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changeset 0:f3fc78cc4c43 draft

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Uploaded
author cpt
date Fri, 17 Jun 2022 12:33:22 +0000
parents
children a99be535e99d
files cpt_disruptin_table/Disruptin_hydrophobicity_helicity_table_package.py cpt_disruptin_table/Disruptin_hydrophobicity_helicity_table_package.xml cpt_disruptin_table/cpt-macros.xml cpt_disruptin_table/macros.xml
diffstat 4 files changed, 293 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_disruptin_table/Disruptin_hydrophobicity_helicity_table_package.py	Fri Jun 17 12:33:22 2022 +0000
@@ -0,0 +1,122 @@
+"""
+This program is intended to create the output table for the disruptin finder workflow
+"""
+from Bio import SeqIO
+from Bio.SeqUtils.ProtParam import ProteinAnalysis
+from Bio.SeqUtils import ProtParamData
+import csv
+import argparse
+import sys
+
+
+def disruptin_table(garnier_file, fasta_file):
+    # Iterable variables
+    position = 1
+    net_charge = 0
+    charge_res = 0
+    record_number = 0
+
+    # loop structures
+    names = []
+    sec_struct = []
+
+    # reading the lines from the garnier csv file
+#    with open(garnier_file,'r') as csvfile:
+#        garnierreader = csv.reader(csvfile)
+    for row in garnier_file:
+        if row[0] == 'Sequence: ':
+            names += [row[1]]
+        elif row[0] in 'HETC':
+	    row = row.split('\t')
+            sec_struct += [''.join(row)]
+			
+    record = []
+    p = []
+    r = []
+    c = []
+    h = []
+    s = []
+
+    # Parse the .fasta file and get the sequence
+    for rec in SeqIO.parse(fasta_file, "fasta"):
+        sequence = str(rec.seq)
+
+        # Set up the information vectors: for position #, residue, hydrophobic/charge/polar/nonpolar, and secondary
+        # structure
+        record += [rec.id]
+        position_vec = []
+        residue_vec = []
+        charge_sym_vec = []
+        sec_struct_vec = []
+
+        for aa in sequence:
+            position_vec += [str(position)]
+            residue_vec += [str(aa)]
+            sec_struct_vec += [str(sec_struct[record_number][position - 1])]
+
+            # For R and K residues a positive charge is given
+            if aa in "RK":
+                symbol = "+"
+            # For D and E residues a negative charge is given
+            elif aa in "DE":
+                symbol = "-"
+            elif aa in "AVMILPWFG":
+                symbol = "N"
+            elif aa in "HSYTCQN":
+                symbol = "P"
+            charge_sym_vec += symbol
+            position += 1
+
+            # Calculating hyrophobicity based on Kyte and Doolittle scale. Using binning value of 9. Since the binning
+            # is 9, the first 4 residues and last 4 residues as set blank so as to center the values to their
+            # approximate position on the sequence.
+            prot_ana_seq = ProteinAnalysis(sequence)
+            hydro = [0] * 4 + prot_ana_seq.protein_scale(ProtParamData.kd, 9) + [0] * 4
+
+        record_number += 1
+        position = 1
+
+        p += [position_vec]
+        r += [residue_vec]
+        c += [charge_sym_vec]
+        h += [hydro]
+        s += [sec_struct_vec]
+
+    # returns values for name of the sequence
+    return record, p, r, c, h, s
+
+
+if __name__ == "__main__":
+    # Grab all of the filters from our plugin loader
+    parser = argparse.ArgumentParser(description="Disruptin Table Output")
+    parser.add_argument(
+        "garnier_file", type=argparse.FileType("r"), help="csv file from garnier reader"
+    )
+    parser.add_argument(
+        "fasta_file",
+        type=argparse.FileType("r"),
+        help="fasta file of disruptin candidates",
+    )
+    args = parser.parse_args()
+
+    # Set up output location
+#    f = open(sys.stdout, 'w', newline='')
+#    writer1 = csv.writer(f)
+
+    iden, position, residue, charge, hydro, struct = disruptin_table(**vars(args))
+
+    for i in range(len(iden)):
+#		 writer1.writerow(['Protein ID']+[iden[i]])
+#        writer1.writerow(['Position'] + [format(x, 's') for x in position[i]])
+#        writer1.writerow(['Residue'] + [format(x, 's') for x in residue[i]])
+#		 writer1.writerow(['Charge'] + [format(x, 's') for x in charge[i]])
+#        writer1.writerow(['Hydrophobicity'] + [format(x, '.3f') for x in hydro[i]])
+#        writer1.writerow(['Secondary Structure'] + [format(x, 's') for x in struct[i]])
+#        writer1.writerow([''])
+
+        print(str(iden[i]))
+        print("Position \t " + "\t".join(position[i]))
+        print("Residue \t" + "\t".join(residue[i]))
+        print("Charge \t" + "\t".join(charge[i]))
+        print("Hydrophobicity \t" + "\t".join(format(x, ".3f") for x in hydro[i]))
+        print("Secondary Structure \t" + "\t".join(struct[i]))
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_disruptin_table/Disruptin_hydrophobicity_helicity_table_package.xml	Fri Jun 17 12:33:22 2022 +0000
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool id="edu.tamu.cpt2.phage.disruptin_table" name="Disruptin Table Output" version="1.0">
+    <description>makes table of disruptin candidates</description>
+    <macros>
+		<import>macros.xml</import>
+		<import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+	<command detect_errors="aggressive"><![CDATA[
+python $__tool_directory__/Disruptin_hydrophobicity_helicity_table_package.py
+$garnier_file
+$fasta_file
+
+
+
+>$output]]></command>
+    <inputs>
+        <param label="Garnier csv file" name="garnier_file" type="data" format="tabular" />
+		<param label="Candidate fasta file" name="fasta_file" type="data" format="fasta" />
+    </inputs>
+    <outputs>
+		<data format="tabular" name="output"/>
+    </outputs>
+    <help><![CDATA[
+**What it does**
+This program takes the parsed output from the garnier tool and the fasta file with disruptin candidate sequences
+and compiles information on each of the sequences into a table format. The table includes the sequence and the position for each residue
+as well as the charge, hydrophobicity (based on the Kyte Doolittle scale), and secondary structure prediction from
+the garnier tool.
+
+        ]]></help>
+		<expand macro="citations" />
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_disruptin_table/cpt-macros.xml	Fri Jun 17 12:33:22 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_table/macros.xml	Fri Jun 17 12:33:22 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>