Merge branch 'master' into 'master'

Add the bam_to_scidx tool.

See merge request !13

tools/bam_to_scidx/.shed.yml

+name: bam_to_scidx
+owner: iuc
+description: Contains a tool that converts a BAM file to an ScIdx file.
+homepage_url:
+long_description: |
+  Contains a tool that converts BAM data to ScIdx, the Strand-specific coordinate count format,
+  which is used by tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used
+  by the Center for Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx
+  files are 1-based.
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx
+type: unrestricted
+categories:
+- Convert Formats

tools/bam_to_scidx/bam_to_scidx.py

+"""
+bam_to_scidx.py
+
+Input: BAM file
+Output: Converted scidx file
+"""
+import optparse
+import os
+import shutil
+import subprocess
+import sys
+import tempfile
+
+BUFF_SIZE = 1048576
+
+
+def get_stderr_exception(tmp_err, tmp_stderr):
+    """
+    Return a stderr string of reasonable size.
+    """
+    tmp_stderr.close()
+    # Get stderr, allowing for case where it's very large.
+    tmp_stderr = open(tmp_err, 'rb')
+    stderr_str = ''
+    buffsize = BUFF_SIZE
+    try:
+        while True:
+            stderr_str += tmp_stderr.read(buffsize)
+            if not stderr_str or len(stderr_str) % buffsize != 0:
+                break
+    except OverflowError:
+        pass
+    tmp_stderr.close()
+    return stderr_str
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+
+parser = optparse.OptionParser()
+parser.add_option('-j', '--jar_file', dest='jar_file', type='string', help='BAMtoIDX.jar')
+parser.add_option('-b', '--input_bam', dest='input_bam', type='string', help='Input dataset in BAM format')
+parser.add_option('-i', '--input_bai', dest='input_bai', type='string', help='Input dataset index')
+parser.add_option('-r', '--read', dest='read', type='int', default=0, help='Reads.')
+parser.add_option('-o', '--output', dest='output', type='string', help='Output dataset in scidx format')
+options, args = parser.parse_args()
+
+tmp_dir = tempfile.mkdtemp(prefix='tmp-scidx-')
+tmp_out = tempfile.NamedTemporaryFile().name
+tmp_stdout = open(tmp_out, 'wb')
+tmp_err = tempfile.NamedTemporaryFile().name
+tmp_stderr = open(tmp_err, 'wb')
+
+# Link input BAM file and associated index file into the working directory.
+input_data_file_name = "input.bam"
+os.link(options.input_bam, os.path.join(tmp_dir, input_data_file_name))
+os.link(options.input_bai, os.path.join(tmp_dir, "%s.bai" % input_data_file_name))
+
+cmd = "java -jar %s -b %s -s %d -o %s" % (options.jar_file, input_data_file_name, options.read, options.output)
+proc = subprocess.Popen(args=cmd, stdout=tmp_stdout, stderr=tmp_stderr, shell=True, cwd=tmp_dir)
+return_code = proc.wait()
+if return_code != 0:
+    error_message = get_stderr_exception(tmp_err, tmp_stderr)
+    stop_err(error_message)
+
+if tmp_dir and os.path.exists(tmp_dir):
+    shutil.rmtree(tmp_dir)

tools/bam_to_scidx/bam_to_scidx.xml

+<tool id="bam_to_scidx" name="Convert BAM to ScIdx" version="1.0.0">
+    <description></description>
+    <command>
+        <![CDATA[
+            python $__tool_directory__/bam_to_scidx.py
+            -j $__tool_directory__/BAMtoIDX.jar
+            -b "$input_bam"
+            -i "${input_bam.metadata.bam_index}"
+            -r $read
+            -o "$output"
+        ]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file" help="BAM file must be sorted and indexed" />
+        <param name="read" type="select" label="Read to output">
+            <option value="0" selected="True">Read1</option>
+            <option value="1">Read2</option>
+            <option value="2">Combined</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="scidx" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="input.bam" ftype="bam" />
+            <param name="read" value="0" />
+            <output name="output" file="output.scidx" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Converts BAM data to ScIdx, the Strand-specific coordinate count format, which is used by
+tools within the Chip-exo Galaxy flavor.  The Chip-exo Galaxy flavor is used by the Center for
+Eukaryotic Gene Regulation labs at The Pennsylvania State University.  ScIdx files are 1-based.
+
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {None},
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
+        }</citation>
+    </citations>
+</tool>

