Repository 'viennarna_rnaaliduplex'
hg clone https://toolshed.g2.bx.psu.edu/repos/rnateam/viennarna_rnaaliduplex

Changeset 2:d688747a6df9 (2017-05-16)
Previous changeset 1:f519bdc9085f (2016-12-21) Next changeset 3:2d43ce0c7006 (2017-07-12)
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna commit b'bd13ffd1c3e126a6dc59dd3c478347ec1b5824a3\n'
modified:
macros.xml
added:
rnafold_SHAPE.py
test-data/sample_3.fa
test-data/sample_3.react
test-data/sample_3_result.txt
b
diff -r f519bdc9085f -r d688747a6df9 macros.xml
--- a/macros.xml Wed Dec 21 17:33:46 2016 -0500
+++ b/macros.xml Tue May 16 16:31:59 2017 -0400
b
@@ -2,6 +2,7 @@
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.2.10">viennarna</requirement>
+            <yield/>
         </requirements>
     </xml>
     <token name="@VERSION@">2.2.10</token>
b
diff -r f519bdc9085f -r d688747a6df9 rnafold_SHAPE.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/rnafold_SHAPE.py Tue May 16 16:31:59 2017 -0400
[
@@ -0,0 +1,45 @@
+### overcoming the problem of SHAPE data working with a single line.
+### creating multiple multiple files containg SHAPE data for a single sequence and running RNAfold for every
+### single sequence.
+
+import os
+import sys
+from os import system
+from Bio import SeqIO
+import re
+from subprocess import Popen, PIPE
+
+params_list = sys.argv[1:]
+param_list_no_shape = [s for s in params_list if not "--shape=" in s ]
+shape_file = [s for s in params_list if "--shape=" in s ]
+assert (len(shape_file) == 1)
+
+shape_file = shape_file[0]
+shape_file = shape_file.replace('--shape=', '')
+
+params_no_shape  =  " ".join(str(x) for x in param_list_no_shape)
+
+pattern = re.compile("^>.*$")
+id_line = ""
+with open(shape_file, 'r') as f:
+    content = f.read()
+    lines = content.split('\n')
+    for line in lines:
+        if pattern.match(line):
+            id_line = line.split()[0]
+            id_line = id_line[1:]
+            continue
+        else:
+            with open(id_line +'.tmp', "a") as clFile:
+                clFile.write(line + "\n")
+                
+input_file = sys.stdin
+
+for record in SeqIO.parse(input_file, "fasta"):
+    seq = ">{}\n{}".format(record.id,record.seq)
+    cmd =  " RNAfold  --shape=" + record.id + '.tmp ' + params_no_shape
+    p = Popen(cmd , stdin=PIPE, shell=True, stdout=PIPE, stderr=PIPE)
+    out,err = p.communicate(seq.encode())
+    if err:
+        raise RuntimeError("Error in calling RNAfold\n{}\n{}\n".format(out, err))
+    print (out.decode('utf-8').strip())
b
diff -r f519bdc9085f -r d688747a6df9 test-data/sample_3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.fa Tue May 16 16:31:59 2017 -0400
b
@@ -0,0 +1,6 @@
+>SECIS_1 test
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+>6S_1 test1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
b
diff -r f519bdc9085f -r d688747a6df9 test-data/sample_3.react
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3.react Tue May 16 16:31:59 2017 -0400
b
@@ -0,0 +1,447 @@
+>SECIS_1
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+4 0.1391216354
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+>6S_1
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+192 0.093087642
+193 0.026770297
+194 0.1003921418
+195 0.731799564
+196 0.3882654324
+>6S_2
+1 5.135077189
+2 0.0137794619
+3 0.0198585136
+4 0.0394762621
+5 0.1032256038
+6 0.0124879331
+7 0.050343991
+8 0.0266906427
+9 0.0867862234
+10 0.0250443701
+11 0.1241682715
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+13 1.72206594665E-17
+14 0.0443782398
+15 0.0331749933
+16 1.190843321
+17 0.0083605324
+18 0.1025127456
+19 0.0318835351
+20 0.6764653014
+21 1.6659553696
+22 0.0532195755
+23 0.1306535914
+24 3.2368938797
+25 0.2999875752
+26 0.1771608894
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+28 1.1463641343
+29 0.3436951718
+30 0.6339043401
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+33 0.3413998482
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+185 0.208503114
\ No newline at end of file
b
diff -r f519bdc9085f -r d688747a6df9 test-data/sample_3_result.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_3_result.txt Tue May 16 16:31:59 2017 -0400
b
@@ -0,0 +1,9 @@
+>SECIS_1
+AUUUUAUCCAUGAAAGUGUUUCCUCUAAACCUAUGUGGAGGAACACCUGAUGUCCAGGAAAAU
+.((((...(((.(..(((.((((((((........))))))))))).).))).....)))).. (-27.97)
+>6S_1
+GAAACCCUAAUGUAUUCGAUAUAGUUCCUGAUAUUUUUGAACCGAACAAUUUUUUAUACCUAGGGAGCUUGGAGUUCCGGCGCGGCGCACAUGCCUUCACACGAGGAAGUGCAAACCGUUAGACAGAGCACCCACCUGCUUUAAUUGAGAGCGGGUUCAAAGGAAGGGAAUCCUAAACGGUACGAUUGGGGUUUCU
+(((((((...(((((.((.....((((((....((((((((((...................(((.((((.....((.((((.(..((((.(.((((.....))))).))))...))))).))..)))).)))....(((((.....))))).))))))))))..))))))......)))))))....))))))). (-110.38)
+>6S_2
+UUGUCCCUGCCGUGCUCGUGACUUGGCCAUACAUUCUCUGAACCUAUGUCUUACGGCAUAUGGGUUGCGGGAGUGUAGAGCUGGAGUGAUCGUCUACUCGUAGACGAACCCGAUGCUCUUCGGAUCGCGACCACCUUGAACCUCAGGGUUCGAGAUGCCGGCCUUGACGGCACAGGCGGGGCAUC
+.((.(((((((((((.(((.(...((((...((.((((.((((((..(((....))).....((((((((...((.(((((.((.((..((((((......))))))))))...))))).))..)))))))).............))))))))))))..)))).).))))))).))))))))).. (-129.27)