Mercurial > repos > peterjc > fastq_pair_names

--- a/tools/fastq_pair_names/README.rst	Thu May 21 10:54:37 2015 -0400
+++ b/tools/fastq_pair_names/README.rst	Wed Feb 01 06:31:10 2017 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to extract FASTQ paired read names
 ==============================================

-This tool is copyright 2014-2015 by Peter Cock, The James Hutton Institute
+This tool is copyright 2014-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).

@@ -55,6 +55,8 @@
 v0.0.2  - Tool definition now embeds citation information.
 v0.0.3  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.4  - Explicit dependency on ``galaxy_sequence_utils``.
+        - Minor internal changes to Python script for error reporting & style.
 ======= ======================================================================


@@ -68,12 +70,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::

-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
     ...

 or::

-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/fastq_pair_names/
     ...

 To just build and check the tar ball, use::
--- a/tools/fastq_pair_names/fastq_pair_names.py	Thu May 21 10:54:37 2015 -0400
+++ b/tools/fastq_pair_names/fastq_pair_names.py	Wed Feb 01 06:31:10 2017 -0500
@@ -16,16 +16,12 @@
 import os
 import sys
 import re
-from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
+from galaxy_utils.sequence.fastq import fastqReader

 if "-v" in sys.argv or "--version" in sys.argv:
     print "Version 0.0.1"
     sys.exit(0)

-def sys_exit(msg, err=1):
-   sys.stderr.write(msg.rstrip() + "\n")
-   sys.exit(err)
-
 msg = """Expects at least 3 arguments:

  - Pair names tabular output filename
@@ -34,21 +30,21 @@
 """

 if len(sys.argv) < 3:
-    sys_exit(msg)
+    sys.exit(msg)

 output_pairs = sys.argv[1]
 output_nonpairs = sys.argv[2]
 input_fastq_filenames = sys.argv[3:]

-#Cope with three widely used suffix naming convensions,
-#Illumina: /1 or /2
-#Forward/revered: .f or .r
-#Sanger, e.g. .p1k and .q1k
-#See http://staden.sourceforge.net/manual/pregap4_unix_50.html
+# Cope with three widely used suffix naming convensions,
+# Illumina: /1 or /2
+# Forward/revered: .f or .r
+# Sanger, e.g. .p1k and .q1k
+# See http://staden.sourceforge.net/manual/pregap4_unix_50.html
 re_f = re.compile(r"(/1|\.f|\.[sfp]\d\w*)$")
 re_r = re.compile(r"(/2|\.r|\.[rq]\d\w*)$")

-#assert re_f.match("demo/1")
+# assert re_f.match("demo/1")
 assert re_f.search("demo.f")
 assert re_f.search("demo.s1")
 assert re_f.search("demo.f1k")
@@ -74,7 +70,7 @@
 assert not re_illumina_r.match("@HWI-ST916:79:D04M5ACXX:1:1101:10000:100326 1:N:0:TGNCCA")

 count = 0
-pairs = set() # Will this scale OK?
+pairs = set()  # Will this scale OK?
 forward = 0
 reverse = 0
 neither = 0
@@ -84,25 +80,25 @@

 for input_fastq in input_fastq_filenames:
     if not os.path.isfile(input_fastq):
-        sys_exit("Missing input FASTQ file %r" % input_fastq)
+        sys.exit("Missing input FASTQ file %r" % input_fastq)
     in_handle = open(input_fastq)

-    #Don't care about the FASTQ type really...
+    # Don't care about the FASTQ type really...
     for record in fastqReader(in_handle, "sanger"):
         count += 1
-        name = record.identifier.split(None,1)[0]
-        assert name[0]=="@", record.identifier #Quirk of the Galaxy parser
+        name = record.identifier.split(None, 1)[0]
+        assert name[0] == "@", record.identifier  # Quirk of the Galaxy parser
         name = name[1:]
         is_forward = False
         suffix = re_f.search(name)
         if suffix:
-            #============
-            #Forward read
-            #============
+            # ============
+            # Forward read
+            # ============
             template = name[:suffix.start()]
             is_forward = True
         elif re_illumina_f.match(record.identifier):
-            template = name #No suffix
+            template = name  # No suffix
             is_forward = True
         if is_forward:
             forward += 1
@@ -113,13 +109,13 @@
             is_reverse = False
             suffix = re_r.search(name)
             if suffix:
-                #============
-                #Reverse read
-                #============
+                # ============
+                # Reverse read
+                # ============
                 template = name[:suffix.start()]
                 is_reverse = True
             elif re_illumina_r.match(record.identifier):
-                template = name #No suffix
+                template = name  # No suffix
                 is_reverse = True
             if is_reverse:
                 reverse += 1
@@ -127,12 +123,12 @@
                     pairs.add(template)
                     out_pairs.write(template + "\n")
             else:
-                #===========================
-                #Neither forward nor reverse
-                #===========================
+                # ===========================
+                # Neither forward nor reverse
+                # ===========================
                 out_nonpairs.write(name + "\n")
                 neither += 1
-    in_handle.close
+    in_handle.close()
 out_pairs.close()
 out_nonpairs.close()
--- a/tools/fastq_pair_names/fastq_pair_names.xml	Thu May 21 10:54:37 2015 -0400
+++ b/tools/fastq_pair_names/fastq_pair_names.xml	Wed Feb 01 06:31:10 2017 -0500
@@ -1,5 +1,8 @@
-<tool id="fastq_pair_names" name="Identify paired reads in FASTQ files" version="0.0.3">
+<tool id="fastq_pair_names" name="Identify paired reads in FASTQ files" version="0.0.4">
     <description>using the read name suffices</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
+    </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/fastq_pair_names/tool_dependencies.xml	Wed Feb 01 06:31:10 2017 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="galaxy_sequence_utils" version="1.0.1">
+        <repository changeset_revision="c38bd3fe9da6" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>