Mercurial > repos > dcorreia > phylogeny_tools

changeset 41:b00618525fd7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 602afc51566ada2f473c4a799c2ba3156eeac76a
author dcorreia
date Tue, 08 Nov 2016 12:18:28 -0500
parents 555f93dfe6cb
children 819529b8d1f3
files fasta2phylip/fasta_to_phylip.py gblock/gblocks.xml gblock/gblocks_onclick.xml muscle/muscle.xml tool_dependencies.xml
diffstat 5 files changed, 15 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/fasta2phylip/fasta_to_phylip.py	Mon Nov 07 08:41:29 2016 -0500
+++ b/fasta2phylip/fasta_to_phylip.py	Tue Nov 08 12:18:28 2016 -0500
@@ -104,30 +104,27 @@
 
     def write_phylip_relaxed_interleave(self, path):
 
-        wrap_length = 80
+        wrap_length = self.name_length - 80
         nb_chunk = 0
 
         with open(path, "w") as f:
             f.write("%s %s\n" % (len(self), self.seqs_length))
 
-            while ((nb_chunk * wrap_length) - self.name_length) < self.seqs_length:
+            while (nb_chunk * wrap_length) < self.seqs_length:
                 for seq in self.sequences:
 
                     if nb_chunk == 0:
-                        chunk_seq = seq.seq[0: (wrap_length - self.name_length)]
 
-                        seq_name = seq.name[:self.name_length].replace(' ', '_')
-                        seq_name = seq_name.ljust(self.name_length)
-
-                        f.write(seq_name)
-                        f.write("%s" % chunk_seq)
-                        f.write("\n")
+                        seq_name = seq.name[:self.name_length].replace(' ', '_') #cut too long name
+                        seq_name = seq_name.ljust(self.name_length) #extend too short name
 
                     else:
-                        chunk_seq = seq.seq[((wrap_length * nb_chunk) - self.name_length): (
-                        (wrap_length * (nb_chunk + 1)) - self.name_length)]
-                        f.write("%s" % chunk_seq)
-                        f.write("\n")
+                        seq_name = "".ljust(self.name_length)
+
+                    chunk_seq = seq.seq[nb_chunk*wrap_length: wrap_length]
+                    f.write(seq_name)
+                    f.write("%s" % chunk_seq)
+                    f.write("\n")
 
                 f.write("\n")
                 nb_chunk += 1
@@ -140,6 +137,7 @@
     parser.add_option("-i", "--input")
     parser.add_option("-o", "--output")
     parser.add_option("--sequencial", action='store_true')
+    parser.add_option("--interleave", action='store_true')
     # parse
     options, args = parser.parse_args()
 
--- a/gblock/gblocks.xml	Mon Nov 07 08:41:29 2016 -0500
+++ b/gblock/gblocks.xml	Tue Nov 08 12:18:28 2016 -0500
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="0.91b">gblocks</requirement>
     </requirements>
-    <command>gblocks 
+    <command>Gblocks
              $input 
              -b1=$b1
              -b2=$b2
--- a/gblock/gblocks_onclick.xml	Mon Nov 07 08:41:29 2016 -0500
+++ b/gblock/gblocks_onclick.xml	Tue Nov 08 12:18:28 2016 -0500
@@ -3,7 +3,7 @@
     <requirements>
         <requirement type="package" version="0.91b">gblocks</requirement>
     </requirements>
-    <command>gblocks 
+    <command>Gblocks
              $input 
              -b1=$b1
              -b2=$b2
@@ -70,7 +70,6 @@
     <tests>
         <test>
             <param name="input" value="nad3.pir"/>
-            <param name="" value="nad3.pir"/>
             <param name="output_aln" value="nad3.pir-gb"/>
             <param name="output_htm" value="nad3.pir-gb.htm"/>
         </test>
--- a/muscle/muscle.xml	Mon Nov 07 08:41:29 2016 -0500
+++ b/muscle/muscle.xml	Tue Nov 08 12:18:28 2016 -0500
@@ -63,10 +63,9 @@
     <tests>
         <test>
             <param name="input" value="seqtest.fasta"/>
-            <param name="output" value="seqtest.aln.fasta"/>
+            <param name="output" value="seqtest_aln.fasta"/>
         </test>
     </tests>
-
     <help>
 
 .. class:: infomark
--- a/tool_dependencies.xml	Mon Nov 07 08:41:29 2016 -0500
+++ b/tool_dependencies.xml	Tue Nov 08 12:18:28 2016 -0500
@@ -3,11 +3,8 @@
     <package name="clustalo" version="1.2.1">
         <repository changeset_revision="8e1916ccca9a" name="package_clustalo_1_2_1" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="biopython" version="1.66">
-        <repository changeset_revision="d86f7eb34488" name="package_biopython_1_66" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
     <package name="gblocks" version="0.91b">
-        <repository changeset_revision="fae18a731740" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="42c0927e0ce6" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 	<package name="muscle" version="3.8.31">
 		<repository changeset_revision="17c53de3f872" name="package_muscle_3_8_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />