# HG changeset patch
# User earlhaminst
# Date 1526515437 14400
# Node ID 92f3966d5bc3b75bdea120639891a499d2f76425
# Parent  9ef7661e8e9c63b72e3968fec080dec7d0abe1ab
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gstf_preparation commit 88ba62ae8c3d9587a0015c72209242ad0c1df0c2

diff -r 9ef7661e8e9c -r 92f3966d5bc3 gstf_preparation.py
--- a/gstf_preparation.py	Wed Apr 25 11:06:03 2018 -0400
+++ b/gstf_preparation.py	Wed May 16 20:03:57 2018 -0400
@@ -1,6 +1,5 @@
 from __future__ import print_function
 
-import collections
 import json
 import optparse
 import sqlite3
@@ -9,7 +8,23 @@
 version = "0.4.0"
 gene_count = 0
 
-Sequence = collections.namedtuple('Sequence', ['header', 'sequence'])
+
+class Sequence(object):
+    def __init__(self, header, sequence_parts):
+        self.header = header
+        self.sequence_parts = sequence_parts
+        self._sequence = None
+
+    @property
+    def sequence(self):
+        if self._sequence is None:
+            self._sequence = ''.join(self.sequence_parts)
+        return self._sequence
+
+    def print(self, fh=sys.stdout):
+        print(self.header, file=fh)
+        for line in self.sequence_parts:
+            print(line, file=fh)
 
 
 def FASTAReader_gen(fasta_filename):
@@ -25,8 +40,7 @@
             while line and line[0] != '>':
                 sequence_parts.append(line.rstrip())
                 line = fasta_file.readline()
-            sequence = "\n".join(sequence_parts)
-            yield Sequence(header, sequence)
+            yield Sequence(header, sequence_parts)
 
 
 def create_tables(conn):
@@ -360,6 +374,10 @@
                 # Extract the transcript id by removing everything after the first space and then removing the version if it is an Ensembl id
                 transcript_id = remove_id_version(entry.header[1:].lstrip().split(' ')[0])
 
+                if len(entry.sequence) % 3 != 0:
+                    print("Transcript '%s' in file '%s' has a coding sequence length which is not multiple of 3" % (transcript_id, fasta_arg), file=sys.stderr)
+                    continue
+
                 gene_id = fetch_gene_id_for_transcript(conn, transcript_id)
                 if not gene_id:
                     print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr)
@@ -383,6 +401,10 @@
                 if options.longestCDS and transcript_id not in selected_transcript_ids:
                     continue
 
+                if len(entry.sequence) % 3 != 0:
+                    print("Transcript '%s' in file '%s' has a coding sequence length which is not multiple of 3" % (transcript_id, fasta_arg), file=sys.stderr)
+                    continue
+
                 species_for_transcript, seq_region_for_transcript = fetch_species_and_seq_region_for_transcript(conn, transcript_id)
                 if not species_for_transcript:
                     print("Transcript '%s' in file '%s' not found in the gene feature information" % (transcript_id, fasta_arg), file=sys.stderr)
@@ -391,14 +413,12 @@
                 if options.headers:
                     # Change the FASTA header to '>TranscriptId_species', as required by TreeBest
                     # Remove any underscore in the species
-                    header = ">%s_%s" % (transcript_id, species_for_transcript.replace('_', ''))
-                else:
-                    header = entry.header
+                    entry.header = ">%s_%s" % (transcript_id, species_for_transcript.replace('_', ''))
 
                 if seq_region_for_transcript.lower() in regions:
-                    filtered_fasta_file.write("%s\n%s\n" % (header, entry.sequence))
+                    entry.print(filtered_fasta_file)
                 else:
-                    output_fasta_file.write("%s\n%s\n" % (header, entry.sequence))
+                    entry.print(output_fasta_file)
 
     conn.close()
 
diff -r 9ef7661e8e9c -r 92f3966d5bc3 gstf_preparation.xml
--- a/gstf_preparation.xml	Wed Apr 25 11:06:03 2018 -0400
+++ b/gstf_preparation.xml	Wed May 16 20:03:57 2018 -0400
@@ -37,7 +37,7 @@
             </param>
         </repeat>
         <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
-        <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding FASTA datasets" help="Each FASTA header line should start with a transcript id" />
+        <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
         <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
         <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
         <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
@@ -111,7 +111,12 @@
 
 This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.
 
-It also filters a CDS FASTA dataset to keep only the transcripts present in the gene feature information. Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).
+It also filters the CDS FASTA datasets to:
+
+- remove coding sequences whose length is not a multiple of 3
+- keep only the transcripts present in the gene feature information.
+
+Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).
 
 Example GFF3 file::
 
