Mercurial > repos > abims-sbr > cds_search
changeset 8:716a45028e55 draft
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 90cfcf697b9f128e81bea1270378e59d63ab0a6f
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--- a/CDS_search.xml Wed Feb 28 10:38:40 2018 -0500 +++ b/CDS_search.xml Mon Mar 12 06:30:49 2018 -0400 @@ -121,8 +121,10 @@ </outputs> <tests> + + <!-- tests with name "orthogroup_x_witn_y_sequences.fasta" --> <test> - <param name="inputs" ftype="fasta" value="inputs/locus1_sp5.fasta,inputs/locus1_sp7.fasta,inputs/locus2_sp4.fasta,inputs/locus2_sp6.fasta" /> + <param name="inputs" ftype="fasta" value="inputs/orthogroup_1_with_4_sequences.fasta,inputs/orthogroup_6_with_4_sequences.fasta,inputs/orthogroup_7_with_3_sequences.fasta,inputs/orthogroup_8_with_4_sequences.fasta,inputs/orthogroup_12_with_5_sequences.fasta,inputs/orthogroup_14_with_4_sequences.fasta" /> <param name="nb_species_keep" value="2" /> <param name="methionine" value="no" /> <section name="length"> @@ -133,32 +135,35 @@ <param name="out_BESTORF" value="both" /> <param name="out_CDS" value="both" /> <param name="out_CDS_filter" value="both" /> - <output name="log" value="cds_search.log" /> <output_collection name="output_BESTORF_aa" type="list"> - <element name="locus1_sp7" value="outputs_ORF_Search_Best_ORF_aa/locus1_sp7.fasta" /> - <element name="locus2_sp6" value="outputs_ORF_Search_Best_ORF_aa/locus2_sp6.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta" /> </output_collection> <output_collection name="output_BESTORF_nuc" type="list"> - <element name="locus1_sp7" value="outputs_ORF_Search_Best_ORF_nuc/locus1_sp7.fasta" /> - <element name="locus2_sp6" value="outputs_ORF_Search_Best_ORF_nuc/locus2_sp6.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta" /> </output_collection> <output_collection name="output_CDS_aa" type="list"> - <element name="locus1_sp7" value="outputs_ORF_Search_CDS_aa/locus1_sp7.fasta" /> - <element name="locus2_sp6" value="outputs_ORF_Search_CDS_aa/locus2_sp6.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_05_CDS_aa/test1/orthogroup_6_with_2_species.fasta" /> </output_collection> <output_collection name="output_CDS_nuc" type="list"> - <element name="locus1_sp7" value="outputs_ORF_Search_CDS_nuc/locus1_sp7.fasta" /> - <element name="locus2_sp6" value="outputs_ORF_Search_CDS_nuc/locus2_sp6.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_6_with_2_species.fasta" /> </output_collection> - <output_collection name="output_filter_aa" type="list"> - <element name="locus2_sp4_sp4" value="outputs_ORF_Search_CDS_without_indel_aa/locus2_sp4_sp4.fasta" /> - </output_collection> - <output_collection name="output_filter_nuc" type="list"> - <element name="locus2_sp4_sp4" value="outputs_ORF_Search_CDS_without_indel_nuc/locus2_sp4_sp4.fasta" /> - </output_collection> + <output_collection name="output_filter_aa" type="list" count="4"/> + <output_collection name="output_filter_nuc" type="list" count="4"/> </test> <test> - <param name="inputs" ftype="fasta" value="inputs/locus2_sp6.fasta" /> + <param name="inputs" ftype="fasta" value="inputs/orthogroup_1_with_4_sequences.fasta,inputs/orthogroup_6_with_4_sequences.fasta,inputs/orthogroup_7_with_3_sequences.fasta,inputs/orthogroup_8_with_4_sequences.fasta,inputs/orthogroup_12_with_5_sequences.fasta,inputs/orthogroup_14_with_4_sequences.fasta" /> <param name="nb_species_keep" value="2" /> <param name="methionine" value="yes" /> <section name="length"> @@ -168,21 +173,90 @@ </section> <param name="out_BESTORF" value="both" /> <param name="out_CDS" value="both" /> - <param name="out_CDS_filter" value="both" /> - <output name="log" value="cds_search_methionine.log" /> + <param name="out_CDS_filter" value="both" /> <output_collection name="output_BESTORF_aa" type="list"> - <element name="locus2_sp6" value="outputs_ORF_Search_Best_ORF_aa/locus2_sp6.fasta" /> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta" /> + </output_collection> + <output_collection name="output_BESTORF_nuc" type="list"> + <element name="orthogroup_1_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta" /> + <element name="orthogroup_2_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta" /> + <element name="orthogroup_3_with_3_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta" /> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta" /> + </output_collection> + <output_collection name="output_CDS_M_aa" type="list"> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_06_CDS_with_M_aa/test1/orthogroup_6_with_2_species.fasta" /> + </output_collection> + <output_collection name="output_CDS_M_nuc" type="list"> + <element name="orthogroup_6_with_2_species" value="outputs_ORF_Search_06_CDS_with_M_nuc/test1/orthogroup_6_with_2_species.fasta" /> + </output_collection> + </test> + + <!-- tests with name "locus_x_spy.fasta" --> + <test> + <param name="inputs" ftype="fasta" value="inputs/locus1_sp5.fasta,inputs/locus1_sp7.fasta,inputs/locus2_sp4.fasta,inputs/locus2_sp6.fasta" /> + <param name="nb_species_keep" value="2" /> + <param name="methionine" value="no" /> + <section name="length"> + <param name="min_length_seq" value="50" /> + <param name="min_length_subseq" value="15" /> + <param name="min_length_nuc" value="50" /> + </section> + <param name="out_BESTORF" value="both" /> + <param name="out_CDS" value="both" /> + <param name="out_CDS_filter" value="both" /> + <output_collection name="output_BESTORF_aa" type="list"> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta" /> </output_collection> <output_collection name="output_BESTORF_nuc" type="list"> - <element name="locus2_sp6" value="outputs_ORF_Search_Best_ORF_nuc/locus2_sp6.fasta" /> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta" /> + </output_collection> + <output_collection