| Previous changeset 2:bb0d4cd765c5 (2015-09-29) Next changeset 4:60b6bd959929 (2016-01-15) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178 |
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modified:
BlastParser_and_hits.py BlastParser_and_hits.xml test-data/output.tab |
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| diff -r bb0d4cd765c5 -r 8f5d48294f70 BlastParser_and_hits.py --- a/BlastParser_and_hits.py Tue Sep 29 06:32:31 2015 -0400 +++ b/BlastParser_and_hits.py Mon Oct 19 12:13:12 2015 -0400 |
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| @@ -15,8 +15,8 @@ the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences") the_parser.add_argument('--mode', action="store", choices=["verbose", "short"], type=str, help="reporting (verbose) or not reporting (short) oases contigs") the_parser.add_argument('--filter_relativeCov', action="store", type=float, default=0, help="filter out relative coverages below the specified ratio (float number)") - the_parser.add_argument('--filter_maxScore', action="store", type=float, default=0, help="filter out maximum BitScore below the specified float number") - the_parser.add_argument('--filter_meanScore', action="store", type=float, default=0, help="filter out maximum BitScore below the specified float number") + the_parser.add_argument('--filter_maxScore', action="store", type=float, default=0, help="filter out best BitScores below the specified float number") + the_parser.add_argument('--filter_meanScore', action="store", type=float, default=0, help="filter out mean BitScores below the specified float number") the_parser.add_argument('--al_sequences', action="store", type=str, help="sequences that have been blast aligned") the_parser.add_argument('--un_sequences', action="store", type=str, help="sequences that have not been blast aligned") args = the_parser.parse_args() @@ -146,7 +146,7 @@ print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"]) print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"]) print >> F, "# Relative Subject Coverage: %s" % (results[subject]["RelativeSubjectCoverage"]) - print >> F, "# Maximum Bit Score: %s" % (results[subject]["maxBitScores"]) + print >> F, "# Best Bit Score: %s" % (results[subject]["maxBitScores"]) print >> F, "# Mean Bit Score: %s" % (results[subject]["meanBitScores"]) for header in results[subject]["HitDic"]: print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) ) @@ -161,7 +161,7 @@ info = "\t".join(info) print >> F, info else: - print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tMaximum Bit Score\tMean Bit Score" + print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tBest Bit Score\tMean Bit Score" for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True): if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov or results[subject]["maxBitScores"]<filter_maxScore or results[subject]["meanBitScores"]<filter_meanScore: continue |
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| diff -r bb0d4cd765c5 -r 8f5d48294f70 BlastParser_and_hits.xml --- a/BlastParser_and_hits.xml Tue Sep 29 06:32:31 2015 -0400 +++ b/BlastParser_and_hits.xml Mon Oct 19 12:13:12 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.1"> +<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.2"> <description>for virus discovery</description> <requirements></requirements> <command interpreter="python"> @@ -23,9 +23,9 @@ <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" /> <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" /> <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/> - <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs"> - <option value="verbose" default="true">verbose</option> - <option value="short">do not report oases contigs</option> + <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs"> + <option value="verbose" default="true">extensive</option> + <option value="short">compact</option> </param> <conditional name="additional_filters"> <param name="use_filters" type="select" label="Use Additional Filters?"> |
