Now that Bio.Fasta is deprecated, must also deprecate the obsolete Bi…

…o.Align.FormatConvert module too

Bio/Align/FormatConvert.py

@@ -1,7 +1,7 @@
 """
-For conversion between different formats for representing alignments (OBSOLETE).
+For conversion between different formats for representing alignments (DEPRECATED).
 
-This module is considered obsolete and likely to be deprecated.  Please use
+This module is considered obsolete and has been deprecated.  Please use
 Bio.AlignIO instead for reading and writing alignments in different file
 formats.
 
@@ -13,6 +13,10 @@
 from Bio.Fasta.FastaAlign import FastaAlignment
 from Bio.Clustalw import ClustalAlignment
 
+import warnings
+warnings.warn("Bio.Align.FormatConvert is deprecated. Please use Bio.AlignIO "
+              "or the Alignment object's format method instead.",
+              DeprecationWarning)
 
 class FormatConverter:
     """Convert between different alignment representation formats.

DEPRECATED

@@ -106,6 +106,11 @@ Bio.Fasta (including Bio.Fasta.FastaAlign)
 Declared obsolete in Release 1.48, and deprecated in Release 1.51.
 Please use the "fasta" support in Bio.SeqIO or Bio.AlignIO instead.
 
+Bio.Align.FormatConvert
+=======================
+Declared obsolete in Release 1.48, and deprecated in Release 1.51.
+Please use Bio.AlignIO or the Alignment object's format method instead.
+
 Bio.Emboss.Primer
 =================
 Deprecated in Release 1.48, this parser was replaced by Bio.Emboss.Primer3

Tests/output/test_align

@@ -804,41 +804,37 @@ Q----VKGITNLDNLAMFNVSGPGMQGM---VGMASRVFSAMSGAGISVILITQSSSEYS
 AKGIAARF------FSALAQAN
 
 Test format conversion...
+As FASTA:
 >gi|6273285|gb|AF191659.1|AF191
 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
 ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCCATTGATTTAGTGTACCAGA
-
 >gi|6273284|gb|AF191658.1|AF191
 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATA--
 ------ATATATTTCAAATTTCCTTATATACCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
-
 >gi|6273287|gb|AF191661.1|AF191
 TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
 ------ATATATTTCAAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
-
 >gi|6273286|gb|AF191660.1|AF191
 TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATA----
 ------ATATATTTATAATTTCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
-
 >gi|6273290|gb|AF191664.1|AF191
 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
 ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
-
 >gi|6273289|gb|AF191663.1|AF191
 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
 ------ATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTATACCAGA
-
 >gi|6273291|gb|AF191665.1|AF191
 TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAATATATATATA
 TATATAATATATTTCAAATTCCCTTATATATCCAAATATAAAAATATCTAATAAATTAGA
 TGAATATCAAAGAATCTATTGATTTAGTGTACCAGA
 
+As Clustal:
 CLUSTAL X (1.81) multiple sequence alignment
 
 
@@ -849,6 +845,7 @@ gi|6273286|gb|AF191660.1|AF191      TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAG
 gi|6273290|gb|AF191664.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
 gi|6273289|gb|AF191663.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
 gi|6273291|gb|AF191665.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
+                                    ******* **** *************************************
 
 gi|6273285|gb|AF191659.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA
 gi|6273284|gb|AF191658.1|AF191      TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA
@@ -857,6 +854,7 @@ gi|6273286|gb|AF191660.1|AF191      TATATA----------ATATATTTATAATTTCCTTATATATCCA
 gi|6273290|gb|AF191664.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
 gi|6273289|gb|AF191663.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
 gi|6273291|gb|AF191665.1|AF191      TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA
+                                    ******          ********  **** ********* *********
 
 gi|6273285|gb|AF191659.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT
 gi|6273284|gb|AF191658.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
@@ -865,6 +863,7 @@ gi|6273286|gb|AF191660.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATT
 gi|6273290|gb|AF191664.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
 gi|6273289|gb|AF191663.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT
 gi|6273291|gb|AF191665.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
+                                    ************************************ *********** *
 
 gi|6273285|gb|AF191659.1|AF191      ACCAGA
 gi|6273284|gb|AF191658.1|AF191      ACCAGA
@@ -873,6 +872,7 @@ gi|6273286|gb|AF191660.1|AF191      ACCAGA
 gi|6273290|gb|AF191664.1|AF191      ACCAGA
 gi|6273289|gb|AF191663.1|AF191      ACCAGA
 gi|6273291|gb|AF191665.1|AF191      ACCAGA
+                                    ******
 
 
 

Tests/test_align.py

@@ -16,7 +16,6 @@
 from Bio import Seq
 from Bio.Alphabet import IUPAC
 from Bio import Clustalw
-from Bio.Align.FormatConvert import FormatConverter
 from Bio.Align import AlignInfo
 from Bio.Fasta import FastaAlign
 from Bio.SubsMat import FreqTable
@@ -159,13 +158,10 @@
 alignment = Clustalw.parse_file(os.path.join(os.curdir, 'Clustalw',
                                              'opuntia.aln'))
 
-converter = FormatConverter(alignment)
-
-fasta_align = converter.to_fasta()
-clustal_align = converter.to_clustal()
-
-print fasta_align
-print clustal_align
+print "As FASTA:"
+print alignment.format("fasta")
+print "As Clustal:"
+print alignment.format("clustal")
 
 """
 # test to find a position in an original sequence given a