Added sam2interval converter

tool_conf.xml.sample

@@ -343,6 +343,7 @@
   </section>
   <section name="SAM Tools" id="samtools">
    <tool file="samtools/sam_bitwise_flag_filter.xml" />
+   <tool file="samtools/sam2interval.xml" />
    <tool file="samtools/sam_to_bam.xml" />
    <tool file="samtools/sam_merge.xml" />
    <tool file="samtools/sam_pileup.xml" />

tools/samtools/sam2interval.py

@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+
+import sys
+import optparse
+import re
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def main():
+    usage = """%prog [options]
+    
+options (listed below) default to 'None' if omitted
+    """
+    parser = optparse.OptionParser(usage=usage)
+
+    parser.add_option(
+        '-f','--input_sam_file',
+        metavar="INPUT_SAM_FILE",
+        dest='input_sam',
+        default = False,
+        help='Name of the SAM file to be filtered. STDIN is default')
+            
+    parser.add_option(
+        '-c','--flag_column',
+        dest='flag_col',
+        default = '2',
+        help='Column containing SAM bitwise flag. 1-based')
+        
+    parser.add_option(
+        '-s','--start_column',
+        dest='start_col',
+        default = '4',
+        help='Column containing position. 1-based')
+
+    parser.add_option(
+        '-g','--cigar_column',
+        dest='cigar_col',
+        default = '6',
+        help='Column containing CIGAR or extended CIGAR string')
+
+    parser.add_option(
+        '-r','--ref_column',
+        dest='ref_col',
+        default = '3',
+        help='Column containing name of the refernce sequence coordinate. 1-based')
+        
+    parser.add_option(
+        '-e','--read_column',
+        dest='read_col',
+        default = '1',
+        help='Column containing read name. 1-based')
+
+    parser.add_option(
+        '-d','--debug',
+        dest='debug',
+        action='store_true',
+        default = False,
+        help='Print debugging info')
+        
+    parser.add_option(
+        '-p','--print_all',
+        dest='prt_all',
+        action='store_true',
+        default = False,
+        help='Print coordinates and original SAM?')
+
+
+    options, args = parser.parse_args()
+
+    if options.input_sam:
+		infile = open ( options.input_sam, 'r')
+    else:
+    	infile = sys.stdin
+
+    cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' )
+
+    for line in infile:
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#,@' ):
+            fields = line.split( '\t' )
+            start = int( fields[ int( options.start_col ) - 1 ] ) - 1
+            end = 0
+            for op in cigar.findall( fields[ int( options.cigar_col) - 1 ] ):
+                end += int( op[ 0:len( op ) - 1 ] )
+                
+            strand = '+' 
+            if bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0010 ):
+                strand = '-'
+            read_name = fields[ int( options.read_col ) - 1 ]
+            ref_name  = fields[ int( options.ref_col ) - 1 ]
+            
+            if options.prt_all:
+                print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
+            else:
+                print '%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand)
+
+if __name__ == "__main__": main()
+

tools/samtools/sam2interval.xml

@@ -0,0 +1,69 @@
+<tool id="sam2interval" name="Convert SAM" version="1.0.0">
+  <description>to interval</description>
+  <command interpreter="python">sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
+  </command>
+  <inputs>
+    <param format="sam" name="input1" type="data" label="Select dataset to convert"/>
+    <param name="print_all" type="select" label="Print all?" help="Do you want to retain original SAM fields? See example below.">
+        <option value="-p">Yes</option>
+        <option value="">No</option>
+    </param>
+  </inputs>
+ <outputs>
+    <data format="interval" name="out_file1" />
+  </outputs>
+<tests>
+    <test>          
+        <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
+        <param name="flags" value="Read is mapped in a proper pair"/>
+        <param name="print_all" value="Yes"/>
+        <output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/>
+    </test>
+    <test>          
+        <param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
+        <param name="flags" value="Read is mapped in a proper pair"/>
+        <param name="print_all" value="No"/>
+        <output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/>
+    </test>
+
+</tests>
+  <help>
+
+**What it does**
+
+Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. To calculate the end position the tool uses the CIGAR string.
+
+-----
+
+**Example**
+
+Converting the following dataset::
+
+ r001 163 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTA *
+ r002   0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *
+ r003   0 ref  9 30       5H6M *  0   0 AGCTAA            * NM:i:1
+ r004   0 ref 16 30    6M14N5M *  0   0 ATAGCTTCAGC       *
+ r003  16 ref 29 30       6H5M *  0   0 TAGGC             * NM:i:0
+ r001  83 ref 37 30         9M =  7 -39 CAGCGCCAT         *
+
+into Interval format will produce the following if *Print all?* is set to **Yes**::
+
+ ref  6 22 + r001 163 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTA *
+ ref  8 19 + r002   0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *
+ ref  8 14 + r003   0 ref  9 30 5H6M       *  0   0 AGCTAA            * NM:i:1
+ ref 15 40 + r004   0 ref 16 30 6M14N5M    *  0   0 ATAGCTTCAGC       *
+ ref 28 33 - r003  16 ref 29 30 6H5M       *  0   0 TAGGC             * NM:i:0
+ ref 36 45 - r001  83 ref 37 30 9M         =  7 -39 CAGCGCCAT         *
+ 
+Setting  *Print all?* is set to **No** will generate the following::
+
+ ref  6 22 + r001
+ ref  8 19 + r002
+ ref  8 14 + r003
+ ref 15 40 + r004
+ ref 28 33 - r003
+ ref 36 45 - r001
+
+
+  </help>
+</tool>