Merge branch 'master' of github.com:jlanga/smsk_trinotate

Snakefile

@@ -37,6 +37,6 @@ rule all:
         # transdecoder + "transdecoder.pep.fai"
         # trinotate + "blastx.tsv",
         # trinotate + "blastp.tsv",
-        # trinotate + "hmmscan.tsv"
-        # trinotate + "init.txt"
+        # trinotate + "hmmscan.tsv",
+        # trinotate + "init.txt",
         trinotate + "trinotate.tsv"

src/config.yaml

@@ -19,5 +19,5 @@ trinotate:
     evalue: 1e-5
     pfam_cutoff: DNC
     rnammer:
-        rnammer_path: /usr/bin/software/rnammer_v1.2/rnammer  # Modify this
+        rnammer_path: ./src/rnammer-1.2/rnammer  # Modify this
         org_type: euk  # arc|bac|euk

src/snakefiles/trinotate.py

@@ -204,20 +204,21 @@
 #     input:
 #         pep = transdecoder + "transdecoder.pep"
 #     output:
-#         tsv = trinotate + "signalp.tsv"
+#         tsv = touch(trinotate + "signalp.tsv")
 #     log:
 #         trinotate + "signalp.log"
 #     benchmark:
 #         trinotate + "signalp.json"
 #     shell:
-#         "signalp "
+#         "./src/signalp-4.1/signalp "
 #             "-f short "
 #             "-n {output.tsv} "
 #             "{input.pep} "
-#         "2> {log}"
-#
-#
-#
+#         "2> {log} 1>&2 "
+
+
+
+
 # rule trinotate_tmhmm:
 #     """
 #     Predict transmembrane regions
@@ -231,35 +232,42 @@
 #     benchmark:
 #         trinotate + "tmhmm.json"
 #     shell:
-#         "tmhmm "
+#         "./src/tmhmm-2.0c/bin/tmhmm "
 #             "--short "
-#         "< transdecoder.pep "
-#         "> tmhmm.out "
-#         "2> {log}"
-#
-#
-#
+#         "< {input.pep} "
+#         "> {output.tsv} "
+#         "2> {log} && "
+#         "rm -rf TMHMM_*"
+
+
+
 # rule trinotate_rnammer:
 #     """
 #     Identify rRNAs
 #     """
 #     input:
 #         assembly = raw + "assembly.fasta",
 #     output:
-#         tsv = trinotate + "rnammer.tsv"
+#         gff = trinotate + "rnammer.gff"
+#         "assembly.fasta.rnammer.gff"
 #     params:
 #         rnammer_path = config["trinotate"]["rnammer"]["rnammer_path"],
-#         org_type = config["trinotate"]["rnammer"]["org_type"]
+#         org_type = config["trinotate"]["rnammer"]["org_type"],
+#         gff_tmp = "assembly.fasta.rnammer.gff"
 #     log:
 #         trinotate + "rnammer.log"
 #     benchmark:
 #         trinotate + "rnammer.json"
 #     shell:
-#         "RnammerTranscriptome.pl "
+#         "./src/Trinotate-3.0.2/util/rnammer_support/RnammerTranscriptome.pl "
 #             "--transcriptome {input.assembly} "
-#             "--path_to_rnammer {params.rnammer_path} "
+#             "--path_to_rnammer  ./src/rnammer-1.2/rnammer "
 #             "--org_type {params.org_type} "
-#         "2> {log}"
+#         "2> {log} 1>&2 ; "
+#         "mv {params.gff_tmp} {output.gff} ; "
+#         "rm tmp.superscaff.rnammer.gff "
+#             "transcriptSuperScaffold.bed "
+#             "transcriptSuperScaffold.fasta"
 
 
 
@@ -278,14 +286,39 @@
         "EMBL_dat_to_Trinotate_sqlite_resourceDB.pl "
             "--sqlite {output.sqlite} "
             "--create "
-        "2> {log}"
+        "2> {log} 1>&2"
 
 
 
