Mercurial > repos > peterjc > seq_filter_by_mapping

changeset 3:481b0a925e66 draft

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v0.0.6 Python 3 compatible print function
author peterjc
date Wed, 17 May 2017 09:24:01 -0400
parents 48e71dfd51b3
children f82868a026ea
files tools/seq_filter_by_mapping/README.rst tools/seq_filter_by_mapping/seq_filter_by_mapping.py tools/seq_filter_by_mapping/seq_filter_by_mapping.xml tools/seq_filter_by_mapping/tool_dependencies.xml
diffstat 4 files changed, 13 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tools/seq_filter_by_mapping/README.rst	Wed May 10 13:16:44 2017 -0400
+++ b/tools/seq_filter_by_mapping/README.rst	Wed May 17 09:24:01 2017 -0400
@@ -70,6 +70,7 @@
         - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
         - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only).
+v0.0.6  - Python 3 compatible print function.
 ======= ======================================================================
 
 
--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.py	Wed May 10 13:16:44 2017 -0400
+++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.py	Wed May 17 09:24:01 2017 -0400
@@ -19,6 +19,8 @@
 Use -v or --version to get the version, -h or --help for help.
 """
 
+from __future__ import print_function
+
 import os
 import re
 import subprocess
@@ -62,7 +64,7 @@
 options, args = parser.parse_args()
 
 if options.version:
-    print "v0.0.5"
+    print("v0.0.6")
     sys.exit(0)
 
 in_file = options.input
@@ -251,7 +253,7 @@
         # Doing the if statement outside the loop for speed
         # (with the downside of three very similar loops).
         if pos_file is not None and neg_file is not None:
-            print "Generating two FASTA files"
+            print("Generating two FASTA files")
             with open(pos_file, "w") as pos_handle:
                 with open(neg_file, "w") as neg_handle:
                     for identifier, record in crude_fasta_iterator(in_handle):
@@ -262,7 +264,7 @@
                             neg_handle.write(record)
                             neg_count += 1
         elif pos_file is not None:
-            print "Generating matching FASTA file"
+            print("Generating matching FASTA file")
             with open(pos_file, "w") as pos_handle:
                 for identifier, record in crude_fasta_iterator(in_handle):
                     if clean_name(identifier) in wanted:
@@ -271,7 +273,7 @@
                     else:
                         neg_count += 1
         else:
-            print "Generating non-matching FASTA file"
+            print("Generating non-matching FASTA file")
             assert neg_file is not None
             with open(neg_file, "w") as neg_handle:
                 for identifier, record in crude_fasta_iterator(in_handle):
@@ -289,10 +291,10 @@
     pos_count = neg_count = 0
     handle = open(in_file, "r")
     if pos_file is not None and neg_file is not None:
-        print "Generating two FASTQ files"
+        print("Generating two FASTQ files")
         positive_handle = open(pos_file, "w")
         negative_handle = open(neg_file, "w")
-        print in_file
+        print(in_file)
         for title, seq, qual in FastqGeneralIterator(handle):
             # print("%s --> %s" % (title, clean_name(title.split(None, 1)[0])))
             if clean_name(title.split(None, 1)[0]) in wanted:
@@ -304,7 +306,7 @@
         positive_handle.close()
         negative_handle.close()
     elif pos_file is not None:
-        print "Generating matching FASTQ file"
+        print("Generating matching FASTQ file")
         positive_handle = open(pos_file, "w")
         for title, seq, qual in FastqGeneralIterator(handle):
             if clean_name(title.split(None, 1)[0]) in wanted:
@@ -314,7 +316,7 @@
                 neg_count += 1
         positive_handle.close()
     elif neg_file is not None:
-        print "Generating non-matching FASTQ file"
+        print("Generating non-matching FASTQ file")
         negative_handle = open(neg_file, "w")
         for title, seq, qual in FastqGeneralIterator(handle):
             if clean_name(title.split(None, 1)[0]) in wanted:
--- a/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Wed May 10 13:16:44 2017 -0400
+++ b/tools/seq_filter_by_mapping/seq_filter_by_mapping.xml	Wed May 17 09:24:01 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.5">
+<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.6">
     <description>from SAM/BAM file</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
--- a/tools/seq_filter_by_mapping/tool_dependencies.xml	Wed May 10 13:16:44 2017 -0400
+++ b/tools/seq_filter_by_mapping/tool_dependencies.xml	Wed May 17 09:24:01 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a12f73c3b116" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.19">
         <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />