Update handling of duplicates

src/aln.c

@@ -3,6 +3,7 @@
 #include <pthread.h>
 #include <stdio.h>
 #include <string.h>
+#include <sys/wait.h>
 #include <unistd.h>
 
 #include "aln.h"

src/pasv.c

@@ -113,7 +113,7 @@ get_aln_posns(char* aln_outfile,
       PANIC_IF(first_ref_seq_found > 1,
                STD_ERR,
                stderr,
-               "Found more than one key ref seq (%s) in file '%s'\n",
+               "Found more than one key ref seq '%s' in file '%s'\n",
                seq->name.s,
                aln_outfile);
 
@@ -123,11 +123,11 @@ get_aln_posns(char* aln_outfile,
     if (tmp_rseq->query_seq == 1) {
       ++query_seq_found;
 
-      PANIC_IF((query_seq_found > 1 && first_ref_seq_found == 0) ||
-               (query_seq_found > 2 && first_ref_seq_found == 1),
+      /* with the naming scheme there should only be one */
+      PANIC_IF(query_seq_found > 1,
                STD_ERR,
                stderr,
-               "Found more than one query seq (%s) in file '%s'\n",
+               "Found more than one pseudo query seq '%s' in file '%s'\n",
                seq->name.s,
                aln_outfile);
 
@@ -213,6 +213,7 @@ get_aln_posns(char* aln_outfile,
 int
 main(int argc, char *argv[])
 {
+  int ret_code = 0;
   tommy_hashlin* header2rseq = NULL;
   tommy_hashlin* type2fs = NULL;
   t2fs_t* t2fs = NULL;
@@ -232,11 +233,11 @@ main(int argc, char *argv[])
   char* query_fname = NULL;
 
   static char version_banner[] =
-    "  Version: 0.0.4\n"
+    "    Version: 0.0.5\n"
     "  Copyright: 2017 Ryan Moore\n"
-    "  Contact: [email protected]\n"
-    "  Website: https://github.com/mooreryan/pasv\n"
-    "  License: GPLv3\n";
+    "    Contact: [email protected]\n"
+    "    Website: https://github.com/mooreryan/pasv\n"
+    "    License: GPLv3\n";
 
   static char intro[] =
     "Trust the Process. Trust the PASV PVCpipe.";
@@ -265,7 +266,7 @@ main(int argc, char *argv[])
   /* TODO base this on actual doc str len */
   char doc_str[10000];
   snprintf(doc_str,
-           9999,
+           10000,
            "\n\n%s\n\n%s\n\nusage: %s %s\n\noptions:\n\n%s\n\n",
            intro,
            version_banner,
@@ -486,22 +487,42 @@ main(int argc, char *argv[])
   while ((l = kseq_read(ref_seq)) >= 0) {
 
     tmp_rseq = rseq_init(ref_seq);
-
     PANIC_IF(tmp_rseq == NULL,
              STD_ERR,
              stderr,
              "Couldn't make rseq");
 
+    /* one for the null and 6 for the ref___ */
+    int new_header_size = tmp_rseq->head_len + 1 + 6;
+    char* new_header = malloc(sizeof *new_header * new_header_size);
+    PANIC_MEM(new_header, stderr);
+    snprintf(new_header,
+             new_header_size,
+             "ref___%s",
+             tmp_rseq->head);
+
+    free(tmp_rseq->head);
+    tmp_rseq->head = new_header;
+    tmp_rseq->head_len = new_header_size - 1;
+
     if (seq_number++ == 0) { /* this is the first seq */
       tmp_rseq->first_ref_seq = 1;
     } else {
       tmp_rseq->first_ref_seq = 0;
     }
-    tmp_rseq->query_seq = 0;
-
-    rseq_try_insert_hashlin(tmp_rseq, header2rseq);
+    tmp_rseq->ref_seq = 1;
 
-    tommy_array_insert(ref_seqs, tmp_rseq);
+    ret_code = rseq_try_insert_hashlin(tmp_rseq, header2rseq);
+    if (ret_code == 1) {
+      tommy_array_insert(ref_seqs, tmp_rseq);
+    } else if (ret_code == 0) {
+      rseq_destroy(tmp_rseq);
+    } else {
+      PANIC_IF(1,
+               STD_ERR,
+               stderr,
+               "Something weird happened...");
+    }
   }
 
   while ((l = kseq_read(query_seq)) >= 0) {
@@ -511,12 +532,19 @@ main(int argc, char *argv[])
              stderr,
              "Couldn't make rseq");
 
-    tmp_rseq->first_ref_seq = 0;
     tmp_rseq->query_seq = 1;
 
