Add samples from FormatSpecimens.jl repo

Cargo.toml

@@ -28,9 +28,8 @@ criterion = "0.3"
 bio = "0.28"
 seq_io = "0.3"
 
-# for testing with the FormatSpecimens.jl repo
-reqwest = "0.9"
-toml = "0.4"
+# for testing with the FormatSpecimens.jl repo samples
+toml = "0.5"
 serde = "1.0"
 serde_derive = "1.0"
 

tests/format_specimens.rs

@@ -1,8 +1,8 @@
+use std::fs;
 use std::io::Read;
 
 use needletail::formats::{FastaParser, FastqParser, RecParser};
 use needletail::{ParseError, ParseErrorType};
-use reqwest::get;
 use serde_derive::Deserialize;
 use toml;
 
@@ -33,33 +33,6 @@ fn test_fasta_file(reader: &mut dyn Read, filename: &str) -> Result<(), ParseErr
     Ok(())
 }
 
-#[test]
-#[ignore]
-fn test_specimen_fasta() {
-    let base_path = "https://raw.githubusercontent.com/BioJulia/FormatSpecimens.jl/master/FASTA";
-    let idx_path = format!("{}/index.toml", base_path);
-    let raw_index = get(&idx_path)
-        .expect("Could not retrieve index")
-        .text()
-        .expect("Could not decode index");
-
-    let index: TestIndex = toml::from_str(&raw_index).expect("Could not deserialize index");
-    for test in index.valid {
-        // what kind of sicko puts comments in FASTAs?
-        if test
-            .tags
-            .unwrap_or_else(Vec::new)
-            .contains(&String::from("comments"))
-        {
-            continue;
-        }
-
-        let test_path = format!("{}/{}", base_path, test.filename);
-        let mut test_reader = get(&test_path).expect("Could not retrieve test data");
-        assert_eq!(test_fasta_file(&mut test_reader, &test.filename), Ok(()));
-    }
-}
-
 fn test_fastq_file(reader: &mut dyn Read, filename: &str) -> Result<(), ParseError> {
     let mut data: Vec<u8> = Vec::new();
     let _ = reader.read_to_end(&mut data)?;
@@ -85,15 +58,28 @@ fn test_fastq_file(reader: &mut dyn Read, filename: &str) -> Result<(), ParseErr
 }
 
 #[test]
-#[ignore]
-fn test_specimen_fastq() {
-    let base_path = "https://raw.githubusercontent.com/BioJulia/FormatSpecimens.jl/master/FASTQ/";
-    let idx_path = format!("{}/index.toml", base_path);
-    let raw_index = get(&idx_path)
-        .expect("Could not retrieve index")
-        .text()
-        .expect("Could not decode index");
+fn test_specimen_fasta() {
+    let raw_index = fs::read_to_string("tests/specimen/FASTA/index.toml").unwrap();
+    let index: TestIndex = toml::from_str(&raw_index).expect("Could not deserialize index");
+    for test in index.valid {
+        // what kind of sicko puts comments in FASTAs?
+        if test
+            .tags
+            .unwrap_or_else(Vec::new)
+            .contains(&String::from("comments"))
+        {
+            continue;
+        }
+
+        let mut test_content =
+            fs::File::open(&format!("tests/specimen/FASTA/{}", test.filename)).unwrap();
+        assert_eq!(test_fasta_file(&mut test_content, &test.filename), Ok(()));
+    }
+}
 