diff -r 9ef7661e8e9c -r 92f3966d5bc3 test-data/test1.sqlite
Binary file test-data/test1.sqlite has changed
diff -r 9ef7661e8e9c -r 92f3966d5bc3 test-data/test4.fasta
--- a/test-data/test4.fasta	Wed Apr 25 11:06:03 2018 -0400
+++ b/test-data/test4.fasta	Wed May 16 20:03:57 2018 -0400
@@ -103,24 +103,6 @@
 GTTCCAGCTTTTGAGATCACCCGCACCTTCTGGGAGAGAAACCTGCCTTCCGTGACCGGG
 CTGCTTAAGATCATCGGATTTTCCACCTCGGTAACTGCCCTGTGGCTTGCCGTGTACAAA
 TTCAGGCTGCTGACCCGATCCTGA
->ENSSSCT00000035258_susscrofa
-TCGCTGCCCGCCATCATGGGCTTCATCCTTGCTCGAAAAGCTGACCGCCTTGCTAAGGTT
-CATAAAGAAATAAGAAAGCGGAAAATCTGTGAGCTCTACGCCAAAGTGCTAGGATCTCAA
-GAAGCTTTACATCCCGTGCACTATGAAGAGAAGAACTGGTGTGAGGAGCAGTACTCGGGG
-GGCTGCTACACTGCCTACTTCCCCCCTGGGATCATGACTCAGTATGGAAGGGTGATCCGC
-CAGCCCGTAGGCAGGATATTCTTTGCTGGCACCGAGACTGCCACACAATGGAGCGGTTAC
-ATGGAAGGAGCAGTAGAAGCCGGCGAACGGGCGGCTAGAGAGGATGTTCCAGCTTTTGAG
-ATCACCCGCACCTTCTGGGAGAGAAACCTGCCTTCCGTGACCGGGCTGCTTAAGATCATC
-GGATTTTCCA
->ENSSSCT00000032764_susscrofa
-ATGGATGACATGGGAAAGAAGATTCCAGCTGATGCACCATGGGAGTCTCCGCATGCAGAG
-GAATGGGATAAGATGACCATGAAAGATCTCATCGATAAAATCTGTTGGACAAAGACTGCT
-AAACGGTTTGCATCTCTCTTTGTAAATATCAATGTGACCTCCGAACCCCACGAAGTGTCT
-GCCCTGTGGTTTTTGTGGTATGTGAAGCAGTGTGGAGGCACCACCCGGATATTCTCTGTT
-ACCAACGGGGGCCAGGAACGGAAGTTTGTAGGCGGATCTGGTCAAGTAAGCGAACGGATA
-ATGCACCTCCTCGGGGACAGAGTGAAGCTGAGGTGTCCTGTCACCTATGTTGACCAGTCA
-GGTGACAACATCATCGTAGAGACATTGAATCATGAACTTTATGAGTGCCAATACGTAATT
-AGTGCCATCCCTCCAACTCT
 >ENSCAFT00000022939_canisfamiliaris
 ATGGCGAGTAGAGAGAAGACGAGTATCGAGGGCCACATGTTTGACGTAGTCGTGATAGGA
 GGCGGCATCTCAGGATTGTCTGCTGCCAAACTCTTAGCCGAACATGAAGTTGATGTCTTA
diff -r 9ef7661e8e9c -r 92f3966d5bc3 test-data/test4.sqlite
Binary file test-data/test4.sqlite has changed
diff -r 9ef7661e8e9c -r 92f3966d5bc3 test-data/test5.ns.fasta
--- a/test-data/test5.ns.fasta	Wed Apr 25 11:06:03 2018 -0400
+++ b/test-data/test5.ns.fasta	Wed May 16 20:03:57 2018 -0400
@@ -103,24 +103,6 @@
 GTTCCAGCTTTTGAGATCACCCGCACCTTCTGGGAGAGAAACCTGCCTTCCGTGACCGGG
 CTGCTTAAGATCATCGGATTTTCCACCTCGGTAACTGCCCTGTGGCTTGCCGTGTACAAA
 TTCAGGCTGCTGACCCGATCCTGA
->ENSSSCT00000035258_susscrofa
-TCGCTGCCCGCCATCATGGGCTTCATCCTTGCTCGAAAAGCTGACCGCCTTGCTAAGGTT
-CATAAAGAAATAAGAAAGCGGAAAATCTGTGAGCTCTACGCCAAAGTGCTAGGATCTCAA
-GAAGCTTTACATCCCGTGCACTATGAAGAGAAGAACTGGTGTGAGGAGCAGTACTCGGGG
-GGCTGCTACACTGCCTACTTCCCCCCTGGGATCATGACTCAGTATGGAAGGGTGATCCGC
-CAGCCCGTAGGCAGGATATTCTTTGCTGGCACCGAGACTGCCACACAATGGAGCGGTTAC
-ATGGAAGGAGCAGTAGAAGCCGGCGAACGGGCGGCTAGAGAGGATGTTCCAGCTTTTGAG
-ATCACCCGCACCTTCTGGGAGAGAAACCTGCCTTCCGTGACCGGGCTGCTTAAGATCATC
-GGATTTTCCA
->ENSSSCT00000032764_susscrofa
-ATGGATGACATGGGAAAGAAGATTCCAGCTGATGCACCATGGGAGTCTCCGCATGCAGAG
-GAATGGGATAAGATGACCATGAAAGATCTCATCGATAAAATCTGTTGGACAAAGACTGCT
-AAACGGTTTGCATCTCTCTTTGTAAATATCAATGTGACCTCCGAACCCCACGAAGTGTCT
-GCCCTGTGGTTTTTGTGGTATGTGAAGCAGTGTGGAGGCACCACCCGGATATTCTCTGTT
-ACCAACGGGGGCCAGGAACGGAAGTTTGTAGGCGGATCTGGTCAAGTAAGCGAACGGATA
-ATGCACCTCCTCGGGGACAGAGTGAAGCTGAGGTGTCCTGTCACCTATGTTGACCAGTCA
-GGTGACAACATCATCGTAGAGACATTGAATCATGAACTTTATGAGTGCCAATACGTAATT
-AGTGCCATCCCTCCAACTCT
 >ENSCAFT00000022939_canisfamiliaris
 ATGGCGAGTAGAGAGAAGACGAGTATCGAGGGCCACATGTTTGACGTAGTCGTGATAGGA
 GGCGGCATCTCAGGATTGTCTGCTGCCAAACTCTTAGCCGAACATGAAGTTGATGTCTTA
diff -r 9ef7661e8e9c -r 92f3966d5bc3 test-data/test5.sqlite
Binary file test-data/test5.sqlite has changed