Mercurial > repos > immport-devteam > check_headers

changeset 0:e88c99a4fb36 draft

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Uploaded
author immport-devteam
date Mon, 27 Feb 2017 12:41:17 -0500
parents
children 05440ef97f8b
files check_headers/getHeaders.py check_headers/getHeaders.xml check_headers/test-data/input1.txt check_headers/test-data/input2.txt check_headers/test-data/input3.txt check_headers/test-data/output.tabular
diffstat 6 files changed, 150 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/getHeaders.py	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,50 @@
+#!/usr/bin/env python
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+from __future__ import print_function
+import sys
+
+from argparse import ArgumentParser
+
+
+def print_headers(files, filenames, outfile):
+    with open(outfile, "w") as outf:
+        for i, eachfile in enumerate(files):
+            with open(eachfile, "r") as ef:
+                headers = ef.readline()
+                outf.write("\t".join([filenames[i], headers]))
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="GetHeaders",
+             description="Gets the headers of all files in given set.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_files",
+            required=True,
+            action='append',
+            help="File location for the text files.")
+
+    parser.add_argument(
+            '-n',
+            dest="file_names",
+            required=True,
+            action='append',
+            help="File names.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    args = parser.parse_args()
+    input_files = [f for f in args.input_files]
+    file_names = [fn for fn in args.file_names]
+    print_headers(input_files, file_names, args.output_file)
+    sys.exit(0)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/getHeaders.xml	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,67 @@
+<tool id="get_headers" name="Check headers" version="1.1">
+  <description>of any set of flowtext files.</description>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+    python $__tool_directory__/getHeaders.py -o "${output_file}"
+ #for $f in $input#
+    -i "${f}"
+    -n "${f.name}"
+ #end for#
+  ]]>
+  </command>
+  <inputs>
+    <param format="flowtext" name="input" type="data_collection" collection_type="list" label="Text files Collection"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="input">
+        <collection type="list">
+          <element name="input1.txt" value="input1.txt"/>
+          <element name="input2.txt" value="input2.txt"/>
+          <element name="input3.txt" value="input3.txt"/>
+        </collection>
+      </param>
+      <output name="output_file" file="output.tabular"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+   This tool returns a table of the headers of a set of text files.
+
+-----
+
+**Input files**
+
+This tool requires collections of txt, flowtext or tabular files as input.
+
+**Output file**
+
+The output file is a table listing the headers for each file.
+
+-----
+
+**Example**
+
+*File1*::
+
+   Marker1 Marker2 Marker3
+   34      45      12
+   33      65      10
+
+*File2*::
+
+   Marker4 Marker5 Marker3
+   19      62      98
+   12      36      58
+
+*Output*::
+
+   File1 Marker1 Marker2 Marker3
+   File2 Marker4 Marker5 Marker3
+  ]]>
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/test-data/input1.txt	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,10 @@
+Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4
+449	157	551	129	169	292
+894	1023	199	277	320	227
+262	73	437	69	0	146
+340	115	509	268	0	74
+316	76	50	0	60	129
+394	144	83	138	335	194
+383	139	499	0	0	224
+800	1023	239	284	288	280
+388	97	534	111	83	177
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/test-data/input2.txt	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,10 @@
+Forward Scatter	Side Scatter	FITC CD4	PE CXCR3	PP CD8	APC CCR5
+363	76	550	200	0	127
+372	126	519	44	51	148
+1023	1023	289	401	362	254
+770	1023	175	361	225	237
+384	111	525	121	0	138
+602	578	385	286	222	131
+788	1023	216	310	270	294
+420	211	552	479	0	62
+668	1019	73	193	227	132
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/test-data/input3.txt	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,10 @@
+Forward Scatter	Side Scatter	FITC CD4	PE CD25	PP CD3	APC CD45RA
+289	56	438	0	626	480
+352	153	30	147	483	386
+383	190	156	228	734	408
+261	62	432	121	598	555
+451	120	537	338	568	201
+373	104	3	110	621	584
+418	105	561	0	610	562
+358	185	0	292	641	327
+733	970	139	227	293	259
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_headers/test-data/output.tabular	Mon Feb 27 12:41:17 2017 -0500
@@ -0,0 +1,3 @@
+input1.txt	Forward Scatter	Side Scatter	FITC CD4	PE CCR3	PP CD8	APC CCR4
+input2.txt	Forward Scatter	Side Scatter	FITC CD4	PE CXCR3	PP CD8	APC CCR5
+input3.txt	Forward Scatter	Side Scatter	FITC CD4	PE CD25	PP CD3	APC CD45RA