+#[test]
+fn test_specimen_fastq() {
+    let raw_index = fs::read_to_string("tests/specimen/FASTQ/index.toml").unwrap();
     let index: TestIndex = toml::from_str(&raw_index).expect("Could not deserialize index");
 
     for test in index.valid {
@@ -102,10 +88,10 @@ fn test_specimen_fastq() {
             // (sequences are one-line, but quality scores are line-wrapped)
             continue;
         }
-        let test_path = format!("{}/{}", base_path, test.filename);
-        let mut test_reader = get(&test_path).expect("Could not retrieve test data");
+        let mut test_content =
+            fs::File::open(&format!("tests/specimen/FASTQ/{}", test.filename)).unwrap();
         assert_eq!(
-            test_fastq_file(&mut test_reader, &test.filename),
+            test_fastq_file(&mut test_content, &test.filename),
             Ok(()),
             "File {} is bad?",
             test.filename
@@ -117,10 +103,10 @@ fn test_specimen_fastq() {
             // we don't care if the sequence ID doesn't match the quality id?
             continue;
         }
-        let test_path = format!("{}/{}", base_path, test.filename);
-        let mut test_reader = get(&test_path).expect("Could not retrieve test data");
+        let mut test_content =
+            fs::File::open(&format!("tests/specimen/FASTQ/{}", test.filename)).unwrap();
         assert!(
-            test_fastq_file(&mut test_reader, &test.filename).is_err(),
+            test_fastq_file(&mut test_content, &test.filename).is_err(),
             format!("File {} is good?", test.filename)
         );
     }

tests/specimen/FASTA/AAC12660.fasta

@@ -0,0 +1,10 @@
+>AAC12660 TAK1 binding protein [Homo sapiens]. 
+MAAQRRSLLQSEQQPSWTDDLPLCHLSGVGSASNRSYSADGKGTESHPPEDSWLKFRSEN
+NCFLYGVFNGYDGNRVTNFVAQRLSAELLLGQLNAEHAEADVRRVLLQAFDVVERSFLES
+IDDALAEKASLQSQLPEGVPQHQLPPQYQKILERLKTLEREISGGAMAVVAVLLNNKLYV
+ANVGTNRALLCKSTVDGLQVTQLNVDHTTENEDELFRLSQLGLDAGKIKQVGIICGQEST
+RRIGDYKVKYGYTDIDLLSAAKSKPIIAEPEIHGAQPLDGVTGFLVLMSEGLYKALEAAH
+GPGQANQEIAAMIDTEFAKQTSLDAVAQAVVDRVKRIHSDTFASGGERARFCPRHEDMTL
+LVRNFGYPLGEMSQPTPSPAPAAGGRVYPVSVPYSSAQSTSKTSVTLSLVMPSQGQMVNG
+AHSASTLDEATPTLTNQSPTLTLQSTNTHTQSSSSSSDGGLFRSRPAHSLPPGEDGRVEP
+YVDFAEFYRLWSVDHGEQSVVTAP

tests/specimen/FASTA/EFTU_BACSU.fasta

@@ -0,0 +1,8 @@
+>sp|P33166|EFTU_BACSU Elongation factor Tu;
+MAKEKFDRSKSHANIGTIGHVDHGKTTLTAAITTVLHKKSGKGTAMAYDQIDGAPEERER
+GITISTAHVEYETETRHYAHVDCPGHADYVKNMITGAAQMDGAILVVSAADGPMPQTREH
+ILLSKNVGVPYIVVFLNKCDMVDDEELLELVEMEVRDLLSEYDFPGDDVPVVKGSALKAL
+EGDAEWEAKIFELMDAVDEYIPTPERDTEKPFMMPVEDVFSITGRGTVATGRVERGQVKV
+GDEVEIIGLQEENKKTTVTGVEMFRKLLDYAEAGDNIGALLRGVSREEIQRGQVLAKPGT
+ITPHSKFKAEVYVLSKEEGGRHTPFFSNYRPQFYFRTTDVTGIIHLPEGVEMVMPGDNTE
+MNVELISTIAIEEGTRFSIREGGRTVGSGVVSTITE

