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changeset 1:141da185be70 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/reprof commit 3aca39eed712c5b3ab8faac62accab588704ffd9
author iuc
date Wed, 02 Dec 2015 15:01:36 -0500
parents 7c33ed152672
children ae7de35846d8
files reprof.py reprof.xml test-data/report.tsv test-data/secondary_structure.gff3 test-data/solvent_accessibility.gff3
diffstat 5 files changed, 98 insertions(+), 55 deletions(-) [+]
line wrap: on
line diff
--- a/reprof.py	Mon Nov 30 20:10:58 2015 -0500
+++ b/reprof.py	Wed Dec 02 15:01:36 2015 -0500
@@ -13,7 +13,7 @@
 def run_reprof(query_path, modeldir):
     outtmp = tempfile.NamedTemporaryFile(delete=False)
     cmd = [
-        './reprof/scripts/reprof',
+        'reprof',
         '-i', query_path,
         '--modeldir=%s' % modeldir,
         '-o', outtmp.name
@@ -75,6 +75,22 @@
     with open(path, 'a') as handle:
         GFF.write([rec], handle)
 
+def storeClassData(path, id, phel):
+    h = float(phel.count('H')) / float(len(phel))
+    e = float(phel.count('E')) / float(len(phel))
+
+    if h > .45 and e < .05:
+        classification = 'all-alpha'
+    elif h < .05 and e > .45:
+        classification = 'all-beta'
+    elif h > .3 and e > .2:
+        classification = 'alpha-beta'
+    else:
+        classification = 'mixed'
+
+    with open(path, 'a') as handle:
+        handle.write("{0}\t{1}\n".format(id, classification))
+
 def main(fasta, modeldir):
     for record in SeqIO.parse(fasta, 'fasta'):
         tmp = tempfile.NamedTemporaryFile(delete=False)
@@ -86,23 +102,24 @@
         for col in ('RI_S', 'P10', 'RI_A', 'PACC', 'PREL', 'pH', 'pE', 'pL'):
             storeWigData(data['idx'], data[col], record.id, col + '.wig')
 
+        eco = ['{ECO:0000255|reprof_1.0.1}']
         storeGff3Data(
             'secondary_structure.gff3', record.id, data['idx'], data['PHEL'],
             {
                 'H': {
                     'type': 'peptide_helix',
-                    'label': ['Helix'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Helix'],
+                    'evidence': eco,
                 },
                 'E': {
                     'type': 'beta_strand',
-                    'label': ['Extended/Sheet'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Extended/Sheet'],
+                    'evidence': eco,
                 },
                 'L': {
                     'type': 'loop',
-                    'label': ['Loop'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Loop'],
+                    'evidence': eco,
                 }
             }
         )
@@ -112,17 +129,19 @@
             {
                 'B': {
                     'type': 'experimental_result_region',
-                    'label': ['Buried'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Buried'],
+                    'evidence': eco,
                 },
                 'E': {
                     'type': 'experimental_result_region',
-                    'label': ['Exposed'],
-                    'evidence': ['ECO:0000255']
+                    'description': ['Exposed'],
+                    'evidence': eco,
                 },
             }
         )
 