-    rseq_try_insert_hashlin(tmp_rseq, header2rseq);
-
-    tommy_array_insert(query_seqs, tmp_rseq);
+    ret_code = rseq_try_insert_hashlin(tmp_rseq, header2rseq);
+    if (ret_code == 1) {
+      tommy_array_insert(query_seqs, tmp_rseq);
+    } else if (ret_code == 0) {
+      rseq_destroy(tmp_rseq);
+    } else {
+      PANIC_IF(1,
+               STD_ERR,
+               stderr,
+               "Something weird happened...");
+    }
   }
 
   for (i = 0; i < num_threads; ++i) {
@@ -586,7 +614,7 @@ main(int argc, char *argv[])
 
   char outfname[1000];
   snprintf(outfname,
-           999,
+           1000,
            "%s/%s.type_info.txt",
            opt_tmp_dir,
            opt_out_base);
@@ -621,22 +649,22 @@ main(int argc, char *argv[])
 
     switch(rseq->spans_region) {
     case -1:
-      snprintf(spans, 9, "NA");
+      snprintf(spans, 10, "NA");
       break;
     case 0:
-      snprintf(spans, 9, "No");
+      snprintf(spans, 10, "No");
       break;
     case 1:
-      snprintf(spans, 9, "Yes");
+      snprintf(spans, 10, "Yes");
       break;
     default:
       assert(0);
     }
 
     if (rseq->spans_region == -1) {
-      snprintf(type, 19, "%s", rseq->key_chars);
+      snprintf(type, 20, "%s", rseq->key_chars);
     } else {
-      snprintf(type, 19, "%s_%s", rseq->key_chars, spans);
+      snprintf(type, 20, "%s_%s", rseq->key_chars, spans);
     }
 
     /* check if type has a fs */
@@ -651,7 +679,7 @@ main(int argc, char *argv[])
       char fname[1000];
       /* TODO validate */
       snprintf(fname,
-               999,
+               1000,
                "%s/%s.type.%s.fa",
                opt_tmp_dir,
                opt_out_base,

src/rseq.c

@@ -112,6 +112,7 @@ rseq_init(kseq_t* kseq)
   rseq->type = NULL;
   rseq->spans_region = 0;
   rseq->first_ref_seq = 0;
+  rseq->ref_seq = 0;
   rseq->query_seq = 0;
 
   return rseq;
@@ -150,7 +151,8 @@ rseq_hash_head(rseq_t* rseq)
   return tommy_strhash_u32(0, rseq->head);
 }
 
-void
+/* Returns 0 if the seq was NOT added, and 1 if it WAS added */
+int
 rseq_try_insert_hashlin(rseq_t* rseq, tommy_hashlin* hash)
 {
   rseq_t* tmp = NULL;
@@ -172,23 +174,14 @@ rseq_try_insert_hashlin(rseq_t* rseq, tommy_hashlin* hash)
              "represents are not equal.",
              rseq->head);
 
-    /* Sometimes a seq can be repeated in both the ref and query
-       files. In this case it's possible that it could be the first
-       ref seq AND a query seq. */
-    /* Now, check if the first_ref_seq and query_seq flags match. If
-       not, the rseq flag will be added to the tmp seq's flag */
-    if (rseq->first_ref_seq == 1 && tmp->first_ref_seq == 0) {
-      tmp->first_ref_seq = 1; /* set it to match the incoming rseq */
-    }
-
-    if (rseq->query_seq == 1 && tmp->query_seq == 0) {
-      tmp->query_seq = 1;
-    }
-
+    /* TODO validate the flags */
+    return 0;
   } else {
     tommy_hashlin_insert(hash,
                          &rseq->node,
                          rseq,
                          hashed_head);
+
+    return 1;
   }
 }

src/rseq.h

@@ -21,6 +21,7 @@ typedef struct rseq_t {
   int seq_len;
   int spans_region;
   int first_ref_seq;
+  int ref_seq;
   int query_seq;
 
 } rseq_t;
@@ -53,7 +54,7 @@ rseq_compare(const void* arg, const void* rseq);
 tommy_uint32_t
 rseq_hash_head(rseq_t* rseq);
 
-void
+int
 rseq_try_insert_hashlin(rseq_t* rseq, tommy_hashlin* hash);
 