-rule trinotate_fill:
+rule trinotate_init:
+    """
+    Initialize db with genes, transcripts and proteins
+    """
     input:
         sqlite = trinotate + "trinotate.sqlite",
         is_created = trinotate + "create.txt",
+        g2t = raw + "gene_to_trans_map.tsv",
+        assembly = raw + "assembly.fasta",
+        proteome = transdecoder + "transdecoder.pep"
+    output:
+        touch(trinotate + "init.txt")
+    log:
+        trinotate + "init.log"
+    benchmark:
+        trinotate + "init.json"
+    shell:
+        "Trinotate {input.sqlite} init "
+            "--gene_trans_map {input.g2t} "
+            "--transcript_fasta {input.assembly} "
+            "--transdecoder_pep {input.proteome} "
+        "2> {log} 1>&2"
+
+
+
+rule trinotate_fill:
+    input:
+        sqlite = trinotate + "trinotate.sqlite",
+        is_init = trinotate + "init.txt",
         eggnog = db + "NOG.annotations.tsv.bulk_load",
         go = db + "go-basic.obo.tab",
         uniprot_index = db + "trinotate.UniprotIndex",
@@ -294,9 +327,9 @@
     output:
         is_filled = touch(trinotate + "fill.txt")
     log:
-        db + "load_trinotate_db.log"
+        db + "fill.log"
     benchmark:
-        db + "load_trinotate_db.json"
+        db + "fill.json"
     shell:
         "EMBL_dat_to_Trinotate_sqlite_resourceDB.pl "
             "--sqlite {input.sqlite} "
@@ -305,62 +338,39 @@
             "--uniprot_index {input.uniprot_index} "
             "--taxonomy_index {input.taxonomy_index} "
             "--pfam {input.pfam} "
-        "> {log} 2>&1"
-
+        "2> {log} 1>&2"
 
 
-rule trinotate_init:
-    """
-    Initialize db with genes, transcripts and proteins
-    """
-    input:
-        sqlite = trinotate + "trinotate.sqlite",
-        is_copied = trinotate + "fill.txt",
-        g2t = raw + "gene_to_trans_map.tsv",
-        assembly = raw + "assembly.fasta",
-        proteome = transdecoder + "transdecoder.pep"
-    output:
-        touch(trinotate + "init.txt")
-    log:
-        trinotate + "init.log"
-    benchmark:
-        trinotate + "init.josn"
-    shell:
-        "Trinotate {input.sqlite} init "
-            "--gene_trans_map {input.g2t} "
-            "--transcript_fasta {input.assembly} "
-            "--transdecoder_pep {input.proteome} "
-        "2> {log}"
 
 
 rule trinotate_load:
     input:
         sqlite = trinotate + "trinotate.sqlite",
-        is_initialized = trinotate + "init.txt",
+        is_filled = trinotate + "fill.txt",
         blastx = trinotate + "blastx.tsv",
         blastp = trinotate + "blastp.tsv",
         pfam = trinotate + "hmmscan.tsv",
         # signalp = trinotate + "signalp.tsv",
         # tmhmm = trinotate + "tmhmm.tsv",
-        # rnammer = trinotate + "rnammer.tsv",
+        # rnammer = trinotate + "rnammer.gff",
     output:
         touch(trinotate + "load.txt")
     log:
         trinotate + "load.log"
     benchmark:
-        trinotate + "load.log"
+        trinotate + "load.json"
     shell:
         "Trinotate {input.sqlite} "
             "LOAD_swissprot_blastp {input.blastp} 2> {log} 1>&2; "
-        "Trinotate {input.sqlite} "
-            "LOAD_swissprot_blastx {input.blastx} 2>> {log} 1>&2; "
         "Trinotate {input.sqlite} "
             "LOAD_pfam {input.pfam} 2>> {log} 1>&2; "
         # "Trinotate {input.sqlite} "
-        #     "LOAD_signalp {input.signalp} 2>> {log} 1>&2; "
-        # "Trinotate {input.sqlite} "
         #     "LOAD_tmhmm {input.tmhmm} 2>> {log} 1>&2; "
         # "Trinotate {input.sqlite} "
+        #     "LOAD_signalp {input.signalp} 2>> {log} 1>&2; "
+        "Trinotate {input.sqlite} "
+            "LOAD_swissprot_blastx {input.blastx} 2>> {log} 1>&2; "
+        # "Trinotate {input.sqlite} "
         #     "LOAD_rnammer {input.rnammer} 2>> {log} 1>&2; "
 