tests/specimen/FASTA/HUMBETGLOA.fasta

@@ -0,0 +1,52 @@
+>HUMBETGLOA Human haplotype C4 beta-globin gene, complete cds. 
+ACCTCCTATTTGACACCACTGATTACCCCATTGATAGTCACACTTTGGGTTGTAAGTGAC
+TTTTTATTTATTTGTATTTTTGACTGCATTAAGAGGTCTCTAGTTTTTTACCTCTTGTTT
+CCCAAAACCTAATAAGTAACTAATGCACAGAGCACATTGATTTGTATTTATTCTATTTTT
+AGACATAATTTATTAGCATGCATGAGCAAATTAAGAAAAACAACAACAAATGAATGCATA
+TATATGTATATGTATGTGTGTACATATACACATATATATATATATATATTTTTTCTTTTC
+TTACCAGAAGGTTTTAATCCAAATAAGGAGAAGATATGCTTAGAACTGAGGTAGAGTTTT
+CATCCATTCTGTCCTGTAAGTATTTTGCATATTCTGGAGACGCAGGAAGAGATCCATCTA
+CATATCCCAAAGCTGAATTATGGTAGACAAAACTCTTCCACTTTTAGTGCATCAACTTCT
+TATTTGTGTAATAAGAAAATTGGGAAAACGATCTTCAATATGCTTACCAAGCTGTGATTC
+CAAATATTACGTAAATACACTTGCAAAGGAGGATGTTTTTAGTAGCAATTTGTACTGATG
+GTATGGGGCCAAGAGATATATCTTAGAGGGAGGGCTGAGGGTTTGAAGTCCAACTCCTAA
+GCCAGTGCCAGAAGAGCCAAGGACAGGTACGGCTGTCATCACTTAGACCTCACCCTGTGG
+AGCCACACCCTAGGGTTGGCCAATCTACTCCCAGGAGCAGGGAGGGCAGGAGCCAGGGCT
+GGGCATAAAAGTCAGGGCAGAGCCATCTATTGCTTACATTTGCTTCTGACACAACTGTGT
+TCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGAGGAGAAGTCTGCCGT
+TACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTT
+GGTATCAAGGTTACAAGACAGGTTTAAGGAGACCAATAGAAACTGGGCATGTGGAGACAG
+AGAAGACTCTTGGGTTTCTGATAGGCACTGACTCTCTCTGCCTATTGGTCTATTTTCCCA
+CCCTTAGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATC
+TGTCCACTCCTGATGCTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGC
+TCGGTGCCTTTAGTGATGGCCTGGCTCACCTGGACAACCTCAAGGGCACCTTTGCCACAC
+TGAGTGAGCTGCACTGTGACAAGCTGCACGTGGATCCTGAGAACTTCAGGGTGAGTCTAT
+GGGACCCTTGATGTTTTCTTTCCCCTTCTTTTCTATGGTTAAGTTCATGTCATAGGAAGG
+GGATAAGTAACAGGGTACAGTTTAGAATGGGAAACAGACGAATGATTGCATCAGTGTGGA
+AGTCTCAGGATCGTTTTAGTTTCTTTTATTTGCTGTTCATAACAATTGTTTTCTTTTGTT
+TAATTCTTGCTTTCTTTTTTTTTCTTCTCCGCAATTTTTACTATTATACTTAATGCCTTA
+ACATTGTGTATAACAAAAGGAAATATCTCTGAGATACATTAAGTAACTTAAAAAAAAACT
+TTACACAGTCTGCCTAGTACATTACTATTTGGAATATATGTGTGCTTATTTGCATATTCA
+TAATCTCCCTACTTTATTTTCTTTTATTTTTAATTGATACATAATCATTATACATATTTA
+TGGGTTAAAGTGTAATGTTTTAATATGTGTACACATATTGACCAAATCAGGGTAATTTTG
+CATTTGTAATTTTAAAAAATGCTTTCTTCTTTTAATATACTTTTTTGTTTATCTTATTTC
+TAATACTTTCCCTAATCTCTTTCTTTCAGGGCAATAATGATACAATGTATCATGCCTCTT
+TGCACCATTCTAAAGAATAACAGTGATAATTTCTGGGTTAAGGCAATAGCAATATCTCTG
+CATATAAATATTTCTGCATATAAATTGTAACTGATGTAAGAGGTTTCATATTGCTAATAG
+CAGCTACAATCCAGCTACCATTCTGCTTTTATTTTATGGTTGGGATAAGGCTGGATTATT
+CTGAGTCCAAGCTAGGCCCTTTTGCTAATCATGTTCATACCTCTTATCTTCCTCCCACAG
+CTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCACCCCA
+CCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAG
+TATCACTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAG
+TCCAACTACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATA
+AAAAACATTTATTTTCATTGCAATGATGTATTTAAATTATTTCTGAATATTTTACTAAAA
+AGGGAATGTGGGAGGTCAGTGCATTTAAAACATAAAGAAATGAAGAGCTAGTTCAAACCT
+TGGGAAAATACACTATATCTTAAACTCCATGAAAGAAGGTGAGGCTGCAAACAGCTAATG
+CACATTGGCAACAGCCCTGATGCATATGCCTTATTCATCCCTCAGAAAAGGATTCAAGTA
+GAGGCTTGATTTGGAGGTTAAAGTTTTGCTATGCTGTATTTTACATTACTTATTGTTTTA
+GCTGTCCTCATGAATGTCTTTTCACTACCCATTTGCTTATCCTGCATCTCTCAGCCTTGA
+CTCCACTCAGTTCTCTTGCTTAGAGATACCACCTTTCCCCTGAAGTGTTCCTTCCATGTT
+TTACGGCGAGATGGTTTCTCCTCGCCTGGCCACTCAGCCTTAGTTGTCTCTGTTGTCTTA
+TAGAGGTCTACTTGAAGAAGGAAAAACAGGGGTCATGGTTTGACTGTCCTGTGAGCCCTT
+CTTCCCTGCCTCCCCCACTCACAGTGACCCGGAATCTGCAGTGCTAGTCTCCCGGAACTA
+TC