 

test_files/queries.fa

@@ -8,3 +8,9 @@ MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSH
 MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH
 >1 query
 MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
+>2 query
+MSNNRPLLLLIDGHALAYRAFHALAEAGLRSSTGEPTYAVFGFTSAMLNAIEEYHPDYAAVAFDVGKTFRDDLYAEYKANRAETPAEFEQQLERIKQVLAAFDIPIYTADGYEADDVIGTLARQATERGVDVLILTGDTDTLQLVDEHVTVLLNNPYVRGSKNTTRYGVADVCARYKGLRPDQLADLRGLKGDPSDNIPGVKGIGEAGAIALLNQFGSIENLYDHLDEAPKRYQKHLEGQRDAALFSKKLATIVRDAPVTLDLPAATLADYDRSRVIAVFQELEFGASLVRRLPPSQTIAAPQALPPVEPPAPLQVDMFAPATPGPDDGPQQLTLFNDMPTPVAPVVEPPAHDAPGEYRAACNDADLEAIVTELKHASLFAFDTETRGTNPLRDDLVGIALATIPGSGWYVPLGHTTGEAQLPRERVIAALRPFFADPARSRIAHNAKFDIEVLERAGIPVAGVAFDTMLAAALLDKRRNLKDLAFYELNLAAPLESIEALIGKGKNQVTFADVPIARATPYAAADADMTLRLKPALEAKLRAAGSVADVFYRLEMPLVPVLVRMEQAGILLDVPYMRALGERMGRELEQIEQQIYAIAGQTFNINSGDQLSEVLFGPKINLPTTGLDRTRTGRYSLTAQALEELQASDTTGIIELILRHRRLSKLKSTYVDELPALVNPETGRVHTDYNQLGAATGRLSSNSPNLQNIPTRTEEGREVRRGFIAAPGHLLIAADYSQIELRVLAHMTGDPNLIQTFIEGRDIHAATAARLFGVGFSAVDKNQRRIAKTVVFGVIYGISPFGLAQRLGISREQARGLIDSLFDQFPRIRDYIDRTLDIGRSEGYVQSLFGRRRPMFDLRVSGPRRQAAEREAINHPIQSTAADIMKLAMIAVDAELQRRQMRTRMLLQVHDELIFEAPEAEVDDVVALVRERMEGVLHGMEPPFAVPLRVEIETGPNWEELTPAG
+>1_e_coli ref
+MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
+>2_phage ref
+MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH

