diff PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py @ 0:7557b48b2872 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_Peptide_Data_Plotting/PDAUG_Peptide_Data_Plotting.py	Wed Oct 28 02:10:12 2020 +0000
@@ -0,0 +1,115 @@
+from modlamp.plot import helical_wheel
+from modlamp.plot import plot_pde
+from modlamp.plot import plot_violin
+from modlamp.plot import plot_aa_distr
+import pandas as pd
+import argparse
+import sys, os
+
+
+
+parser = argparse.ArgumentParser(description='Deployment tool')
+subparsers = parser.add_subparsers()
+
+HelWhl = subparsers.add_parser('HelWhl')
+
+HelWhl.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
+HelWhl.add_argument("-C","--colorcoding", required=False, default='rainbow', help="available: , charge, polar, simple, amphipathic, none")
+HelWhl.add_argument("-L","--lineweights", required=False, default=True, help="(boolean) defines whether connection lines decrease in thickness along the sequence")
+HelWhl.add_argument("-F","--filename", required=False, default="out.png", help="")
+HelWhl.add_argument("-s","--seq", required=False, default=False, help="")
+HelWhl.add_argument("-M","--movment", required=False, default=False, help="")
+HelWhl.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
+
+
+PltPde = subparsers.add_parser('PltPde')
+PltPde.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
+PltPde.add_argument("-l", "--ClmList", required=True, default=None, help="")
+PltPde.add_argument("-F","--filename", required=False, default="out.png", help="filename where to safe the plot. default = None > show the plot")
+PltPde.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
+
+PltVio = subparsers.add_parser('PltVio')
+PltVio.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
+PltVio.add_argument("-l", "--ClmList", required=True, default=None, help="Column list")
+PltVio.add_argument("-C","--colors", required=False, default=None, help='Data to be plotted')
+PltVio.add_argument("-B","--bp", required=False, default=False, help="Print a box blot inside violin")
+PltVio.add_argument("-T","--title", required=False, default=None, help="Title of the plot.")
+PltVio.add_argument("-a","--axlabels", required=False, default=None, help="list containing the axis labels for the plot")
+PltVio.add_argument("-M","--y_max", required=False, default=1, help='y-axis maximum.')
+PltVio.add_argument("-m","--y_min", required=False, default=0, help="y-axis minimum.")
+PltVio.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
+
+
+PltAaDis = subparsers.add_parser('PltAaDis')
+PltAaDis.add_argument("-I","--InFile", required=True, default=None, help="Input data file")
+PltAaDis.add_argument("-O", "--OutFile", required=False, default="out.png", help="OutFile")
+
+args = parser.parse_args()
+
+
+if sys.argv[1] == 'HelWhl':
+
+    f = open(args.InFile)
+    lines = f.readlines()
+    sequence = lines[1].strip('\n')
+
+    if args.movment == 'true':
+        mvt = True
+    else:
+      mvt = False
+
+    if args.seq == 'true':
+        sq = True
+    else:
+      sq = False
+
+    if args.lineweights == 'true':
+        lw = True
+    else:
+      lw = False
+
+    helical_wheel(sequence, colorcoding=args.colorcoding, lineweights=args.lineweights, filename=args.OutFile, seq=args.seq, moment=mvt)
+
+
+elif sys.argv[1] == 'PltPde':
+
+    df = pd.read_csv(args.InFile, sep="\t")
+
+    data = df[args.ClmList.split(',')].as_matrix().T
+
+    plot_pde(data, filename=args.OutFile)
+
+elif sys.argv[1] == 'PltVio':
+
+    df = pd.read_csv(args.InFile, sep="\t")
+
+    data = df[args.ClmList.split(',')].as_matrix().T
+
+    c = ['#0B486B']*len(args.ClmList.split(','))
+
+    plot_violin(data, colors=c, bp=True, filename=args.OutFile)
+
+
+elif sys.argv[1] == 'PltAaDis':
+
+    f = open(args.InFile)
+    lines = f.readlines()
+
+    sequences = []
+
+    for line in lines:
+        if '>' in line:
+            pass
+        else:
+            sequences.append(line.strip('\n'))
+
+    plot_aa_distr(sequences, color='#0B486B', filename=args.OutFile) 
+
+
+
+
+
+
+
+
+