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| diff -r bb0d4cd765c5 -r 8f5d48294f70 test-data/output.tab --- a/test-data/output.tab Tue Sep 29 06:32:31 2015 -0400 +++ b/test-data/output.tab Mon Oct 19 12:13:12 2015 -0400 |
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| b'@@ -5,7 +5,7 @@\n # Suject Length: 3005\n # Total Subject Coverage: 3001\n # Relative Subject Coverage: 0.998668885191\n-# Maximum Bit Score: 5413.0\n+# Best Bit Score: 5413.0\n # Mean Bit Score: 3241.5\n Locus_42_Transcript_2/2_Confidence_0.333_Length_597\t100.0\t593\t2409\t3001\t99.2\t0.0\t1070.0\n Locus_42_Transcript_1/2_Confidence_0.333_Length_3138\t100.0\t3001\t1\t3001\t95.6\t0.0\t5413.0\n@@ -14,7 +14,7 @@\n # Suject Length: 6780\n # Total Subject Coverage: 6765\n # Relative Subject Coverage: 0.997787610619\n-# Maximum Bit Score: 8001.0\n+# Best Bit Score: 8001.0\n # Mean Bit Score: 2184.97272727\n Locus_10_Transcript_7/8_Confidence_0.111_Length_255\t100.0\t26\t6549\t6524\t9.8\t0.001\t48.2\n Locus_7_Transcript_10/11_Confidence_0.154_Length_4093\t99.66\t4093\t542\t4628\t100.0\t0.0\t7319.0\n@@ -43,7 +43,7 @@\n # Suject Length: 6780\n # Total Subject Coverage: 6765\n # Relative Subject Coverage: 0.997787610619\n-# Maximum Bit Score: 8001.0\n+# Best Bit Score: 8001.0\n # Mean Bit Score: 2184.97272727\n Locus_10_Transcript_7/8_Confidence_0.111_Length_255\t100.0\t26\t6549\t6524\t9.8\t0.001\t48.2\n Locus_7_Transcript_10/11_Confidence_0.154_Length_4093\t99.66\t4093\t542\t4628\t100.0\t0.0\t7319.0\n@@ -72,7 +72,7 @@\n # Suject Length: 4806\n # Total Subject Coverage: 4708\n # Relative Subject Coverage: 0.979608822305\n-# Maximum Bit Score: 5317.0\n+# Best Bit Score: 5317.0\n # Mean Bit Score: 1797.4\n Locus_63_Transcript_1/1_Confidence_0.000_Length_371\t95.96\t371\t3781\t3411\t99.7\t3e-170\t601.0\n Locus_42_Transcript_2/2_Confidence_0.333_Length_597\t97.81\t594\t2761\t3354\t99.3\t0.0\t1012.0\n@@ -84,7 +84,7 @@\n # Suject Length: 4806\n # Total Subject Coverage: 4708\n # Relative Subject Coverage: 0.979608822305\n-# Maximum Bit Score: 5317.0\n+# Best Bit Score: 5317.0\n # Mean Bit Score: 1797.4\n Locus_63_Transcript_1/1_Confidence_0.000_Length_371\t95.96\t371\t3781\t3411\t99.7\t3e-170\t601.0\n Locus_42_Transcript_2/2_Confidence_0.333_Length_597\t97.81\t594\t2761\t3354\t99.3\t0.0\t1012.0\n@@ -96,7 +96,7 @@\n # Suject Length: 3014\n # Total Subject Coverage: 3004\n # Relative Subject Coverage: 0.996682149967\n-# Maximum Bit Score: 2296.0\n+# Best Bit Score: 2296.0\n # Mean Bit Score: 1733.0\n Locus_21_Transcript_1/1_Confidence_0.000_Length_919\t100.0\t919\t813\t1731\t99.9\t0.0\t1658.0\n Locus_12_Transcript_1/1_Confidence_0.000_Length_1279\t100.0\t1273\t3014\t1742\t99.5\t0.0\t2296.0\n@@ -107,7 +107,7 @@\n # Suject Length: 3260\n # Total Subject Coverage: 3150\n # Relative Subject Coverage: 0.966257668712\n-# Maximum Bit Score: 3952.0\n+# Best Bit Score: 3952.0\n # Mean Bit Score: 1617.5\n Locus_15_Transcript_1/1_Confidence_0.000_Length_436\t100.0\t436\t35\t470\t99.8\t0.0\t787.0\n Locus_9_Transcript_2/3_Confidence_0.333_Length_2216\t99.59\t2217\t972\t3186\t100.0\t0.0\t3952.0\n@@ -120,7 +120,7 @@\n # Suject Length: 3243\n # Total Subject Coverage: 3016\n # Relative Subject Coverage: 0.930003083565\n-# Maximum Bit Score: 1734.0\n+# Best Bit Score: 1734.0\n # Mean Bit Score: 1205.8\n Locus_17_Transcript_3/3_Confidence_0.200_Length_456\t98.9\t456\t1652\t2107\t99.8\t0.0\t800.0\n Locus_43_Transcript_1/1_Confidence_0.000_Length_1002\t98.4\t1003\t2189\t3191\t99.9\t0.0\t1734.0\n@@ -132,7 +132,7 @@\n # Suject Length: 3243\n # Total Subject Coverage: 3016\n # Relative Subject Coverage: 