test_files/refs.fa

@@ -2,7 +2,15 @@
 MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
 >2_phage ref
 MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH
+>1 query
+MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
+>2 query
+MSNNRPLLLLIDGHALAYRAFHALAEAGLRSSTGEPTYAVFGFTSAMLNAIEEYHPDYAAVAFDVGKTFRDDLYAEYKANRAETPAEFEQQLERIKQVLAAFDIPIYTADGYEADDVIGTLARQATERGVDVLILTGDTDTLQLVDEHVTVLLNNPYVRGSKNTTRYGVADVCARYKGLRPDQLADLRGLKGDPSDNIPGVKGIGEAGAIALLNQFGSIENLYDHLDEAPKRYQKHLEGQRDAALFSKKLATIVRDAPVTLDLPAATLADYDRSRVIAVFQELEFGASLVRRLPPSQTIAAPQALPPVEPPAPLQVDMFAPATPGPDDGPQQLTLFNDMPTPVAPVVEPPAHDAPGEYRAACNDADLEAIVTELKHASLFAFDTETRGTNPLRDDLVGIALATIPGSGWYVPLGHTTGEAQLPRERVIAALRPFFADPARSRIAHNAKFDIEVLERAGIPVAGVAFDTMLAAALLDKRRNLKDLAFYELNLAAPLESIEALIGKGKNQVTFADVPIARATPYAAADADMTLRLKPALEAKLRAAGSVADVFYRLEMPLVPVLVRMEQAGILLDVPYMRALGERMGRELEQIEQQIYAIAGQTFNINSGDQLSEVLFGPKINLPTTGLDRTRTGRYSLTAQALEELQASDTTGIIELILRHRRLSKLKSTYVDELPALVNPETGRVHTDYNQLGAATGRLSSNSPNLQNIPTRTEEGREVRRGFIAAPGHLLIAADYSQIELRVLAHMTGDPNLIQTFIEGRDIHAATAARLFGVGFSAVDKNQRRIAKTVVFGVIYGISPFGLAQRLGISREQARGLIDSLFDQFPRIRDYIDRTLDIGRSEGYVQSLFGRRRPMFDLRVSGPRRQAAEREAINHPIQSTAADIMKLAMIAVDAELQRRQMRTRMLLQVHDELIFEAPEAEVDDVVALVRERMEGVLHGMEPPFAVPLRVEIETGPNWEELTPAG
 >1_e_coli ref
 MVQIPQNPLILVDGSSYLYRAYHAFPPLTNSAGEPTGAMYGVLNMLRSLIMQYKPTHAAVVFDAKGKTFRDELFEHYKSHRPPMPDDLRAQIEPLHAMVKAMGLPLLAVSGVEADDVIGTLAREAEKAGRPVLISTGDKDMAQLVTPNITLINTMTNTILGPEEVVNKYGVPPELIIDFLALMGDSSDNIPGVPGVGEKTAQALLQGLGGLDTLYAEPEKIAGLSFRGAKTMAAKLEQNKEVAYLSYQLATIKTDVELELTCEQLEVQPPAAEELLGLFKKYEFKRWTADVEAGKWLQAKGVKPAARPQETSVADEAPEVTATVISYDNYVTILDEETLKEWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH
 >2_phage ref
 MLYPWENMYASDIETTGLLEQMRKQAAPRLHNIGYIDVLTREETVIEWTDRKSIQAFLDTGPTLIMHNGATFDFEALRFLGYDVSKCTLIDTLFISWYLQPRRVKHGLEGYGEEFGVPKPVIEDWENQTQEEYNHRVMEDCKIQLKLWEQQYIQLLKIYKSPSEVKRFVEYLMTKARQQVIQQRTRWKLNIEKALAFKAKLEPMIKEKTDALEASMPRIPEYVIKTRPAKCHKMNGQLSATGIKWKAVCDANGLDWKDPDLAIKVLKGYKEPNAGSHVQIKDWLFSLGWEPETFKFDRNKETGETRQIPQITVKDEDGNPEICPSLHKLAERNPESGIQHLIGMGVYKHRLSVVNGFLRDVDEDGYLTARCGGLTNTLRLKHRELVNLPSIRVFGGEELRSMLEAWREDYEQLGSDLCSLEDRCKHHFQWMYDPEYVKKQLAPDYDAHLAIGVIGGFITEQESQDHKDGIKKCKQRPMFKTTNYACQYGAGVPTVARSAGCDQTTAARLHKAYWDLNWSIKEIAANTKVITVDGQMWQQNPVNKFWYSLRTEKDRFSTLCQGTGAYVFDIWCNNIIAICNERWGCDPLLSGQFHDELILQVKKGFRDLWTDLLNEAMDRTNKELKLNRDCACDVQFGDNYAEIH
+>1 query
+MIVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH
+>2 query
+MSNNRPLLLLIDGHALAYRAFHALAEAGLRSSTGEPTYAVFGFTSAMLNAIEEYHPDYAAVAFDVGKTFRDDLYAEYKANRAETPAEFEQQLERIKQVLAAFDIPIYTADGYEADDVIGTLARQATERGVDVLILTGDTDTLQLVDEHVTVLLNNPYVRGSKNTTRYGVADVCARYKGLRPDQLADLRGLKGDPSDNIPGVKGIGEAGAIALLNQFGSIENLYDHLDEAPKRYQKHLEGQRDAALFSKKLATIVRDAPVTLDLPAATLADYDRSRVIAVFQELEFGASLVRRLPPSQTIAAPQALPPVEPPAPLQVDMFAPATPGPDDGPQQLTLFNDMPTPVAPVVEPPAHDAPGEYRAACNDADLEAIVTELKHASLFAFDTETRGTNPLRDDLVGIALATIPGSGWYVPLGHTTGEAQLPRERVIAALRPFFADPARSRIAHNAKFDIEVLERAGIPVAGVAFDTMLAAALLDKRRNLKDLAFYELNLAAPLESIEALIGKGKNQVTFADVPIARATPYAAADADMTLRLKPALEAKLRAAGSVADVFYRLEMPLVPVLVRMEQAGILLDVPYMRALGERMGRELEQIEQQIYAIAGQTFNINSGDQLSEVLFGPKINLPTTGLDRTRTGRYSLTAQALEELQASDTTGIIELILRHRRLSKLKSTYVDELPALVNPETGRVHTDYNQLGAATGRLSSNSPNLQNIPTRTEEGREVRRGFIAAPGHLLIAADYSQIELRVLAHMTGDPNLIQTFIEGRDIHAATAARLFGVGFSAVDKNQRRIAKTVVFGVIYGISPFGLAQRLGISREQARGLIDSLFDQFPRIRDYIDRTLDIGRSEGYVQSLFGRRRPMFDLRVSGPRRQAAEREAINHPIQSTAADIMKLAMIAVDAELQRRQMRTRMLLQVHDELIFEAPEAEVDDVVALVRERMEGVLHGMEPPFAVPLRVEIETGPNWEELTPAG