name="output_CDS_aa" type="list"> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_05_CDS_aa/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_05_CDS_aa/test2/orthogroup_4_with_6_species.fasta" /> + </output_collection> + <output_collection name="output_CDS_nuc" type="list"> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_4_with_6_species.fasta" /> + </output_collection> + <output_collection name="output_filter_aa" type="list"> + <element name="orthogroup_1_with_4_species" value="outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_1_with_4_species.fasta" /> + </output_collection> + <output_collection name="output_filter_nuc" type="list"> + <element name="orthogroup_1_with_4_species" value="outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_1_with_4_species.fasta" /> + </output_collection> + </test> + <test> + <param name="inputs" ftype="fasta" value="inputs/locus1_sp5.fasta,inputs/locus1_sp7.fasta,inputs/locus2_sp4.fasta,inputs/locus2_sp6.fasta" /> + <param name="nb_species_keep" value="2" /> + <param name="methionine" value="yes" /> + <section name="length"> + <param name="min_length_seq" value="50" /> + <param name="min_length_subseq" value="15" /> + <param name="min_length_nuc" value="50" /> + </section> + <param name="out_BESTORF" value="both" /> + <param name="out_CDS" value="both" /> + <param name="out_CDS_filter" value="both" /> + <output_collection name="output_BESTORF_aa" type="list"> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta" /> + </output_collection> + <output_collection name="output_BESTORF_nuc" type="list"> + <element name="orthogroup_2_with_7_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta" /> </output_collection> <output_collection name="output_CDS_M_aa" type="list"> - <element name="locus2_sp6" value="outputs_ORF_Search_CDS_with_M_aa/locus2_sp6.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_06_CDS_with_M_aa/test2/orthogroup_4_with_6_species.fasta" /> </output_collection> <output_collection name="output_CDS_M_nuc" type="list"> - <element name="locus2_sp6" value="outputs_ORF_Search_CDS_with_M_nuc/locus2_sp6.fasta" /> + <element name="orthogroup_4_with_6_species" value="outputs_ORF_Search_06_CDS_with_M_nuc/test2/orthogroup_4_with_6_species.fasta" /> </output_collection> - </test> + </test> </tests> <help>
--- a/scripts/S01_find_orf_on_multiple_alignment.py Wed Feb 28 10:38:40 2018 -0500 +++ b/scripts/S01_find_orf_on_multiple_alignment.py Mon Mar 12 06:30:49 2018 -0400 @@ -1,6 +1,8 @@ #!/usr/bin/python +# coding: utf8 ## Author: Eric Fontanillas -## Last modification: 03/09/14 by Julie BAFFARD +## Modification: 03/09/14 by Julie BAFFARD +## Last modification : 05/03/18 by Victor Mataigne ## Description: Predict potential ORF on the basis of 2 criteria + 1 optional criteria ## CRITERIA 1 ## Longest part of the alignment of sequence without codon stop "*", tested in the 3 potential ORF @@ -294,24 +296,16 @@ ################################### - - - - ############################################################ ###### DEF 7 : Reverse complement DNA sequence ###### ###### Reference: http://crazyhottommy.blogspot.fr/2013/10/python-code-for-getting-reverse.html ############################################################ - - def ReverseComplement2(seq): # too lazy to construct the dictionary manually, use a dict comprehension seq1 = 'ATCG-TAGC-atcg-tagc-' seq_dict = { seq1[i]:seq1[i+5] for i in range(20) if i < 5 or 10<=i<15 } return "".join([seq_dict[base] for base in reversed(seq)]) - -################################### - +############################ ####################### @@ -344,25 +338,35 @@ os.mkdir("06_CDS_with_M_aa") Path_OUT6 = "06_CDS_with_M_aa" - - - ### Get the Bash corresponding to an alignment file in fasta format count_file_processed = 0 count_file_with_CDS = 0 count_file_without_CDS = 0 count_file_with_CDS_plus_M = 0 +# ! : Currently, files are named "Orthogroup_x_y_sequences.fasta, where x is the number of the orthogroup (not important, juste here to make a distinct name), +# and y is the number of sequences/species in the group. These files are outputs of blastalign, where species can be removed. y is then modified. + +name_elems = ["orthogroup", "0", "with", "0", "species.fasta"] + +# by fixing the counter here, there will be some "holes" in the outputs directories (missing numbers), but the groups between directories will correspond +n0 = 0 for file in list_file: + n0 += 1 + count_file_processed = count_file_processed + 1 fasta_file_path = "./%s" %file bash_fasta = dico(fasta_file_path) ### DEF 1 ### BESTORF_nuc, BESTORF_nuc_CODING, BESTORF_nuc_CDS_with_M, BESTORF_aa, BESTORF_aa_CODING, BESTORF_aa_CDS_with_M = find_good_ORF_criteria_3(bash_fasta, bash_codeUniversel) ### DEF 4 - PART 2 - ### + + name_elems[1] = str(n0) ## a ## OUTPUT BESTORF_nuc if BESTORF_nuc != {}: + name_elems[3] = str(len(BESTORF_nuc.keys())) + new_name = "_".join(name_elems) count_file_with_CDS = count_file_with_CDS +1 - OUT1 = open("%s/%s" %(Path_OUT1,file), "w") + OUT1 = open("%s/%s" %(Path_OUT1,new_name), "w") for fasta_name in BESTORF_nuc.keys(): seq = BESTORF_nuc[fasta_name] OUT1.write("%s\n" %fasta_name) @@ -371,10 +375,11 @@ else: count_file_without_CDS = count_file_without_CDS + 1 - ## b ## OUTPUT BESTORF_nuc_CODING ===> THE MOST INTERESTING!!! if BESTORF_aa != {}: - OUT2 = open("%s/%s" %(Path_OUT2,file), "w") + name_elems[3] = str(len(BESTORF_aa.keys())) + new_name = "_".join(name_elems) + OUT2 = open("%s/%s" %(Path_OUT2,new_name), "w") for fasta_name in BESTORF_aa.keys(): seq = BESTORF_aa[fasta_name] OUT2.write("%s\n" %fasta_name) @@ -383,7 +388,9 @@ ## c ## OUTPUT BESTORF_aa if BESTORF_nuc_CODING != {}: - OUT3 = open("%s/%s" %(Path_OUT3,file), "w") + name_elems[3] = str(len(BESTORF_nuc_CODING.keys())) + new_name = "_".join(name_elems) + OUT3 = open("%s/%s" %(Path_OUT3,new_name), "w") for fasta_name in BESTORF_nuc_CODING.keys(): seq = BESTORF_nuc_CODING[fasta_name] OUT3.write("%s\n" %fasta_name) @@ -392,7 +399,9 @@ ## d ## OUTPUT BESTORF_aa_CODING if BESTORF_aa_CODING != {}: - OUT4 = open("%s/%s" %(Path_OUT4,file), "w") + name_elems[3] = str(len(BESTORF_aa_CODING.keys())) + new_name = "_".join(name_elems) + OUT4 = open("%s/%s" %(Path_OUT4,new_name), "w") for fasta_name in BESTORF_aa_CODING.keys(): seq = BESTORF_aa_CODING[fasta_name] OUT4.write("%s\n" %fasta_name) @@ -401,8 +410,10 @@ ## e ## OUTPUT BESTORF_nuc_CDS_with_M if BESTORF_nuc_CDS_with_M != {}: + name_elems[3] = str(len(BESTORF_nuc_CDS_with_M.keys())) + new_name = "_".join(name_elems) count_file_with_CDS_plus_M = count_file_with_CDS_plus_M + 1 - OUT5 = open("%s/%s" %(Path_OUT5,file), "w") + OUT5 = open("%s/%s" %(Path_OUT5,new_name), "w") for fasta_name in BESTORF_nuc_CDS_with_M.keys(): seq = BESTORF_nuc_CDS_with_M[fasta_name] OUT5.write("%s\n" %fasta_name) @@ -411,7 +422,9 @@ ## f ## OUTPUT BESTORF_aa_CDS_with_M if BESTORF_aa_CDS_with_M != {}: - OUT6 = open("%s/%s" %(Path_OUT6,file), "w") + name_elems[3] = str(len(BESTORF_aa_CDS_with_M.keys())) + new_name = "_".join(name_elems) + OUT6 = open("%s/%s" %(Path_OUT6,new_name), "w") for fasta_name in BESTORF_aa_CDS_with_M.keys(): seq = BESTORF_aa_CDS_with_M[fasta_name] OUT6.write("%s\n" %fasta_name)
--- a/scripts/S02_remove_too_short_bit_or_whole_sequence.py Wed Feb 28 10:38:40 2018 -0500 +++ b/scripts/S02_remove_too_short_bit_or_whole_sequence.py Mon Mar 12 06:30:49 2018 -0400 @@ -1,10 +1,11 @@ #!/usr/bin/python +# coding: utf8 ## Author: Eric Fontanillas -## Last modification: 03/09/14 by Julie BAFFARD +## Modification: 03/09/14 by Julie BAFFARD +## Last modification : 05/03/18 by Victor Mataigne ## Description : find and remove indels - ################### ###### DEF 9 ###### ################### @@ -35,8 +36,6 @@ #################################### - - ####################### ##### RUN RUN RUN ##### ####################### @@ -52,12 +51,12 @@ MAX_sp = MIN_SPECIES_NB dicoco = {} dico_dico = {} -list_sp = [] list_new_file = [] n0 = 0 e=0 j=0 i=1 +name_elems = ["orthogroup", "0", "with", "0", "species.fasta"] ### 1 ### IN if sys.argv[2] == "oui" : @@ -94,7 +93,6 @@ seq = string.replace(seq, "?", "-") if "?" in seq_nuc: seq_nuc = string.replace(seq_nuc, "?", "-") - ## 4.1 ## [FILTER 1] : Detect and Replace short internal indel symbole (= "-" as for other longer gaps) by a "?" ## aa @@ -107,7 +105,6 @@ for pos_short_indels in list_sublist_pos: for pos in pos_short_indels: seq_nuc = seq_nuc[:pos] + "?" + seq_nuc[pos+1:] - ## 4.2 ## [FILTER 2] : Remove short bits of sequence (<"MIN_LENGTH_BIT_OF_SEQUENCE_aa") LIST_sublist_aa=[] @@ -116,7 +113,6 @@ if len(element) > MIN_LENGTH_BIT_OF_SEQUENCE_aa: LIST_sublist_aa.append(element) - ## 4.3 ## [FILTER 3] : Remove all the sequence if the total length of all subsequences < "MIN_LENGTH_ALL_aa") seq_all = "" for bit_of_sequence in LIST_sublist_aa: @@ -125,7 +121,6 @@ if len(seq_all) < MIN_LENGTH_ALL_aa: LIST_sublist_aa = [] - ## 4.4 ## [FILTER 4] : Detect sublist position in the original sequence, and recreate the filtered sequence from these positions: seq_gap = "-" * len(seq) ## 4.4.1 ## generate a sequence with only gaps inside seq_gap_nuc = "-" * len(seq_nuc) @@ -139,7 +134,6 @@ START_nuc = START*3 END_nuc = END*3 seq_gap_nuc = seq_gap_nuc[:START_nuc] + seq_nuc[START_nuc:END_nuc] + seq_gap_nuc[END_nuc:] - ## 4.5 ## Save new sequence in bash if not empty seq_empty_test = string.replace(seq_gap, "-", "") @@ -150,34 +144,13 @@ if seq_empty_test != "": new_bash_nuc[fasta_name] = seq_gap_nuc - ## 4.6 ## Correct the nb of sequence in the output name, if necessary - sp_nb = len(new_bash_aa.keys()) - lis = string.split(file, "_") - new_lis = string.split(lis[1], ".") - nb = "sp%d" % sp_nb - - old_nb = new_lis[0] - max_old_nb = string.split(old_nb, "sp") - max_old_nb = "".join(max_old_nb) - - if old_nb == nb: - new_file = lis[0] + "_" + nb + "." + new_lis[1] - else: - new_file = lis[0] + "_NEW_"+ nb + "." + new_lis[1] - list_new_file.append(new_file) - dico_dico[new_file] = [new_bash_aa, new_bash_nuc] - n0+=1 #number of locus traited - - if list_sp == [] and nb!="sp0" : - list_sp.append(nb) - else : - if nb not in list_sp and nb != "sp0" : - list_sp.append(nb) - -# [FILTER 5]: check if the number of locus with the max number of species isn't 0 -#if it is : MIN_SPECIES_NB - 1 -if len(list_sp) < MIN_SPECIES_NB : - MIN_SPECIES_NB = len(list_sp) + # 4.6 ## Correct the nb of sequence in the output name, if necessary + n0 += 1 + name_elems[1] = str(n0) + name_elems[3] = str(len(new_bash_nuc.keys())) + new_name = "_".join(name_elems) + dico_dico[new_name] = [new_bash_aa, new_bash_nuc] + list_new_file.append(new_name) ## [FILTER 6]: print output only if at least "MIN_SPECIES_NB" species remaining in the alignment for name in list_new_file : @@ -191,11 +164,11 @@ file_OUTnuc = open("%s/%s" %(path_OUT2, name), "w") for fasta_name in dico_aa.keys() : - seq_aa = dico_aa[fasta_name] + seq_aa = dico_aa[fasta_name] file_OUTaa.write("%s\n" %fasta_name) file_OUTaa.write("%s\n" %seq_aa) - for fasta_name in dico_nuc.keys() : - seq_nuc = dico_nuc[fasta_name] + for fasta_name in dico_nuc.keys() : + seq_nuc = dico_nuc[fasta_name] file_OUTnuc.write("%s\n" %fasta_name) file_OUTnuc.write("%s\n" %seq_nuc) @@ -205,36 +178,10 @@ else: e+=1 - ###Print if sys.argv[2] == "oui" : print "\nIn locus with CDS considering Methionine : \n" else : print "\nIn locus with CDS regardless of the Methionine : \n" -print "*************** 1st filter : selection of the locus ***************" -print "\nTotal number of locus recorded = %d" %n0 - -list_sp.sort() -for sp in list_sp : - dicoco[sp] = [] - for files in list_new_file : - nb_sp = string.split(files, "_NEW") - nb_sp = "".join(nb_sp) - nb_sp = string.split(nb_sp,'_') - nb_sp = nb_sp[1] - nb_sp = string.split(nb_sp, ".") - nb_sp = nb_sp[0] - if nb_sp == sp : - dicoco[sp].append(files) - new_sp = sp.split("sp") - new_sp = int(new_sp[1]) - if new_sp == i : - print "\tNumber of locus with %d species : %d" %(i, len(dicoco[sp])) - elif i <= MAX_sp : - print "\tNumber of locus with %d species : 0" %i - i+=1 -if len(list_sp) != int(MAX_sp) : - print "\tNumber of locus with %d species : 0" %int(MAX_sp) - -print "Number of locus excluded (exclude if not at least %d species in the alignment)= %d\n" %(MIN_SPECIES_NB,e) +print "\nTotal number of locus recorded = %d" %n0 \ No newline at end of file