tools/bam_to_scidx/test-data/output.scidx

+#2015-11-23 20:18:56.51;input.bam;READ1
+chrom	index	forward	reverse	value
+chr17	1820100	0	1	1
+chr17	1849175	1	0	1
+chr17	2778159	0	1	1
+chr17	3205518	0	1	1
+chr17	12974350	1	0	1
+chr17	20624912	0	1	1
+chr17	27071176	0	1	1
+chr17	34920819	1	0	1
+chr17	39810583	0	1	1
+chr17	43542379	0	1	1
+chr17	45800656	1	0	1
+chr17	47124830	0	1	1
+chr17	48697995	0	1	1
+chr17	54474619	0	1	1
+chr17	64901353	0	1	1
+chr17	69072332	1	0	1
+chr17	76184543	1	0	1
+chr17	76518878	0	1	1
+chr17	76941015	1	0	1

tools/cwpair2/cwpair2.py

@@ -27,7 +27,6 @@ if __name__ == '__main__':
     parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
     parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
     parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.')
-    parser.add_argument('--sort_chromosome', dest='sort_chromosome', default='asc', help='Sort output by chromosome.')
     parser.add_argument('--sort_score', dest='sort_score', default='no', help='Sort output by score.')
     parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
     args = parser.parse_args()
@@ -50,7 +49,6 @@ if __name__ == '__main__':
                                           args.down_distance,
                                           args.binsize,
                                           args.output_files,
-                                          args.sort_chromosome,
                                           args.sort_score)
         statistics.extend(stats)
     # Accumulate statistics.

tools/cwpair2/cwpair2.xml

@@ -22,7 +22,6 @@
                 --relative_threshold $threshold_format_cond.relative_threshold
             #end if
             --output_files $output_files
-            --sort_chromosome $sort_chromosome
             --sort_score $sort_score
             --statistics_output "$statistics_output"
         ]]>
@@ -56,10 +55,6 @@
             <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option>
             <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option>
         </param>
-        <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" >
-            <option value="asc" selected="True">ascending order</option>
-            <option value="desc">descending order</option>
-        </param>
         <param name="sort_score" type="select" label="Sort output by score?">
             <option value="no" selected="True">No</option>
             <option value="asc">Yes, in ascending order</option>
@@ -151,7 +146,6 @@
             <param name="threshold_format" value="relative_threshold" />
             <param name="relative_threshold" value="0.0" />
             <param name="output_files" value="simple" />
-            <param name="sort_chromosome" value="asc" />
             <param name="sort_score" value="asc" />
             <output_collection name="closest_S" type="list">
                 <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" />
@@ -173,7 +167,6 @@
             <param name="threshold_format" value="relative_threshold" />
             <param name="relative_threshold" value="0.0" />
             <param name="output_files" value="all" />
-            <param name="sort_chromosome" value="asc" />
             <param name="sort_score" value="no" />
             <output_collection name="closest_D" type="list">
                 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" />

tools/cwpair2/cwpair2_util.py

@@ -225,7 +225,7 @@ def create_directories(method):
 
 
 def process_file(dataset_path, galaxy_hid, method, threshold, up_distance,
-                 down_distance, binsize, output_files, sort_chromosome, sort_score):
+                 down_distance, binsize, output_files, sort_score):
     if method == 'all':
         match_methods = METHODS.keys()
     else:
@@ -240,7 +240,6 @@ def process_file(dataset_path, galaxy_hid, method, threshold, up_distance,
                                 down_distance,
                                 binsize,
                                 output_files,
-                                sort_chromosome,
                                 sort_score)
         statistics.append(stats)
     if output_files == 'all' and method == 'all':
@@ -251,7 +250,7 @@ def process_file(dataset_path, galaxy_hid, method, threshold, up_distance,
 
 
 def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
-                    down_distance, binsize, output_files, sort_chromosome, sort_score):
+                    down_distance, binsize, output_files, sort_score):
     output_details = output_files in ["all", "simple_orphan_detail"]
     output_plots = output_files in ["all"]
     output_orphans = output_files in ["all", "simple_orphan", "simple_orphan_detail"]
@@ -367,27 +366,12 @@ def perform_process(dataset_path, galaxy_hid, method, threshold, up_distance,
                 orphan_output.writerow((cname, cpeak[0], cpeak[1], cpeak[2], cpeak[3]))
         # Keep track of orphans for statistics.
         orphans += len(crick)
-    # Sort output by chromosome if specified.
-    if sort_chromosome == "asc":
-        try:
-            x.sort(key=lambda data: int(data[3]))
-            x.sort(key=lambda data: int(data[0]))
-        except:
-            # Cannot sort because chromosome number is not a numeric.
-            pass
-    elif sort_chromosome == "desc":
-        try:
-            x.sort(key=lambda data: int(data[0]), reverse=True)
-            x.sort(key=lambda data: int(data[3]), reverse=True)
-        except:
-            # Cannot sort because chromosome number is not a numeric.
-            pass
     # Sort output by score if specified.
     if sort_score == "desc":
         x.sort(key=lambda data: float(data[5]), reverse=True)
     elif sort_score == "asc":
         x.sort(key=lambda data: float(data[5]))
-    # Writing a summary to txt or gff format file
+    # Writing a summary to gff format file
     for row in x:
         row_tmp = list(row)
         # Dataset in tuple cannot be modified in Python, so row will

tools/genetrack/genetrack_util.py

@@ -9,11 +9,6 @@ import tempfile
 GFF_EXT = 'gff'
 SCIDX_EXT = 'scidx'
 
-ROMAN = ['0', 'I', 'II', 'III', 'IV', 'V', 'VI', 'VII', 'VIII', 'IX', 'X',
-         'XI', 'XII', 'XIII', 'XIV', 'XV', 'XVI', 'XVII', 'XVIII', 'XIX', 'XX',
-         'XXI', 'XXII', 'XXIII', 'XXIV', 'XXV', 'XXVI', 'XXVII', 'XXVIII', 'XXIX',
-         'XXX']
-
 
 def noop(data):
     return data
@@ -27,39 +22,9 @@ def numeric_to_zeropad(data):
     return re.sub(r'chr(\d([^\d]|$))', r'chr0\1', data)
 
 
-def roman_to_numeric(data):
-    def convert(match):
-        """
-        Converts a single roman numeral to a number
-        """
-        numeral = match.group(1)
-        numeral = numeral.upper()
-        if numeral not in ROMAN:
-            # Unable to convert detected Roman numeral
-            return match.group(0)
-        return 'chr'+str(ROMAN.index(numeral))+(match.group(2) or '')
-    r = re.compile('chr([IVX]+)([^IVX]|$)', flags=re.IGNORECASE)
-    data = r.sub(convert, data)
-    return data
-
-
-def numeric_to_roman(data):
-    def convert(match):
-        """
-        Converts a number to a roman numeral
-        """
-        number = int(match.group(1))
-        if number >= len(ROMAN):
-            # Number is out of range to convert to a Roman numeral
-            return match.group(0)
-        return 'chr'+ROMAN[number]+(match.group(2) or '')
-    r = re.compile('chr(\d+)([^\d]|$)')
-    data = r.sub(convert,  data)
-    return data
-
-FORMATS = ['zeropad', 'numeric', 'roman']
-IN_CONVERT = {'zeropad': zeropad_to_numeric, 'roman': roman_to_numeric, 'numeric': noop}
-OUT_CONVERT = {'zeropad': numeric_to_zeropad, 'roman': numeric_to_roman, 'numeric': noop}
+FORMATS = ['zeropad', 'numeric']
+IN_CONVERT = {'zeropad': zeropad_to_numeric, 'numeric': noop}
+OUT_CONVERT = {'zeropad': numeric_to_zeropad, 'numeric': noop}
 
 
 def conversion_functions(in_fmt, out_fmt):
@@ -69,19 +34,7 @@ def conversion_functions(in_fmt, out_fmt):
     return [IN_CONVERT[in_fmt], OUT_CONVERT[out_fmt]]
 
 
-def autodetect_format(data):
-    if re.search('chr0\d', data):
-        fmt = 'zeropad'
-    elif re.search('chr[IVXivx]', data):
-        fmt = 'roman'
-    else:
-        fmt = 'numeric'
-    return fmt
-
-
 def convert_data(data, in_fmt, out_fmt):
-    if in_fmt == 'autodetect':
-        in_fmt = autodetect_format(data)
     for fn in conversion_functions(in_fmt, out_fmt):
         data = fn(data)
     return data
@@ -425,12 +378,12 @@ def process_chromosome(cname, data, writer, process_bounds, width, sigma, down_w
             write(cname, '-', peak)
 
 
-def sort_chromosome_reads_by_index( input_path ):
+def sort_chromosome_reads_by_index(input_path):
     """
     Return a gff file with chromosome reads sorted by index.
     """
     # Will this sort produce different results across platforms?
-    output_path = tempfile.NamedTemporaryFile( delete=False ).name
+    output_path = tempfile.NamedTemporaryFile(delete=False).name
     command = 'sort -k 1,1 -k 4,4n "%s" > "%s"' % (input_path, output_path)
     p = subprocess.Popen(command, shell=True)
     p.wait()