Mercurial > repos > galaxy-australia > alphafold2

changeset 18:e4a053d67e24 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ef97511263dcac81f8563ae6a98d1db2400fcf1d
author galaxy-australia
date Fri, 01 Sep 2023 00:09:46 +0000
parents 5b85006245f3
children 2f7702fd0a4c
files alphafold.xml scripts/validate_fasta.py
diffstat 2 files changed, 5 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/alphafold.xml	Wed May 31 01:30:22 2023 +0000
+++ b/alphafold.xml	Fri Sep 01 00:09:46 2023 +0000
@@ -3,7 +3,7 @@
     <macros>
       <token name="@TOOL_VERSION@">2.3.1</token>
       <token name="@TOOL_MINOR_VERSION@">2.3</token>
-      <token name="@VERSION_SUFFIX@">3</token>
+      <token name="@VERSION_SUFFIX@">4</token>
       <import>macro_output.xml</import>
       <import>macro_test_output.xml</import>
     </macros>
--- a/scripts/validate_fasta.py	Wed May 31 01:30:22 2023 +0000
+++ b/scripts/validate_fasta.py	Fri Sep 01 00:09:46 2023 +0000
@@ -6,6 +6,7 @@
 from typing import List
 
 MULTIMER_MAX_SEQUENCE_COUNT = 10
+STRIP_SEQUENCE_CHARS = ['\n', '\r', '\t', ' ']
 
 
 class Fasta:
@@ -67,6 +68,9 @@
                 fasta_count = len(self.fastas)
                 header = f'>sequence_{fasta_count}'
 
+            for char in STRIP_SEQUENCE_CHARS:
+                sequence = sequence.replace(char, '')
+
             # Create new Fasta
             self.fastas.append(Fasta(header, sequence))
 
@@ -109,7 +113,6 @@
                     'Multimer mode requires multiple input sequence.'
                     f' Only {fasta_count} sequences were detected in'
                     ' the provided file.')
-                self.fasta_list = self.fasta_list
 
             elif fasta_count > MULTIMER_MAX_SEQUENCE_COUNT:
                 sys.stderr.write(