--- a/scripts/S03_remove_site_with_not_enough_species_represented.py Wed Feb 28 10:38:40 2018 -0500 +++ b/scripts/S03_remove_site_with_not_enough_species_represented.py Mon Mar 12 06:30:49 2018 -0400 @@ -1,6 +1,8 @@ #!/usr/bin/python +# coding: utf8 ## Author: Eric Fontanillas -## Last modification: 03/09/14 by Julie BAFFARD +## Modification: 03/09/14 by Julie BAFFARD +## Last modification : 05/03/18 by Victor Mataigne ## Description : find and remove indels @@ -93,7 +95,7 @@ ####################### ##### RUN RUN RUN ##### ####################### -import string, os, time, re, sys, zipfile +import string, os, time, re, sys from dico import dico ### 0 ### PARAMETERS @@ -106,7 +108,7 @@ list_new_file = [] dicoco = {} list_file = [] - +name_elems = ["orthogroup", "0", "with", "0", "species.fasta"] ### 1 ### IN path_IN1 = "./07_CDS_aa/" @@ -130,7 +132,7 @@ dico_nuc = dico(file_INnuc) ### DEF 1 ### if len(dico_aa) < MIN_SPECIES_NB : - list_file.append(file) + list_file.append(file) if list_file == lenght : MIN_SPECIES_NB == MIN_SPECIES_NB - 1 @@ -153,14 +155,11 @@ seq0 = filtered_bash_nuc[k0] new_leng_nuc = len(seq0) - ## 4.3 ## Change file name for output, depending the number of species remaining in the alignment - LS = string.split(file, "_NEW") - LS = "".join(LS) - LS = string.split(LS, "_") - ln_aa = len(filtered_bash_aa.keys()) - nb = "sp%d" %ln_aa - new_name = LS[0] + "_" + nb + "_" + LS[1] + ## 4.3 ## Change file name for output, depending the number of species remaining in the alignment n0+=1 + name_elems[1] = str(n0) + name_elems[3] = str(len(filtered_bash_aa.keys())) + new_name = "_".join(name_elems) ## 4.5 ## Write filtered alignment in OUTPUTs ## aa @@ -173,7 +172,7 @@ OUTaa.close() # nuc if filtered_bash_nuc != {} and new_leng_nuc >= MIN_LENGTH_FINAL_ALIGNMENT_NUC: - good+=1 + good+=1 OUTnuc=open("%s/%s" %(path_OUT2, new_name), "w") for fasta_name in filtered_bash_nuc.keys(): seq_nuc = filtered_bash_nuc[fasta_name] @@ -181,7 +180,7 @@ OUTnuc.write("%s\n" %seq_nuc) OUTnuc.close() else: - bad+=1 + bad+=1 ## 5 ## Print @@ -189,4 +188,4 @@ print "\nTotal number of locus recorded = %d" %n0 print "\tTotal number of locus with no indels (SAVED) = %d" %good print "\tTotal number of locus, when removing indel, wich are empty (EXCLUDED) = %d" %bad -print "" +print "" \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_12_with_5_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Ac689_1/1_1.000_714 +ccgtccaaacgtgacgaatacgcggccgagctggccaaatacatcgacgtcgacgtctacggaaagtgcggcacgctgacgtgtccgaaggatgagaaggtcgactgcgaacagatgtgggccgaaacgtacaagtttcacttgtcctttgagaacacgatttgtcaagattacatcacg +>Ap6163_1/1_1.000_569 +-------------------------------tggccaagtacatcgacgtagacgtctatggcaagtgcggca----------------------------------------------------------------------------------------------------------- +>Pu6544_1/1_1.000_249 +------------------------------------------------------------------------------------------------------------------------------acgtacaagtttca----------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_14_with_4_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap1491_1/1_1.000_963 +cgaagaaacatgacggagcaaatgacgcttcgcggtaccctccaagggcacggaggatgggtaacccaaattgctacaacgccacaatttcctgatatcattttgtcggcttctagagacaaatcgctcattctgtggcagctgactcgcgaggaatcgcgttacggcttccctcgcaaggccttgcgcggacatggacacttcgtgtctgacgtcgtcatgtcatcagatggacagttcgccctgtctggatcctgggatggaacccttcgtttgtgggatcttggcactggtcagacaactcgtaggtttgttggacacacgaaggacgtgctaagtgtggctttctcagctgataaccgtcagattgtgtcaggttcacgtgacaagaccatcaagttgtggaacactcttggggtgtgcaagtataccattcaggaagatgggcacacagagtgggtatcatgtgttcgattctcaccaaacacccagaatcccatcattgtgtcctgtggctgggacaaactggttaaggtgtggaatctgacaaactgcaagctaaaaacaaaccacttcggacactcaggttatctgaactgtgtcactgtgtcccctgatggatctttgtgcgcttctggtggaaaagatggccaggcaatgttatgggatttgaatgaaggcaagcatctgtacacattggatggtggtgatgtcatcaactcactgtgcttcagccccaacagatactggctttgtgctgcttctggaccaagcataaagatctgggatctggaaggcaaggttgttgtggatgagctgcgtccagaagtgatcagcaccagtgccagtgccgagccacctcagtgtatatccctggcttggtcagctgatggccagacactgtttgctggatacacagacaacctgattcgtgtgtggcaggtatctatggcagctacccga +>Ac6688_1/1_1.000_963 +cgaagaaacatgacggagcaaatgacgcttcgcggtaccctccaagggcacggaggatgggtaactcaaattgctacaacgccacaatttcccgatattattttgtcggcttcaagagacaaatcgctcatcctgtggcagctgactcgtgaggaatcgcgctacggtttccctcgcaaggccttgcgtggacatggacatttcgtgtctgacgttgttatgtcatcagatggacagttcgctctgtctggatcctgggatggaacccttcgtttgtgggatcttggcactggtcagacaactcgtaggtttgtcggacacacaaaagatgtgctaagcgtggccttctcagctgataaccgccagattgtgtcaggttcacgtgacaagaccatcaagttgtggaacactctcggtgtatgcaagtacaccattcaggaagatggacacacagagtgggtatcatgtgttcgcttctcaccaaacactcagaatcccatcattgtgtcttgtggctgggacaaactggttaaggtttggaatctgacaaactgcaaactaaaaacaaaccactttggacactcaggttacctgaactgtgtcaccgtgtcccctgatggatctttgtgtgcttctggtggtaaggatggccaggcaatgttgtgggatttgaatgaaggcaagcatctgtacacattggatggtggtgatgtcatcaactcactgtgcttcagccccaacagatattggctttgtgctgcctctggaccaagcataaagatctgggatctggaaggcaaggttgttgtggatgagttgcgtccagaagtgatcagtaccagtgccagcgctgaaccaccccagtgtatatccctggcatggtcagctgatggccagacgctgtttgcaggatacacagacaacctgatccgtgtctggcaggtgtccatggcagctacccga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_1_with_4_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Ac3644_1/1_1.000_1626 +attggcacagcatcatttgaaagccttgttgagttagttaaatattacaagaagaacccactttacagaaaaatgaaactcagatatgctgttaatgaggaagttgttcaacaacaaggaatggatccagatgaacaggcaatttacagtggagaaatgtacacaaatccaaatgattttgtatctaagattaaagtgagggctttgtatgactacaagaaacaacgtgaagatgaactg +>Ap2303_1/1_1.000_424 +attggcacagcatcctttgagagccttgttgagttagttaagtattacaagaagaacccactttacagaaaaatgaaactcagatatgcggttaatgaggaagttgtccagcaacaaggaatggatccagatgaacaggcaatatacagtggagaaatgtacacaaatccaaatgattttgtatctaagattaaag-------------------------------------------- +>Am7472_1/1_1.000_254 +attggtaccgcatcatttgagagtctggtagagctagtggaatactacaagaaaaaccc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_6_with_4_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac1013_1/1_1.000_525 +ttgaccttcaaggagctgaaaaaagccctcaaggccaaaggctacaaggtcaagggcaaacaactcaaggctcaattcaaacagtttgataaagatggcgataagaaaataacccttcaagaatacttgatcgcgatgggccaagtcccggatgcctaccacaaagaggcagccatgcggcaggctttcgagcgggcggacaaaaacaaagacggaagcttggacatcggcgaggttaacgccattttccaagagatgaacaccttccttgatccagacgagctcttcaagatcgtccacgccatcgacaaggaccacagcggacggatcaactacgacgaattcttgaccttcttcatgaagcagcaaaatgtcaactttgagagcagcgacagcgactgggac +>Ap5072_1/1_1.000_437 +ttgaccttcaaggagctgaaaaaggccctgaaggccaagggctacaaggtcaagggcaaacagctcaaggcccaattcaaacagtttgataaagacggcgacaagaaaatatcccttcaagaatacctgatcgcgatgggtcaagtcccggatgtctaccacaaagaggccgccatgcggcaggctttcgagcgggcggacaaaaacaaagacggaagcttggacatcggcgagatcaacgccatcttccgggagatgaacaccttcctcaatccagacgagctctttcagatcgtccacgaaatcgacaaggaccacagcggacggatcaactacaacgaattcctgaccttcttcatgaagcagcaaaatgtcaacttcgagagcagtgacagcgattggga-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_7_with_3_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Ac2173_1/1_1.000_330 +gcttggagaaggtcagaagcgttgaaaatgttgcagagagctcttcgtcttaaccagcttactcgtcgattttccacaagtgtggttcggcgaagtgaagaatggcaacaaaggggtcttcccggatctaacatgcctttcgatatgaacaaccgatacaagttgatggcttggttcatcctcttttttggttctggcttgggagtgccatatctcttagtccgccaccagcttctgaaggag +>Ap5050_1/1_1.000_243 +gcttggggaaggtcagaagctgtgaaaatgttgcagagagctcttcgtcttaatcaacttactcgtcgattttccacaagtgtggttcgacggagtgaagaatggcaacagaggggtcttcccggatctaacatgcctttcgacatgaacaaccgatacaaattgatggcgtggttcatcctcttttttggttctggcttgggagtgccatatctcttagtccgccaccagcttctgaaggag +>Am3527_1/1_1.000_270 +-------------------------------------------------------------ctcgtcgtttttccacaagtgtggtcagacaaagccaagaatggcaacagcttggagtacctggatcgaacatgccatttgacatcaacaacagatacaa----------------------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs/orthogroup_8_with_4_sequences.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Am6963_1/1_1.000_854 +gataagtcgtcaggagtacattatggcatcataacctgtgagggctgcaagggatttttc +>Pg7693_1/1_1.000_511 +---------------------------------acctgtgagggctg-------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_1_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +?????????????????????????????????????????????????????????????VFLVVFH*LYQTLK*CGTN +>Ap2303_1/1_1.000_424 +???????????????FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN*LNKALKGCCAN +>Ac3644_1/1_1.000_1626 +QFIFTLFLVVIQSPHFNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN*LNKAFK*CCAN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +PNRCHCSRS*HFAAS*RRSGIRCS*SVRCGPCRFRGRSERARLD*GRCSSPGRWR*SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV*IGP*AVCP*PCSPWPSGPFSAP*RS +>Ac1013_1/1_1.000_525 +PSRCRCSQS*HFAAS*RRSRIRRS*SVRCGPCRWRGRS*RARLDQGRCSSLGKWR*PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV*IEP*VVCP*PCSLWP*GLFSAP*RS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +????????????????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT????????????????????? +>Ap5050_1/1_1.000_243 +LLQKLVAD*EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF*PSPS +>Ac2173_1/1_1.000_330 +LLQKLVAD*EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF*PSPS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +RVAAMDTCQTRIRLSVYPANSVWPSADHARDIHWGGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFQTLTSLSQPQDTMMGF*VFGEKRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTIWRLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDITTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKIISGNCGVVAI*VTHPPCPWRVPRSVICSVMFL +>Ap1491_1/1_1.000_963 +RVAAIDTCHTRIRLSVYPANSVWPSADQARDIH*GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR*PECPKWFVFSLQFVRFHTLTSLSQPQDTMMGFWVFGENRTHDTHSVCPSS*MVYLHTPRVFHNLMVLSREPDTI*RLSAEKATLSTSFVCPTNLRVV*PVPRSHKRRVPSQDPDRANCPSDDMTTSDTKCPCPRKALRGKP*RDSSRVSCHRMSDLSLEADKMISGNCGVVAIWVTHPPCPWRVPRSVICSVMFL
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,14 @@ +>Ac72851/110 +??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +>Te17661/110 +??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +>Ap26441/110 +??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +>Th39471/110 +??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? +>Pf20921/110 +??????????????LSSFQKRRCSHT????????????????????LAQRS*LSPDGSVHQSTVNRVLFLLNRCRFLGRVFAV???????????????????????????????????????????????????????? +>Pu7631/1100 +???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????DYHI*PERISEES??????? +>Am31481/110 +SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS*WSLGESTRQSIANRALV*PDRFLFPGPVSAVDVYPVPPVD*LRLDV*PP*EHAPLVFSCLYSC*QEQDCHISPEMRLEESF*FLSGF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +??????????????????????????????????????????????????FANKQM?????????????????????????????????????????????????????????????????????????? +>Te26821/110 +???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY??????????????????????? +>Ph73091/110 +?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA?????????????????????????????????????????????????????????????????????????????? +>Am30661/110 +???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE*???? +>Ac28061/110 +PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD*SSVF +>Pg28571/110 +?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD?????
