diff extract_min_max_lines.py @ 0:42e4aee6b1fa draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/extract_min_max_lines commit 5c45ed58045ce1686aa069403f8a9426ea20bac5-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_min_max_lines.py	Tue Apr 12 02:58:49 2016 -0400
@@ -0,0 +1,63 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+import time
+
+def extract_lines(input_content, column_id, extraction_type, extraction_nb):
+    conserved_lines = []
+    for line in input_content:
+        split_line = line[:-1].split('\t')
+        value = float(split_line[column_id])
+
+        if len(conserved_lines) < extraction_nb:
+            conserved_lines.append(split_line)
+        else:
+            best_pos = None
+            #print value
+            #print conserved_lines
+            for i in range(len(conserved_lines)-1,-1,-1):
+                compared_value = float(conserved_lines[i][column_id])
+                if extraction_type(value, compared_value) == value:
+                    print value, compared_value, extraction_type(value, compared_value)
+                    best_pos = i
+                else:
+                    break
+            if best_pos != None:
+                print best_pos
+                tmp_conserved_lines = conserved_lines
+                conserved_lines = tmp_conserved_lines[:best_pos]
+                conserved_lines += [split_line]
+                conserved_lines += tmp_conserved_lines[best_pos:-1]
+                print conserved_lines
+                print 
+    return conserved_lines
+
+def extract_min_max_lines(args):
+    if args.extraction_type == 'max':
+        extraction_type = max
+    elif args.extraction_type == 'min':
+        extraction_type = min
+
+    with open(args.input_file, 'r') as input_file:
+        input_content = input_file.readlines()
+        conserved_lines = extract_lines(input_content, args.column_id - 1, 
+            extraction_type, args.extraction_nb)
+
+    with open(args.output_file, 'w') as output_file:
+        for line in conserved_lines:
+            output_file.write('\t'.join(line) + "\n")
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input_file', required=True)
+    parser.add_argument('--output_file', required=True)
+    parser.add_argument('--column_id', required=True, type=int)
+    parser.add_argument('--extraction_type', required=True, choices = ['min','max'])
+    parser.add_argument('--extraction_nb', required=True, type=int)
+    args = parser.parse_args()
+
+    extract_min_max_lines(args)
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