+        storeClassData('report.tsv', record.id, data['PHEL'])
+
 
 if __name__ == '__main__':
     # Grab all of the filters from our plugin loader
--- a/reprof.xml	Mon Nov 30 20:10:58 2015 -0500
+++ b/reprof.xml	Wed Dec 02 15:01:36 2015 -0500
@@ -54,6 +54,28 @@
 Three states of secondary structure are predicted: helix (H; includes alpha-,
 pi- and 3_10-helix), (beta-)strand (E = extended strand in beta-sheet
 conformation of at least two residues length) and loop (L).
+
+Protein Classification
+----------------------
+
+Proteins can be classified as mixed given the following classes:
+
+-  'all-alpha': %H > 45% AND %E < 5%
+-  'all-beta': %H < 5% AND %E > 45%
+-  'alpha-beta': %H > 30% AND %E > 20%
+-  'mixed': All others
+
+Gff3 Data and Evidence Codes
+----------------------------
+
+In order to facilitate interoperability with other downstream analyses, and to
+document provenance, the Galaxy tool author has opted to apply ECO:0000255 to
+all annotated features in the GFF3 file. Per the `UniPro Evidence page <http://www.uniprot.org/help/evidences#ECO:0000255>`__
+
+    The ECO code ECO:0000255 is also used for information which has been
+    generated by various sequence analysis programs that are used during the
+    manual curation process and which has been verified by a curator.
+
       ]]></help>
   <citations>
     <citation type="doi">10.1186/1471-2105-10-S13-O3</citation>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report.tsv	Wed Dec 02 15:01:36 2015 -0500
@@ -0,0 +1,2 @@
+test	all-alpha
+test2	all-alpha
--- a/test-data/secondary_structure.gff3	Mon Nov 30 20:10:58 2015 -0500
+++ b/test-data/secondary_structure.gff3	Wed Dec 02 15:01:36 2015 -0500
@@ -1,14 +1,14 @@
 ##gff-version 3
 ##sequence-region test 1 4
-test	feature	loop	1	3	.	.	.	evidence=ECO:0000255;label=Loop
-test	feature	peptide_helix	4	19	.	.	.	evidence=ECO:0000255;label=Helix
-test	feature	loop	20	24	.	.	.	evidence=ECO:0000255;label=Loop
-test	feature	peptide_helix	25	76	.	.	.	evidence=ECO:0000255;label=Helix
-test	feature	loop	77	78	.	.	.	evidence=ECO:0000255;label=Loop
+test	feature	loop	1	3	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
+test	feature	peptide_helix	4	19	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Helix
+test	feature	loop	20	24	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
+test	feature	peptide_helix	25	76	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Helix
+test	feature	loop	77	78	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
 ##gff-version 3
 ##sequence-region test2 1 4
-test2	feature	loop	1	4	.	.	.	evidence=ECO:0000255;label=Loop
-test2	feature	peptide_helix	5	64	.	.	.	evidence=ECO:0000255;label=Helix
-test2	feature	loop	65	68	.	.	.	evidence=ECO:0000255;label=Loop
-test2	feature	peptide_helix	69	75	.	.	.	evidence=ECO:0000255;label=Helix
-test2	feature	loop	76	78	.	.	.	evidence=ECO:0000255;label=Loop
+test2	feature	loop	1	4	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
+test2	feature	peptide_helix	5	64	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Helix
+test2	feature	loop	65	68	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
+test2	feature	peptide_helix	69	75	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Helix
+test2	feature	loop	76	78	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Loop
--- a/test-data/solvent_accessibility.gff3	Mon Nov 30 20:10:58 2015 -0500
+++ b/test-data/solvent_accessibility.gff3	Wed Dec 02 15:01:36 2015 -0500
@@ -1,38 +1,38 @@
 ##gff-version 3
 ##sequence-region test 1 4
-test	feature	experimental_result_region	1	6	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	7	14	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	15	16	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	17	17	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	18	29	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	30	30	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	31	33	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	34	34	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	35	36	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	37	37	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	38	40	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	41	41	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	42	54	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	55	55	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	56	64	.	.	.	evidence=ECO:0000255;label=Exposed
-test	feature	experimental_result_region	65	65	.	.	.	evidence=ECO:0000255;label=Buried
-test	feature	experimental_result_region	66	78	.	.	.	evidence=ECO:0000255;label=Exposed
+test	feature	experimental_result_region	1	6	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	7	14	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	15	16	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	17	17	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	18	29	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	30	30	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	31	33	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	34	34	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	35	36	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	37	37	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	38	40	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	41	41	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	42	54	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	55	55	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	56	64	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test	feature	experimental_result_region	65	65	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test	feature	experimental_result_region	66	78	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
 ##gff-version 3
 ##sequence-region test2 1 4
-test2	feature	experimental_result_region	1	8	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	9	9	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	10	12	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	13	13	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	14	22	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	23	23	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	24	26	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	27	27	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	28	36	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	37	37	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	38	40	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	41	41	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	42	50	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	51	58	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	59	61	.	.	.	evidence=ECO:0000255;label=Exposed
-test2	feature	experimental_result_region	62	62	.	.	.	evidence=ECO:0000255;label=Buried
-test2	feature	experimental_result_region	63	78	.	.	.	evidence=ECO:0000255;label=Exposed
+test2	feature	experimental_result_region	1	8	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	9	9	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	10	12	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	13	13	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	14	22	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	23	23	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	24	26	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	27	27	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	28	36	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	37	37	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	38	40	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	41	41	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	42	50	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	51	58	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	59	61	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed
+test2	feature	experimental_result_region	62	62	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Buried
+test2	feature	experimental_result_region	63	78	.	.	.	evidence={ECO:0000255|reprof_1.0.1};description=Exposed