update tests for different input processing

lib/Bio/PanGenome/PrepareInputFiles.pm

@@ -16,7 +16,7 @@ Take in a mixture of FASTA and GFF input files and output FASTA proteomes only
 
 use Moose;
 use Bio::PanGenome::Exceptions;
-use Bio::PanGenome::ExtractProteomeFromGFF;
+use Bio::PanGenome::ExtractProteomeFromGFFs;
 use Cwd;
 
 has 'input_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
@@ -25,7 +25,7 @@ has '_input_fasta_files' => ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, b
 has '_derived_fasta_files' =>
   ( is => 'ro', isa => 'Maybe[ArrayRef]', lazy => 1, builder => '_build__derived_fasta_files' );
 has '_extract_proteome_obj' =>
-  ( is => 'ro', isa => 'Bio::PanGenome::ExtractProteomeFromGFF', lazy => 1, builder => '_build__extract_proteome_obj' );
+  ( is => 'ro', isa => 'Bio::PanGenome::ExtractProteomeFromGFFs', lazy => 1, builder => '_build__extract_proteome_obj' );
 
 sub _build__input_gff_files {
     my ($self) = @_;
@@ -41,7 +41,7 @@ sub _build__input_fasta_files {
 
 sub _build__extract_proteome_obj {
     my ($self) = @_;
-    return Bio::PanGenome::ExtractProteomeFromGFF->new( gff_files => $self->_input_gff_files );
+    return Bio::PanGenome::ExtractProteomeFromGFFs->new( gff_files => $self->_input_gff_files );
 }
 
 sub _build__derived_fasta_files {

t/Bio/PanGenome/ExtractProteomeFromGFFs.t

@@ -20,12 +20,14 @@ ok(
     'initialise object'
 );
 
+my @sorted_fasta_files = sort(@{$plot_groups_obj->fasta_files()});
+my @sorted_expected_files = sort((
+$plot_groups_obj->_extract_proteome_objects->{'t/data/example_annotation_2.gff'}->_working_directory_name . '/example_annotation_2.faa',
+     $plot_groups_obj->_extract_proteome_objects->{'t/data/example_annotation.gff'}->_working_directory_name . '/example_annotation.faa',));
+
 is_deeply(
-    $plot_groups_obj->fasta_files(),
-    [
-        $plot_groups_obj->_extract_proteome_objects->{'t/data/example_annotation.gff'}->_working_directory_name . '/example_annotation.faa',
-        $plot_groups_obj->_extract_proteome_objects->{'t/data/example_annotation_2.gff'}->_working_directory_name . '/example_annotation_2.faa'
-    ],
+    \@sorted_fasta_files,
+\@sorted_expected_files,
     'one file created'
 );
 

t/Bio/PanGenome/PrepareInputFiles.t

@@ -23,20 +23,23 @@ ok(
     'initalise'
 );
 
+my @sorted_fasta_files = sort @{$obj->fasta_files};
+my @expected_fasta_files = sort((
+    't/data/example_1.faa',
+    't/data/example_2.faa',
+    $obj->_extract_proteome_obj->_extract_proteome_objects->{'t/data/example_annotation.gff'}->_working_directory_name . '/example_annotation.faa',
+    $obj->_extract_proteome_obj->_extract_proteome_objects->{'t/data/example_annotation_2.gff'}->_working_directory_name . '/example_annotation_2.faa'
+));
+
 is_deeply(
-    $obj->fasta_files,
-    [
-        't/data/example_1.faa',
-        't/data/example_2.faa',
-        $obj->_extract_proteome_obj->_working_directory_name . '/example_annotation.faa',
-        $obj->_extract_proteome_obj->_working_directory_name . '/example_annotation_2.faa'
-    ],
+    \@sorted_fasta_files,
+    \@expected_fasta_files,
     'proteome extracted from gff files, input fasta files left alone'
 );
 
 is_deeply(
     $obj->lookup_fasta_files_from_unknown_input_files( [ 't/data/example_annotation_2.gff', 't/data/example_1.faa' ] ),
-    [$obj->_extract_proteome_obj->_working_directory_name . '/example_annotation_2.faa','t/data/example_1.faa'],
+    [$obj->_extract_proteome_obj->_extract_proteome_objects->{'t/data/example_annotation_2.gff'}->_working_directory_name . '/example_annotation_2.faa','t/data/example_1.faa'],
     'previously created faa file looked up from gff filename'
 );
 

t/data/expected_example_annotation_1.faa

@@ -1,65 +1,30 @@
->abc_00001
-MKTRIVSSVTTTLLLGSILMNPVANAADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGM
-HKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNE
-VAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFK
-TILESPTDKKVGWKVIFNNMVNQNWGPYDRDSWNPVYGNQLFMKTRNGSMKAAENFLDPN
-KASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKW
-TDRSSERYKIDWEKEEMTN*
->abc_00002
+>abc_00001 [revcomp]:[translate(1)]
+MKTRIVSSVTTTLLLGSILMNPVANAADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWGPYDRDSWNPVYGNQLFMKTRNGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKASKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN*
+>abc_00002 [translate(1)]
 MKLFYIVFLIIIWLNIFLGNEIIHTLTVLITTLYIVNSRKGIKNDRVE*
->abc_00003
-MTELNNIINSLQSLFESESGYKISKNSGVPYQTVQDLRNGKTKLEDARFRTIIKLYSYYV
-SLKEH*
->abc_00004
-MSKNITKNIILTTTLLLLGTVLPQNQKPVFSFYSEAKAYSIGQDETNINELIKYYTQPHF
-SFSNKWLYQYDNGNIYVELKRYSWSAHISLWGAESWGNINQLKDRYVDVFGLKDKDTDQL
-WWSYRETFTGGVTPAAKPSDKTYNLFVQYKDKLQTIIGAHKIYQGNKPVLTLKEIDFRAR
-EALIKNKILYTENRNKGKLKITGGGNNYTIDLSKRLHSDLANVYVKNPNKITVDVLFD*
->abc_00005
-MNNNITKKIILSTTLLLLGTAFTQFPNTPINSSSEAKAYYINQNETNVNELTKYYSQKYL
-TFSNSTLWQKDNGTIHATLLQFSWYSHIQVYGPESWGNINQLRNKSVDIFGIKDQETIDS
-FALSQETFTGGVTPAATSNDKHYKLNVTYKDKAETFTGGFPVYEGNKPVLTLKELDFRIR
-QTLIKSKKLYNNSYNKGQIKITGTDNNYTIDLSKRLPSTDANRYVKKPQNAKIEVILEKS
-N*
->abc_00006
-MKKNIMNKLVLSTALLLLGTTSTQLPKTPISFSSEAKAYNISENETNINELIKYYTQPHF
-SLSGKWLWQKPNGSIHATLQTWVWYSHIQVFGSESWGNINQLRNKYVDIFGTKDEDTVEG
-YWTYDETFTGGVTPAATSSDKPYRLFLKYSDKQQTIIGGHEFYKGNKPVLTLKELDFRIR
-QTLIKNKKLYNGEFNKGQIKITADGNNYTIDLSKKLKLTDTNRYVKNPKNAQIEVILEKS
-N*
->abc_00007
-MKNLRNRSFLTLLDFSRQEVEFLLTLSEDLKRAKYIGTEKPMLKNKNIALLFEKDSTRTR
-CAFEVAAHDQGANVTYLGPTGSQMGKKETTKDTARVLGGMYDGIEYRGFSQRTVETLAEN
-SGVPVWNGLTDEDHPTQVLADFLTAKEVLKKDYADINFTYVGDGRNNVANALMQGAAIMG
-MNFHLVCPKELNPTDELLNRCKNIAAENGGNILITDDIDQGVKGSDVIYTDVWVSMGEPD
-EVWKERLELLKPYQVNKEMMDKTGNPNVIFEHCLPSFHNADTKIGQQIFEKYGIREMEVT
-DEVFESKASVVFQEAENRMHTIKAVMVATLGEF*
->abc_00008
-MMAKIVVALGGNALGKSPQEQLELVKNTAKSLVGLITKGHEIVISHGNGPQVGSINLGLN
