changeset 6:e951f9d38339 tip

Added metaphlan2krona
author Dannon Baker <dannonbaker@me.com>
date Tue, 08 Apr 2014 14:16:46 -0400
parents 73f082e9fa2d
children
files metaphlan2krona.py metaphlan_to_krona.xml
diffstat 2 files changed, 66 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan2krona.py	Tue Apr 08 14:16:46 2014 -0400
@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+
+# ============================================================================== 
+# Conversion script: from MetaPhlAn output to Krona text input file
+# Author: Daniel Brami (daniel.brami@gmail.com)
+# ==============================================================================
+
+import sys
+import optparse
+import re
+
+def main():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' )
+    parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krona output file name' )
+    ( options, spillover ) = parser.parse_args()
+
+    if not options.profile or not options.krona:
+        parser.print_help()
+        sys.exit()
+
+    re_candidates = re.compile(r"s__|unclassified\t")
+    re_replace = re.compile(r"\w__")
+    re_bar = re.compile(r"\|")
+
+    metaPhLan = list()
+    with open(options.profile,'r') as f:
+        metaPhLan = f.readlines()
+    f.close()
+
+    krona_tmp = options.krona 
+    metaPhLan_FH = open(krona_tmp, 'w')
+
+    for aline in (metaPhLan):
+        if(re.search(re_candidates, aline)):
+            x=re.sub(re_replace, '\t', aline)
+            x=re.sub(re_bar, '', x)
+
+            x_cells = x.split('\t')
+            lineage = '\t'.join(x_cells[0:(len(x_cells) -1)])
+            abundance = float(x_cells[-1].rstrip('\n')) 
+
+            metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage))
+
+    metaPhLan_FH.close()
+
+if __name__ == '__main__':
+    main()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_to_krona.xml	Tue Apr 08 14:16:46 2014 -0400
@@ -0,0 +1,17 @@
+<tool id="meta_to_krona" name="MetaPhlAn to Krona" version="1.0.0">
+ <description>Converter</description>
+ <command interpreter="python">
+metaphlan2krona.py -p $input -k $output
+ </command>
+ <inputs>
+  <param name="input" type="data" format="tabular" label="Input MetaPhlAn File"/>
+ </inputs>
+ <outputs>
+    <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> 
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  MetaPhlAn to Krona Converter
+ </help>
+</tool>