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_1_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gggtttttcttgtagtattccactagctctaccagactctcaaatgatgcggtaccaat +>Ap2303_1/1_1.000_424 +--------------------------------------------ctttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaactaactcaacaaggctctcaaaggatgctgtgccaat +>Ac3644_1/1_1.000_1626 +cagttcatcttcacgttgtttcttgtagtcatacaaagccctcactttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaactaactcaacaaggctttcaaatgatgctgtgccaat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +cccaatcgctgtcactgctctcgaagttgacattttgctgcttcatgaagaaggtcaggaattcgttgtagttgatccgtccgctgtggtccttgtcgatttcgtggacgatctgaaagagctcgtctggattgaggaaggtgttcatctcccggaagatggcgttgatctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtttgaattgggccttgagctgtttgcccttgaccttgtagcccttggccttcagggcctttttcagctccttgaaggtca +>Ac1013_1/1_1.000_525 +cccagtcgctgtcgctgctctcaaagttgacattttgctgcttcatgaagaaggtcaagaattcgtcgtagttgatccgtccgctgtggtccttgtcgatggcgtggacgatcttgaagagctcgtctggatcaaggaaggtgttcatctcttggaaaatggcgttaacctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtttgaattgagccttgagttgtttgcccttgaccttgtagcctttggccttgagggcttttttcagctccttgaaggtca
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +----------------------------------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag------------------------------------------------------------- +>Ap5050_1/1_1.000_243 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttctgaccttccccaagc +>Ac2173_1/1_1.000_330 +ctccttcagaagctggtggcggactaagagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttctgaccttctccaagc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +cgggtagctgccatggacacctgccagacacggatcaggttgtctgtgtatcctgcaaacagcgtctggccatcagctgaccatgccagggatatacactggggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcaggtaacctgagtgtccaaagtggtttgtttttagtttgcagtttgtcagattccaaaccttaaccagtttgtcccagccacaagacacaatgatgggattctgagtgtttggtgagaagcgaacacatgatacccactctgtgtgtccatcttcctgaatggtgtacttgcatacaccgagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctggcggttatcagctgagaaggccacgcttagcacatcttttgtgtgtccgacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagagcgaactgtccatctgatgacataacaacgtcagacacgaaatgtccatgtccacgcaaggccttgcgagggaaaccgtagcgcgattcctcacgagtcagctgccacaggatgagcgatttgtctcttgaagccgacaaaataatatcgggaaattgtggcgttgtagcaatttgagttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt +>Ap1491_1/1_1.000_963 +cgggtagctgccatagatacctgccacacacgaatcaggttgtctgtgtatccagcaaacagtgtctggccatcagctgaccaagccagggatatacactgaggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcagataacctgagtgtccgaagtggtttgtttttagcttgcagtttgtcagattccacaccttaaccagtttgtcccagccacaggacacaatgatgggattctgggtgtttggtgagaatcgaacacatgatacccactctgtgtgcccatcttcctgaatggtatacttgcacaccccaagagtgttccacaacttgatggtcttgtcacgtgaacctgacacaatctgacggttatcagctgagaaagccacacttagcacgtccttcgtgtgtccaacaaacctacgagttgtctgaccagtgccaagatcccacaaacgaagggttccatcccaggatccagacagggcgaactgtccatctgatgacatgacgacgtcagacacgaagtgtccatgtccgcgcaaggccttgcgagggaagccgtaacgcgattcctcgcgagtcagctgccacagaatgagcgatttgtctctagaagccgacaaaatgatatcaggaaattgtggcgttgtagcaatttgggttacccatcctccgtgcccttggagggtaccgcgaagcgtcatttgctccgtcatgtttctt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,14 @@ +>Ac72851/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Te17661/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Ap26441/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Th39471/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pf20921/110 +-----------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagttgattgtcacctgacggatcagttcatcaaagcactgtgaatagagttctcttcttattgaacagatgccggtttctcgggcgagtctttgctgtag----------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pu7631/1100 +--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggattatcatatttaaccagagaggatttcggaggaatcat-------------------- +>Am31481/110 +tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagttaatggtcacttggcgaatcaactcgtcaaagcattgcgaatagagctctcgtctgaccggacagattcctgtttcccgggcctgtctctgctgtagacgtctatccagttcctcctgtagattgactacgtctagacgtgtagccaccttgagagcacgcgcccttggtgttttcttgtctgtattcctgctaacaagaacaggattgtcatatttcaccagagatgcgtttggaggaatcattttgatttttgtcgggtttt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_04_Best_ORF_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Te26821/110 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt------------------------------------------------------------------- +>Ph73091/110 +-------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Am30661/110 +---------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaataaag---------- +>Ac28061/110 +ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgactaaagcagcgtgttt +>Pg28571/110 +---gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac---------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_1_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +?????????????????????????????????????????????????????????????VFLVVFH +>Ap2303_1/1_1.000_424 +???????????????FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN +>Ac3644_1/1_1.000_1626 +QFIFTLFLVVIQSPHFNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV +>Ac1013_1/1_1.000_525 +PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +???????????????????VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT???????????????? +>Ap5050_1/1_1.000_243 +EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF +>Ac2173_1/1_1.000_330 +EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,14 @@ +>Ac72851/110 +??????????????????????????????????????????????????? +>Te17661/110 +??????????????????????????????????????????????????? +>Ap26441/110 +??????????????????????????????????????????????????? +>Th39471/110 +??????????????????????????????????????????????????? +>Pf20921/110 +??????????????LSSFQKRRCSHT????????????????????LAQRS +>Pu7631/1100 +??????????????????????????????????????????????????? +>Am31481/110 +SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? +>Te26821/110 +???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? +>Ph73091/110 +?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? +>Am30661/110 +???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE +>Ac28061/110 +PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD +>Pg28571/110 +?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_1_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am7472_1/1_1.000_254 +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gggtttttcttgtagtattccac +>Ap2303_1/1_1.000_424 +--------------------------------------------ctttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaac +>Ac3644_1/1_1.000_1626 +cagttcatcttcacgttgtttcttgtagtcatacaaagccctcactttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt +>Ac1013_1/1_1.000_525 +cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +-------------------------------------------------------ttgtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacgag---------------------------------------------- +>Ap5050_1/1_1.000_243 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc +>Ac2173_1/1_1.000_330 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_2_with_7_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,14 @@ +>Ac72851/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------- +>Te17661/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------- +>Ap26441/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------- +>Th39471/110 +--------------------------------------------------------------------------------------------------------------------------------------------------------- +>Pf20921/110 +-----------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagt +>Pu7631/1100 +--------------------------------------------------------------------------------------------------------------------------------------------------------- +>Am31481/110 +tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_05_CDS_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Te26821/110 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- +>Ph73091/110 +-------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Am30661/110 +---------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa +>Ac28061/110 +ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac +>Pg28571/110 +---gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_06_CDS_with_M_aa/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_06_CDS_with_M_aa/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? +>Te26821/110 +???