-YAAEHNQGPAFPFAECGAMSQAYIGYQLQESLQNELHSIGMDKQVVTLVTQVEVDENDPA
-FNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKN
-DTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINF
-NTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAA
-LEGKVGTVIKK*
->abc_00010
-MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGV
-PSEMIKDRQRKNNGV*
->abc_00011
-MRLQKAPLVTSGLVLGLLGLGNLLKDLSLTLNAVCGIFAFLIWIHLLCTMIKYFNNVKEQ
-LNSPLVSSVFTTFFMSGFLGTTYLNTFFSNITFINSLITPIWILCLVGIMTHMIIFSIKY
-LKDFSLENVYPSWTVLFIGIAIAGLTAPVSGCFFIGQLTVIYGFVATCIVLPIVFKRLKA
-FPLQTSIKPNTSTICAPFSLVAAAYVIAFPKANAFIVIIFLILAQIFYFYIIIQLPKLLK
-EPFSPVFSAFTFPLVISATALKNSLPVLMFPDIWKGLLFIEVLLATVIVLRVFIGYLHFF
-LKKENQDKFLRNASQ*
->abc_00012
-MRNQIQKLLDSDLSSLHISKQTGVPQSTIHRMRKKERSLDNMSLKNAELLYKFANSIFSN
-EN*
->abc_00014
+>abc_00003 [translate(1)]
+MTELNNIINSLQSLFESESGYKISKNSGVPYQTVQDLRNGKTKLEDARFRTIIKLYSYYVSLKEH*
+>abc_00004 [revcomp]:[translate(1)]
+MSKNITKNIILTTTLLLLGTVLPQNQKPVFSFYSEAKAYSIGQDETNINELIKYYTQPHFSFSNKWLYQYDNGNIYVELKRYSWSAHISLWGAESWGNINQLKDRYVDVFGLKDKDTDQLWWSYRETFTGGVTPAAKPSDKTYNLFVQYKDKLQTIIGAHKIYQGNKPVLTLKEIDFRAREALIKNKILYTENRNKGKLKITGGGNNYTIDLSKRLHSDLANVYVKNPNKITVDVLFD*
+>abc_00005 [revcomp]:[translate(1)]
+MNNNITKKIILSTTLLLLGTAFTQFPNTPINSSSEAKAYYINQNETNVNELTKYYSQKYLTFSNSTLWQKDNGTIHATLLQFSWYSHIQVYGPESWGNINQLRNKSVDIFGIKDQETIDSFALSQETFTGGVTPAATSNDKHYKLNVTYKDKAETFTGGFPVYEGNKPVLTLKELDFRIRQTLIKSKKLYNNSYNKGQIKITGTDNNYTIDLSKRLPSTDANRYVKKPQNAKIEVILEKSN*
+>abc_00006 [revcomp]:[translate(1)]
+MKKNIMNKLVLSTALLLLGTTSTQLPKTPISFSSEAKAYNISENETNINELIKYYTQPHFSLSGKWLWQKPNGSIHATLQTWVWYSHIQVFGSESWGNINQLRNKYVDIFGTKDEDTVEGYWTYDETFTGGVTPAATSSDKPYRLFLKYSDKQQTIIGGHEFYKGNKPVLTLKELDFRIRQTLIKNKKLYNGEFNKGQIKITADGNNYTIDLSKKLKLTDTNRYVKNPKNAQIEVILEKSN*
+>abc_00007 [translate(1)]
+MKNLRNRSFLTLLDFSRQEVEFLLTLSEDLKRAKYIGTEKPMLKNKNIALLFEKDSTRTRCAFEVAAHDQGANVTYLGPTGSQMGKKETTKDTARVLGGMYDGIEYRGFSQRTVETLAENSGVPVWNGLTDEDHPTQVLADFLTAKEVLKKDYADINFTYVGDGRNNVANALMQGAAIMGMNFHLVCPKELNPTDELLNRCKNIAAENGGNILITDDIDQGVKGSDVIYTDVWVSMGEPDEVWKERLELLKPYQVNKEMMDKTGNPNVIFEHCLPSFHNADTKIGQQIFEKYGIREMEVTDEVFESKASVVFQEAENRMHTIKAVMVATLGEF*
+>abc_00008 [translate(1)]
