIWLVMYCATGS # add C and T --> This is what is being used__ | ||
| * Lysines can be present in the hydrophobic stretch if within 3 residues of the domain boundary (lysine snorkeling) | ||
| * <s>Currently, I'm not checking for lysine snorkels as the hydrophobic region present will still be caught.</s> | ||
| * Snorkelers are found by if a Lys is on the first or last index of the sequence range being inspected, checks for hydrophobic residues between it and either the beginning or end of the sequence. | ||
| * More refinement will be necessary to verify a "K_nonhydro_nonhydro_nonhydro_hydro..hydro_" | ||
| * I would think the argument of tuning it anymore is that the method currently would still catch the hydrophobic domains with within a given range. | ||
| * Topology check | ||
| * N term (net positive charge) | ||
| * C term catalytic domain | ||
| 3. Return candidates and multi fasta. | ||
| 4. Return candidates in multi gff3. | ||
| 5. Write statistics to output file in table format | ||
| * <s>identifier :: length of peptide :: topology orientation :: %G and %A :: likely more later</s> | ||
| * Been reworked to include what is currently in tab-separated format: | ||
| * ["Name","Protein Sequence","Protein Length","SAR Length","Putative SAR Sequence","SAR Start Location","[res%]","N-term Sequence","N-term net Charge"] | ||
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| # File Summaries | ||
| * `SAR_functions.py` | ||
| * Has the SAR class and accompanying methods | ||
| * `SAR_finder.py` | ||
| * The executed script by Galaxy | ||
| * `biopython_parsing.py` | ||
| * _might scale to a_ sym link for parsing bio related files, otherwise will just be related to addressing this experiment. | ||
| * `file_operations.py` | ||
| * _mich scale to a_ sym link for operating on files and exporting them, otherwise will just be related to addressing this experiment, and writing the outputs. | ||
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| # Testing | ||
| * Mu (mu-proteins.fa) for a TP | ||
| * Phage-21 for a TP | ||
| * simple-proteins.fa includes TP from Mu and TN from Mu. Used with Planemo. |
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| import sys | ||
| import argparse | ||
| import os | ||
| import re | ||
| from biopython_parsing import FASTA_parser | ||
| from file_operations import fasta_from_SAR_dict, gff3_from_SAR_dict, tab_from_SAR_dict | ||
| from SAR_functions import CheckSequence | ||
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| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser(description="SAR Finder") | ||
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| parser.add_argument("fa",type=argparse.FileType("r"),help="organism's multi fasta file") | ||
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| parser.add_argument("--min",type=int,default=20,help="minimum size of candidate peptide") | ||
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| parser.add_argument("--max",type=int,default=200,help="maximum size of candidate peptide") | ||
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| parser.add_argument("--sar_min",type=int,default=15,help="minimum size of candidate peptide TMD domain") | ||
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| parser.add_argument("--sar_max",type=int,default=20,help="maximum size of candidate peptide TMD domain") | ||
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| parser.add_argument("--out_fa",type=argparse.FileType("w"),help="multifasta output of candidate SAR proteins",default="candidate_SAR.fa") | ||
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| parser.add_argument("--out_stat",type=argparse.FileType("w"),help="summary statistic file for candidate SAR proteins, tab separated",default="candidate_SAR_stats.tsv") | ||
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| parser.add_argument("--out_gff3",type=argparse.FileType("w"),help="multigff3 file for candidate SAR proteins",default="candidate_SAR.gff3") | ||
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| args = parser.parse_args() | ||
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| fa_dict = FASTA_parser(fa=args.fa).multifasta_dict() | ||
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| sars = {} | ||
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| for protein_name, protein_data in fa_dict.items(): | ||
| sar = CheckSequence(protein_name, protein_data) | ||
| #sar.check_sizes(min=args.min,max=args.max) | ||
| hydros = sar.shrink_results(sar_min=args.sar_min, sar_max=args.sar_max) | ||
| sars.update(hydros) | ||
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| gff3_from_SAR_dict(sars, args.out_gff3) | ||
| tab_from_SAR_dict(sars,args.out_stat,"SGAT",sar_min=args.sar_min, sar_max=args.sar_max) | ||
| fasta_from_SAR_dict(sars,args.out_fa) | ||
| #stat_file_from_SAR_dict(sars,args.out_stat,sar_min=args.sar_min,sar_max=args.sar_max) # fix this whenever ready. |
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| <tool id="edu.tamu.cpt.sar.sar_finder" name="SAR Finder" version="1.0"> | ||
| <description>SAR Domain Finder</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"> | ||
| </expand> | ||
| <command detect_errors="aggressive"><![CDATA[ | ||
| python $__tool_directory__/SAR_finder.py | ||
| $fa | ||
| --sar_min $sar_min | ||
| --sar_max $sar_max | ||
| --out_fa $out_fa | ||
| --out_gff3 $out_gff3 | ||
| --out_stat $out_stat | ||
| ]]></command> | ||
| <inputs> | ||
| <param label="Multi FASTA File" name="fa" type="data" format="fasta" /> | ||
| <param label="SAR domain minimal size" name="sar_min" type="integer" value="15" /> | ||
| <param label="SAR domain maximum size" name="sar_max" type="integer" value="20" /> | ||
| </inputs> | ||
| <outputs> | ||
| <data format="tabular" name="out_stat" label="candidate_SAR_stats.tsv"/> | ||
| <data format="fasta" name="out_fa" label="candidate_SAR.fa"/> | ||
| <data format="gff3" name="out_gff3" label="candidate_SAR.gff3"/> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="fa" value="simple-proteins.fa"/> | ||
| <param name="sar_min" value="15"/> | ||
| <param name="sar_max" value="20"/> | ||
| <output name="out_stat" file="candidate_SAR_stats.tsv"/> | ||
| <output name="out_fa" file="candidate_SAR.fa"/> | ||
| <output name="out_gff3" file="candidate_SAR.gff3"/> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| A tool that analyzes protein sequence within the first 50 residues for a weakly hydrophobic domain sometimes found in endolysins called Signal-Anchor-Release (aka SAR) | ||
| Definition: A Signal-Arrest-Release (SAR) domain is a N-terminal, weakly hydrophobic transmembrane region rich is Gly/Ala and/or Ser residues sometimes found in phage lysis proteins, including endolysins and holins. The SAR domain can be released from the membrane in a proton motive force-dependent manner. | ||
| This tool finds proteins that contain a stretch (default 15-20 residues) of hydrophobic residues (Ile, Leu, Val, Phe, Tyr, Trp, Met, Gly, Ala, Ser) and calculates the % Gly/Ala/Ser/Thr residues in the hydrophobic stretch. The net charge on the N-terminal region is also displayed to aid in determining the SAR topology.[1] | ||
| INPUT : Protein Multi FASTA | ||
| OUTPUT : | ||
| * Multi FASTA of candidate proteins that pass the SAR domain criteria | ||
| * Text summary file containing each protein that passes the SAR domain criteria | ||
| * Multi GFF3 | ||
| ]]></help> | ||
| <citations> | ||
| <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation> | ||
| <citation type="bibtex"> | ||
| @unpublished{galaxyTools, | ||
| author = {C. Ross}, | ||
| title = {CPT Galaxy Tools}, | ||
| year = {2020-}, | ||
| note = {https://github.com/tamu-cpt/galaxy-tools/} | ||
| } | ||
| </citation> | ||
| </citations> | ||
| </tool> |
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