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? +>Ph73091/110 +?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? +>Am30661/110 +???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE +>Ac28061/110 +PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD +>Pg28571/110 +?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_06_CDS_with_M_nuc/test1/orthogroup_6_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_06_CDS_with_M_nuc/test2/orthogroup_4_with_6_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,12 @@ +>Th44731/110 +------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Te26821/110 +---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- +>Ph73091/110 +-------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Am30661/110 +---------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa +>Ac28061/110 +ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac +>Pg28571/110 +---gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_1_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +GGSALALVLITSGRNSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSLPPEAHKDPSGDTVTQFR +>Ap1491_1/1_1.000_963 +GGSALALVLITSGRSSSTTTLPSRSQIFMLGPEAAQSQYLLGLKHSELMTSPPSNVYRCLPSFKSHNIAWPSFPPEAHKDPSGDTVTQFR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap2303_1/1_1.000_424 +FNLRYKIIWICVHFSTVYCLFIWIHSLLLDNFLINRISEFHFSVKWVLLVILN +>Ac3644_1/1_1.000_1626 +FNLRYKIIWICVHFSTVNCLFIWIHSLLLNNFLINSISEFHFSVKWVLLVIFN
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +-------------------VSVVDVKWHVRSRYSKLLPFLALSDHTCGKTT---------------- +>Ap5050_1/1_1.000_243 +EIWHSQARTKKEDEPRHQFVSVVHVERHVRSGKTPLLPFFTPSNHTCGKSTSKLIKTKSSLQHFHSF +>Ac2173_1/1_1.000_330 +EIWHSQARTKKEDEPSHQLVSVVHIERHVRSGKTPLLPFFTSPNHTCGKSTSKLVKTKSSLQHFQRF
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test1/orthogroup_4_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +SRRCPSFRLCFCPPARKPAAWRPLCGRHPGLDPSRSGILEGIFSCRRLYQTV +>Ac1013_1/1_1.000_525 +PRRCPSFRLCFCPPARKPAAWLPLCGRHPGLGPSRSSILEGLFSYRHLYQTV
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_aa/test2/orthogroup_1_with_4_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,8 @@ +>Ac28061/110 +EAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD +>Pg28571/110 +EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD +>Ph73091/110 +----RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA------------------------------------------------------------------------- +>Am30661/110 +----------KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK---------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_1_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ac6688_1/1_1.000_963 +ggtggttcagcgctggcactggtactgatcacttctggacgcaactcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaggcagcacaaagccaatatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccacaacattgcctggccatccttaccaccagaagcacacaaagatccatcaggggacacggtgacacagttcagg +>Ap1491_1/1_1.000_963 +ggtggctcggcactggcactggtgctgatcacttctggacgcagctcatccacaacaaccttgccttccagatcccagatctttatgcttggtccagaagcagcacaaagccagtatctgttggggctgaagcacagtgagttgatgacatcaccaccatccaatgtgtacagatgcttgccttcattcaaatcccataacattgcctggccatcttttccaccagaagcgcacaaagatccatcaggggacacagtgacacagttcaga
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_2_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap2303_1/1_1.000_424 +tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtatattgcctgttcatctggatccattccttgttgctggacaacttcctcattaaccgcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatacttaac +>Ac3644_1/1_1.000_1626 +tttaatcttagatacaaaatcatttggatttgtgtacatttctccactgtaaattgcctgttcatctggatccattccttgttgttgaacaacttcctcattaacagcatatctgagtttcatttttctgtaaagtgggttcttcttgtaatatttaac
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_3_with_3_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,6 @@ +>Am3527_1/1_1.000_270 +---------------------------------------------------------gtatctgttgttgatgtcaaatggcatgttcgatccaggtactccaagctgttgccattcttggctttgtctgaccacacttgtggaaaaacgacg------------------------------------------------ +>Ap5050_1/1_1.000_243 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccacgccatcaatttgtatcggttgttcatgtcgaaaggcatgttagatccgggaagacccctctgttgccattcttcactccgtcgaaccacacttgtggaaaatcgacgagtaagttgattaagacgaagagctctctgcaacattttcacagcttc +>Ac2173_1/1_1.000_330 +gagatatggcactcccaagccagaaccaaaaaagaggatgaaccaagccatcaacttgtatcggttgttcatatcgaaaggcatgttagatccgggaagacccctttgttgccattcttcacttcgccgaaccacacttgtggaaaatcgacgagtaagctggttaagacgaagagctctctgcaacattttcaacgcttc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test1/orthogroup_4_with_2_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,4 @@ +>Ap5072_1/1_1.000_437 +tctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggcggcctctttgtggtagacatccgggacttgacccatcgcgatcaggtattcttgaagggatattttcttgtcgccgtctttatcaaactgtt +>Ac1013_1/1_1.000_525 +cctcgccgatgtccaagcttccgtctttgtttttgtccgcccgctcgaaagcctgccgcatggctgcctctttgtggtaggcatccgggacttggcccatcgcgatcaagtattcttgaagggttattttcttatcgccatctttatcaaactgtt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_ORF_Search_08_CDS_without_indel_nuc/test2/orthogroup_1_with_4_species.fasta Mon Mar 12 06:30:49 2018 -0400 @@ -0,0 +1,8 @@ +>Ac28061/110 +gaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac +>Pg28571/110 +gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac +>Ph73091/110 +------------cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Am30661/110 +------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag---------------------------------------------------------------------------------------------------------------------------------------------------------
--- a/test-data/outputs_ORF_Search_Best_ORF_aa/locus1_sp7.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Te17661/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Ap26441/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Th39471/110 -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->Pf20921/110 -??????????????LSSFQKRRCSHT????????????????????LAQRS*LSPDGSVHQSTVNRVLFLLNRCRFLGRVFAV???????????????????????????????????????????????????????? ->Pu7631/1100 -???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????DYHI*PERISEES??????? ->Am31481/110 -SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS*WSLGESTRQSIANRALV*PDRFLFPGPVSAVDVYPVPPVD*LRLDV*PP*EHAPLVFSCLYSC*QEQDCHISPEMRLEESF*FLSGF
--- a/test-data/outputs_ORF_Search_Best_ORF_aa/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM?????????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY??????????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA?????????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE*???? ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD*SSVF ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD?????