+MMAKIVVALGGNALGKSPQEQLELVKNTAKSLVGLITKGHEIVISHGNGPQVGSINLGLNYAAEHNQGPAFPFAECGAMSQAYIGYQLQESLQNELHSIGMDKQVVTLVTQVEVDENDPAFNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKNDTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINFNTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAALEGKVGTVIKK*
+>abc_01705 [translate(1)]
+VENTINESEKKKRFKLKMPGAFMILFILTVVAVIATWVIPAGAYSKLSYEPSSQELKIVNPHNQVKKVPGTQQELDKMGVKIKIEQFKSGAINKPVSIPNTYERLKQHPAGPEQITSSMVEGTIEAVDIMVFILVLGGLIGVVQASGSFESGLLALTKKTKGHEFMLIVFVSILMIIGGTLCGIEEEAVAFYPILVPIFIALGYDSIVSVGAIFLASSVGSTFSTINPFSVVIASNAAGTTFTDGLYWRIGACIVGAIFVISYLYWYCKKIKNDPKASYSYEDKDAFEQQWSVLKDDDSAHFTLRKKIILTLFVLPFPIMVWGVMTQGWWFPVMASAFLIFTIIIMFIAGTGKSGLGEKGTVDAFVNGASSLVGVSLIIGLARGINLVLNEGMISDTILHFSSSLVQHMSGPLFIIVLLFIFFCLGFIVPSSSGLAVLSMPIFAPLADTVGIPRFVIVTTYQFGQYAMLFLAPTGLVMATLQMLNMRYSHWFRFVWPVVAFVLIFGGGVLITQVLIYS*
+>abc_00010 [translate(1)]
+MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGVPSEMIKDRQRKNNGV*
+>abc_00011 [revcomp]:[translate(1)]
+MRLQKAPLVTSGLVLGLLGLGNLLKDLSLTLNAVCGIFAFLIWIHLLCTMIKYFNNVKEQLNSPLVSSVFTTFFMSGFLGTTYLNTFFSNITFINSLITPIWILCLVGIMTHMIIFSIKYLKDFSLENVYPSWTVLFIGIAIAGLTAPVSGCFFIGQLTVIYGFVATCIVLPIVFKRLKAFPLQTSIKPNTSTICAPFSLVAAAYVIAFPKANAFIVIIFLILAQIFYFYIIIQLPKLLKEPFSPVFSAFTFPLVISATALKNSLPVLMFPDIWKGLLFIEVLLATVIVLRVFIGYLHFFLKKENQDKFLRNASQ*
+>abc_00012 [translate(1)]
+MRNQIQKLLDSDLSSLHISKQTGVPQSTIHRMRKKERSLDNMSLKNAELLYKFANSIFSNEN*
+>abc_00014 [translate(1)]
 MEGLFNAIKDTVTAAINNDGAKLGTSIVSIVENGVGLLGKLFGF*
->abc_00015
+>abc_00015 [translate(1)]
 MTGLAEAIANTVQAAQQHDSVKLGTSIVDIVANGVGLLGKLFGF*
->abc_00016
-LGYKNILIDFDDTIVDFYDAEEWAFHYMANVFNHKATKDDFLTFKKINHQHWEAFQQNKL
-TKSEVLSERFVNYFKHHQMEVDGHRADVLFRNGLAEAKVKYFDQTLETIVELSKRHDLYI
-VTNGVTETQKRRLNQTPLHKYIKKIFISEETGYQKPNPEFFNYVFNDIGEDERQHSIIVG
-DSLTSDILGGINAGIATCWFNFRGFDHNPGIIPDYEINSWKQLNDIVR*
+>abc_00016 [translate(1)]
+LGYKNILIDFDDTIVDFYDAEEWAFHYMANVFNHKATKDDFLTFKKINHQHWEAFQQNKLTKSEVLSERFVNYFKHHQMEVDGHRADVLFRNGLAEAKVKYFDQTLETIVELSKRHDLYIVTNGVTETQKRRLNQTPLHKYIKKIFISEETGYQKPNPEFFNYVFNDIGEDERQHSIIVGDSLTSDILGGINAGIATCWFNFRGFDHNPGIIPDYEINSWKQLNDIVR*