0.930003083565\n-# Maximum Bit Score: 1734.0\n+# Best Bit Score: 1734.0\n # Mean Bit Score: 1205.8\n Locus_17_Transcript_3/3_Confidence_0.200_Length_456\t98.9\t456\t1652\t2107\t99.8\t0.0\t800.0\n Locus_43_Transcript_1/1_Confidence_0.000_Length_1002\t98.4\t1003\t2189\t3191\t99.9\t0.0\t1734.0\n@@ -144,7 +144,7 @@\n # Suject Length: 3360\n # Total Subject Coverage: 2526\n # Relative Subject Coverage: 0.751785714286\n-# Maximum Bit Score: 978.0\n+# Best Bit Score: 978.0\n # Mean Bit Score: 445.75\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t99.39\t164\t546\t383\t99.4\t3e-77\t291.0\n Locus_62_Transcript_1/1_Confidence_0.000_Length_130\t98.46\t130\t1733\t1862\t99.2\t8e-58\t226.0\n@@ -163,7 +163,7 @@\n # Suject Length: 3360\n # Total Subject Coverage: 2526\n # Relative Subject Coverage: 0.751785714286\n-# Maximum Bit Score: 978.0\n+# Best Bit Score: 978.0\n # Mean Bit Score: 445.75\n Locus_69_T'..b'e-04\t50.0\n #\n@@ -1701,7 +1701,7 @@\n # Suject Length: 3040\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0269736842105\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t409\t328\t49.4\t2e-04\t50.0\n #\n@@ -1709,7 +1709,7 @@\n # Suject Length: 3193\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0256811775759\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t539\t458\t49.4\t2e-04\t50.0\n #\n@@ -1717,7 +1717,7 @@\n # Suject Length: 3262\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0251379521766\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t538\t457\t49.4\t2e-04\t50.0\n #\n@@ -1725,7 +1725,7 @@\n # Suject Length: 3260\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0251533742331\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t538\t457\t49.4\t2e-04\t50.0\n #\n@@ -1733,7 +1733,7 @@\n # Suject Length: 3260\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0251533742331\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t538\t457\t49.4\t2e-04\t50.0\n #\n@@ -1741,7 +1741,7 @@\n # Suject Length: 1356\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0604719764012\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t408\t327\t49.4\t2e-04\t50.0\n #\n@@ -1749,7 +1749,7 @@\n # Suject Length: 3084\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.026588845655\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t446\t365\t49.4\t2e-04\t50.0\n #\n@@ -1757,7 +1757,7 @@\n # Suject Length: 3039\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0269825600526\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t408\t327\t49.4\t2e-04\t50.0\n #\n@@ -1765,7 +1765,7 @@\n # Suject Length: 3040\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0269736842105\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t409\t328\t49.4\t2e-04\t50.0\n #\n@@ -1773,7 +1773,7 @@\n # Suject Length: 1356\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0604719764012\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t408\t327\t49.4\t2e-04\t50.0\n #\n@@ -1781,7 +1781,7 @@\n # Suject Length: 1356\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0604719764012\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t408\t327\t49.4\t2e-04\t50.0\n #\n@@ -1789,7 +1789,7 @@\n # Suject Length: 3184\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0257537688442\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t532\t451\t49.4\t2e-04\t50.0\n #\n@@ -1797,7 +1797,7 @@\n # Suject Length: 1356\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0604719764012\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t408\t327\t49.4\t2e-04\t50.0\n #\n@@ -1805,6 +1805,6 @@\n # Suject Length: 3085\n # Total Subject Coverage: 82\n # Relative Subject Coverage: 0.0265802269044\n-# Maximum Bit Score: 50.0\n+# Best Bit Score: 50.0\n # Mean Bit Score: 50.0\n Locus_69_Transcript_1/1_Confidence_0.000_Length_164\t73.17\t82\t454\t373\t49.4\t2e-04\t50.0\n' |