--- a/test-data/outputs_ORF_Search_Best_ORF_nuc/locus1_sp7.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te17661/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Ap26441/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th39471/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pf20921/110 ------------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagttgattgtcacctgacggatcagttcatcaaagcactgtgaatagagttctcttcttattgaacagatgccggtttctcgggcgagtctttgctgtag----------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pu7631/1100 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggattatcatatttaaccagagaggatttcggaggaatcat-------------------- ->Am31481/110 -tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagttaatggtcacttggcgaatcaactcgtcaaagcattgcgaatagagctctcgtctgaccggacagattcctgtttcccgggcctgtctctgctgtagacgtctatccagttcctcctgtagattgactacgtctagacgtgtagccaccttgagagcacgcgcccttggtgttttcttgtctgtattcctgctaacaagaacaggattgtcatatttcaccagagatgcgtttggaggaatcattttgatttttgtcgggtttt
--- a/test-data/outputs_ORF_Search_Best_ORF_nuc/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt------------------------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaataaag---------- ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgactaaagcagcgtgttt ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac---------------
--- a/test-data/outputs_ORF_Search_CDS_aa/locus1_sp7.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 -??????????????????????????????????????????????????? ->Te17661/110 -??????????????????????????????????????????????????? ->Ap26441/110 -??????????????????????????????????????????????????? ->Th39471/110 -??????????????????????????????????????????????????? ->Pf20921/110 -??????????????LSSFQKRRCSHT????????????????????LAQRS ->Pu7631/1100 -??????????????????????????????????????????????????? ->Am31481/110 -SFSPCRPCLVLLVRLSSYQKLQSSHTGSGRQRSSYGSHHEHVVTTNLAQHS
--- a/test-data/outputs_ORF_Search_CDS_aa/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- a/test-data/outputs_ORF_Search_CDS_nuc/locus1_sp7.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->Ac72851/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te17661/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Ap26441/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Th39471/110 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Pf20921/110 ------------------------------------------gctttcctcattccaaaagcgacgctgctctcataca-----------------------------------------------------------cctcgctcagcgcagt ->Pu7631/1100 ---------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am31481/110 -tctttctctccatgtcggccttgccttgttctgcttgtaaggctttcctcataccaaaagctacagagctctcatacagggtctggtaggcagcgatcgtcatacggatctcatcacgaacacgtagtaacaacaaacctcgctcagcacagt
--- a/test-data/outputs_ORF_Search_CDS_nuc/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- a/test-data/outputs_ORF_Search_CDS_with_M_aa/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -??????????????????????????????????????????????????FANKQM????????????????????????????????????????????????????????????????????? ->Te26821/110 -???????????????????????????????????????????????????????????????????????????????????????????NEDEDSPHKLYTLVTY?????????????????? ->Ph73091/110 -?????RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA????????????????????????????????????????????????????????????????????????? ->Am30661/110 -???????????KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK??????????????????????????????????????????QTVNVESSE ->Ac28061/110 -PEAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -?EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD
--- a/test-data/outputs_ORF_Search_CDS_with_M_nuc/locus2_sp6.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ ->Th44731/110 -------------------------------------------------------------------------------------------------------------------------------------------------------tttgccaacaagcagatggg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Te26821/110 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgaggatgaagattcaccgcacaaactttatacattagtgacctatgt---------------------------------------------------- ->Ph73091/110 --------------cacgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcct-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 ----------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaaggg---------------------------------------------------------------------------------------------------------------------------ccagaccgtgaatgtggagagcagtgaa ->Ac28061/110 -ccggaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 ----gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac
--- a/test-data/outputs_ORF_Search_CDS_without_indel_aa/locus2_sp4_sp4.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Ac28061/110 -EAMTRREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFAYKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Pg28571/110 -EAMARREKGKKKSVTNEVVTREYTVNIHKRIHGIGFKKRAPRAIKAIRQFAFKQMGTEDVRIETRLNKHIWSKGIRNVPFRVRVRLARKRNEDEDSPHKLYTLVSYVPVTTFKGTQTVNVESSD ->Ph73091/110 -----RREKGKKKSVTNEVVTREYTINIHKRIHGIGFKKRAPRAIKAIRQFA------------------------------------------------------------------------- ->Am30661/110 -----------KKSVTQEVVTREYTINIHKRIHGIGFKRRAPRAVKAIREFAFKQMGTEDVRIETRLNKHVWSK---------------------------------------------------
--- a/test-data/outputs_ORF_Search_CDS_without_indel_nuc/locus2_sp4_sp4.fasta Wed Feb 28 10:38:40 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ ->Ac28061/110 -gaagcgatgacacgccgcgagaaaggcaagaagaagtctgtcaccaacgaggtggtgacacgggaatacaccatcaacatccacaagcgaatccatggaatagggttcaagaagagggcgccacgggctataaaggctatcagacaatttgcctacaagcagatgggaactgaagatgtacgcatagagacaagactgaacaaacacatttggtccaagggaattagaaatgttccattcagagtacgagttcgattggctcgtaagaggaatgaggatgaggactcgcctcacaagctttacaccttggtgtcctatgtacctgtcaccacattcaaaggtacccagacagtaaatgtagagagcagtgac ->Pg28571/110 -gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac ->Ph73091/110 -------------cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ->Am30661/110 -------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag---------------------------------------------------------------------------------------------------------------------------------------------------------