tests/specimen/FASTA/P02456.fasta

@@ -0,0 +1,2 @@
+>sp|P02456|CO1A1_RABIT Collagen alpha-1(I) chain (Fragment) OS=Oryctolagus cuniculus GN=COL1A1 PE=1 SV=1
+SYGYBZKSAGVSVPGPMGPSGPRGLPGPPGAPGPZGFZGPPGZPGZPGSSGPM

tests/specimen/FASTA/alnfile.fasta

@@ -0,0 +1,9 @@
+>BS1-fragment 7fab light chain variable region
+TISCTGSSSNIGAGNHVKWYQQLPG
+>BS2-fragment 2fb4 light chain variable region
+VTISCTGTSSNIGSITVNWYQQLPG
+>BS3-fragment 2fb4 heavy chain variable region
+LRLSCSSSGFIFSSYAMYWVRQAPG
+>BS4-fragment 7fab heavy chain variable region 
+LSLTCTVSGTSFDDYYSTWVRQPPG
+

tests/specimen/FASTA/amino.fasta

@@ -0,0 +1,10 @@
+>CYS1_DICDI fragment
+SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGE
+
+>ALEU_HORVU
+MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
+SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
+AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
+GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
+QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
+IATCASYPVVAA

tests/specimen/FASTA/aster.fasta

@@ -0,0 +1,3 @@
+>gi|3298468|dbj|BAA31520.1| SAMIPF
+GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVGVTNALVFEIV
+MTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI

tests/specimen/FASTA/badfasta.fasta

@@ -0,0 +1,27 @@
+>CEESC12R
+gcacgagtccatctccatatgccaccacaacantggtcctgtcgaaccaa
+caaccagcttggctcaatgacaaaatgcttcgcgcgccanaatgccaaca
+aatcccgtgccaccagagccaccggcgcgatatgcagatcataccgctgg
+aagacgatctcgatcgagccgtgcatccgatgggagaggaactctgaatg
+gcggactccatcaccggactagcggaagtcaacggtcggatagtccacct
+cacacagatgtgagctatgttcagcttcactcatccgatggaactggtag
+tagtaaggaaagaantngggagcggagaacaccaccgaataaa
+>CEESC13F
+cttgcttgaaaaatttatataaatatttaagagaagaaaaataaataatc
+gcatctaatgacgtctgtccttgtatccctggtttccattgactggtgca
+ctttcctgtctttgaggacatggacaatattcggcatcagttcctggctc
+tccctcctctcctggtgctccagcagaaccgttctctccattatctccct
+tgtctccacgtggtccacgctctcctggtgctcctggaataccttgagct
+ccctcgtgccgaattcctgcagcccgggggatccactagttctagagcgg
+ccgccaccgcggtgggagctccagcttttgttncctttagtgagggttaa
+
+tttcgagcttggcgtaatcatggtcatagctgtttcctg
+>CEESC13R
+gcacgagggagctcaaggtattccaggagcaccaggagagcgtggaccac
+gtggagacaagggagataatggagagaacggttctgctggagcaccagga
+
+gaggagggagagccaggaactgatgccgaatattgtccatgtcctcaaag
+acaggaaagtgcaccagtcaatggaaaccagggatacaagaacagacgtc
+attagatgcgattatttatttttcttctcttaaatatttatataaatttt
+tcaagcaag
+

tests/specimen/FASTA/bug2901.fasta

@@ -0,0 +1,8 @@
+>seq1
+GGTACCAGCAGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
+>seq2
+GGTACCAGCTGGTGGGCCGCCTACTGCGCACGCGCGGGTTTGCGGGCAGCCGC
+>seq3
+GGTACCAGCAGGTGGTCCGCCTA------------------------------
+>seq4
+--------------------------CGCACGCGCGTGTTTGCGGGCAGCCGC

tests/specimen/FASTA/centaurea.fasta

@@ -0,0 +1,18 @@
+>gi|4104054|gb|AH007193.1|SEG_CVIGS Centaurea vallesiaca 18S ribosomal RNA gene, partial sequence
+CCTGTCACTTAACTTTTTGTTCATAAGGTATATATGGGGGGGTGTGTGTCTTCGGACACACTTTCGATTG
+GGCCATGGTGCCCCCCTGCCAGGCAAAGGGATGCCTGGGCATGGCCACCCGGGAAAATGCGCTTCACTTC
+TTGCATGCCAGTCGTTTTTAAAAACGGCTGCGGCTCGTGTATCGTATTTTCCCCGGGATCGGTGACGCTT
+AGATGACGACGGCCCTTGACGGATATAGATGAAGGAATTGACGGATATGCAGATCGGTTGCCTATTGACC
+CTTGTCGNTACTATGTAGGCTACATCCCGGTCATGGTGGGTTCGATTGTGGGTTTGTTACTTTCGCATCG
+TTCGGTGCATTTTGGGGGCTGTTTTGGCTTTTCGTTGCTTGCTTGACCTTTTTTGGTTGGGTGGGTGGCT
+TCTAGTTGGGCGGCTTTCGGGAATGTCGACCGGGGAGGTGCATGAGTGGTGATTGGTATGTTACGTGTGG
+ATGGCTGTTTGCTCGCGCACCAACGTTCACGCTTCATACCTCTTCAGTTTTGCGTCAAGACTTGATTTGT
+CTTGAGCAATGTCGTGGGTTTCCTGTGTTGCATACCTAATTGACGGTAACGTGTGGGCTTTACGGTTATC
+TATTTCGTCATGTGTCGTTCATGCGGCGTGGGATGAACAATGAAACGGCCTTTGTGATCCACAGTGGTGT
+TGCGTTTGCAACAACGATGTGGCCTATGAAGCATCGTTTGGTCTCTTGTATACGGAACCTGATGTGGGCA
+TGGGTCTTCATAAGATCTTCATTATGCCCTCGTTAAGCGTTCTCGCTTCTCCAAAACGATTGCCTGCCAT
+GTTACGGCTTTGTTCGTTCATGGTGGGCTACGTCGAAGAGGAATGCTACCTGGTTGATCCTGCCAGTAGT
+CATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTACGAACAAATTCAGACTGTGAAACTGCGAA
+TGGCTCATTAAATCAGTTAGAG
+
+

