diff PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py @ 0:2df11ea23f10 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.py	Wed Oct 28 02:36:27 2020 +0000
@@ -0,0 +1,57 @@
+import os
+import argparse
+
+
+def TSVtoFASTA(InFile, Method, Positive, Negative, OutFile):
+
+    if Method == 'WithClassLabel':
+
+        f = open(InFile)
+        lines = f.readlines()
+
+        of1 = open(Positive,'w')
+        of2 = open(Negative,'w')
+
+        n = 0
+        m = 0
+
+        for line in lines:
+
+            if '1' in line.split('\t')[1].strip('\n'):
+                n= n+1
+                of1.write('>peptide_'+str(n)+'\n')
+                of1.write(line.split('\t')[0]+'\n')
+
+            if '0' in line.split('\t')[1].strip('\n'):
+                m= m+1
+                of2.write('>peptide_'+str(m)+'\n')
+                of2.write(line.split('\t')[0]+'\n')
+
+    elif Method == 'NoClassLabel':
+
+        f = open(InFile)
+        lines = f.readlines()
+        of1 = open(OutFile,'w')
+
+        for i, line in enumerate(lines[1:]):
+            of1.write('>peptide_'+str(i)+'\n')
+            of1.write(line.split('\t')[0]+'\n')
+
+    else:
+        pass
+
+if __name__=="__main__":
+
+    import argparse
+
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("-I", "--InFile", required=True, default=None, help=".fasta or .tsv")
+    parser.add_argument("-P", "--Postvs", required=False, default='Positive.fasta', help="Path to target tsv file")
+    parser.add_argument("-N", "--Negtvs", required=False, default='Negative.fasta', help="Path to target tsv file")
+    parser.add_argument("-O", "--OutFile", required=False, default='OutFile.fasta', help="Path to target tsv file")
+    parser.add_argument("-M", "--Method", required=True, default=None, help="Path to target tsv file")
+    args = parser.parse_args()
+
+    TSVtoFASTA(args.InFile, args.Method, args.Postvs, args.Negtvs, args.OutFile)
+