tests/specimen/FASTA/cysprot.fasta

@@ -0,0 +1,58 @@
+>CYS1_DICDI
+MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
+ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
+SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
+ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
+PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
+
+
+>ALEU_HORVU
+MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
+SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
+AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
+GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
+QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
+IATCASYPVVAA
+
+
+>CATH_HUMAN
+MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN
+GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS
+CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK
+DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN
+HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV
+
+
+>CATH_RAT
+MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN
+HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW
+TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG
+QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA
+VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV
+
+
+>CATL_HUMAN
+MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK
+HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA
+FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES
+CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV
+VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
+
+
+>CATL_RAT
+MTPLLLLAVLCLGTALATPKFDQTFNAQWHQWKSTHRRLYGTNEEEWRRAVWEKNMRMIQLHNGEYSNGK
+HGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQIPKTVDWREKGCVTPVKNQGQCGSCWA
+FSASGCLEGQMFLKTGKLISLSEQNLVDCSHDQGNQGCNGGLMDFAFQYIKENGGLDSEESYPYEAKDGS
+CKYRAEYAVANDTGFVDIPQQEKALMKAVATVGPISVAMDASHPSLQFYSSGIYYEPNCSSKDLDHGVLV
+VGYGYEGTDSNKDKYWLVKNSWGKEWGMDGYIKIAKDRNNHCGLATAASYPIVN
+
+
+>PAPA_CARPA
+MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFE
+IFKDNLKYIDETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDW
+RQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQ
+YGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGG
+IFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
+
+
+

tests/specimen/FASTA/cysprot1.fasta

@@ -0,0 +1,6 @@
+>CYS1_DICDI
+MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
+ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
+SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
+ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
+PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII

tests/specimen/FASTA/cysprot1a.fasta

@@ -0,0 +1,24 @@
+>CYS1_DICDI
+MKVILLFVLAVFTVFVSSRGIPPEEQSQFLEFQDKFNKKYSHEEYLERFEIFKSNLGKIEELNLIAINHK
+ADTKFGVNKFADLSSDEFKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRGAVTPVKNQGQCG
+SCWSFSTTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQT
+ESSYPYTAETGTQCNFNSANIGAKISNFTMIPKNETVMAGYIVSTGPLAIAADAVEWQFYIGGVFDIPCN
+PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQGYIYLRRGKNTCGVSNFVSTSII
+
+
+>ALEU_HORVU
+MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGK
+SYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRD
+AAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNG
+GLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAF
+QVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCA
+IATCASYPVVAA
+
+
+>CATH_HUMAN
+MWATLPLLCAGAWLLGVPVCGAAELSVNSLEKFHFKSWMSKHRKTYSTEEYHHRLQTFASNWRKINAHNN
+GNHTFKMALNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPPSVDWRKKGNFVSPVKNQGACGS
+CWTFSTTGALESAIAIATGKMLSLAEQQLVDCAQDFNNYGCQGGLPSQAFEYILYNKGIMGEDTYPYQGK
+DGYCKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVTQDFMMYRTGIYSSTSCHKTPDKVN
+HAVLAVGYGEKNGIPYWIVKNSWGPQWGMNGYFLIERGKNMCGLAACASYPIPLV
+