 
@@ -382,6 +392,6 @@
     shell:
         "Trinotate {input.sqlite} report "
             "-E {params.evalue} "
-            "--pfam_cutoff {params.pfam_cutoff}"
+            "--pfam_cutoff {params.pfam_cutoff} "
         "> {output} "
         "2> {log}"

transcript.fa

@@ -97,4 +97,89 @@ ATATATCAAAGAGTATTTTATTTACTGGGCTTTAGTGCTGAATCTACTGATGTGGGCTAG
 CGTCACTGACTTGACCATATGAATACAATCTGGTGCAAATATGTGAAATATTGTAGAGAA
 TAATGAAGTGCTTTGATGTGTAAAAATGTTTGAGATACATTTATACTGTGTGTGGCATAT
 AAATTAATACAAGAAAACAAAAAAAAA
->TRINITY_DN66968_c0_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+>TRINITY_DN99999_c0_g1_i1
+TACGTGGTTTCCTTCATGCATTTGCCCGCTTACCTGGATGATCAATTAATATTAGATAAA
+TTAGAAGGCTGGGGAGTATTTCCCATAACAAAAATTAAAAGAAGGGTATATCCGGGCACA
+GAAATAGAAGATGGAACTCGATATCTCAAAGTGAGATTCCCCAGAGAAGTGATATCTCTC
+CCTTACAGCACAAGACTGGAAACGGCAGAAGGTCAGCAATATTTTAGGGTGATGCACAGC
+CACCAGGTTAAGACTTGTAGGCTGTGCATGAGCCCTGACCATATGGTCAAAGATTGCCCA
+GACTTTAAATGCCATAAATGTGAGGAAAGGGGACATTTTGCCAGAGACTGCGATGCTATT
+AAGTGCCCGGACTGCCAGAACTATTTAAGTAAGTGTGAATGTTGGATGGAGGAAGAGGAG
+GAGGAGGATGAGATCCAGGTGAGTGGGCAAATGCATGAAGGAAACAGTGAAAAGGAAAGT
+AATGAAGAGGAACAAACAACGACACAAACAATACAAACTACAACAGAGGAAATAACATTG
+AAGGAGGAGAATGCAAAAAAAGAAAAGGAAAAAGAAACAGAAACAGACAGTCAACAAATA
+GAGCATGAAGAGGAGGTAGCATGGACACCAATGGACATAACTTCTAGCTTCAAAAACGTT
+TTGGATGTAATTGAAAAAGAGGATCTTAAAGAACAAAGCAAGGGAACGGACAGAGAGACT
+GGAAAACATGAGGAGGAAGTAGAAAAAGACAAACTTGAGAAAAGACAAACAAGACGATCG
+GCAAAAGTTTTATCAAAATTAGAAACTGCAAGAAAAAAGGGTTTGAAAAAAGGACAACTG
+AAAAGCCACAACAGATATGATTCTTTGAGAGGTTTGGGAGAAGAAGAGGACTAAGATGAC
+GGTTTTTATTTCCTTTTTCCTTCTTTTAATGGTTTTAAATTGCGTGTCTTTTAATGCAAG
+AGGTTTAATGGACTTAAGAAAATTTAATAATGTAAAGGAAAAATGTAAAAGAGAAGAAAT
+AATTATTTTACAAGAAACAAATTGGAAAAATGAGGTGATGGACATATATAAAAAAGAATG
+GGATGGGGACTTTTATTATAGTAATGGAGATACGAAAGCTGGGAGAGGAGTAGCAATTTT
+AATAAAGAAGAATGCACTGCAAATGAGTAAAGTAATATATAAAGACAAACAAGGAAAATG
+TATGATCTTAGAAATAAAATATGAAGGGAAAGATATTATTTTAGTTAATGTGCATGCACC
+AAATGAAGAGAGTGAAAAGAAAAGTTTTTTTAACATATTAAGAAGGTTTTTAAAAAACTA
+TAAACAAATAATAGTATGTGGGGATTTTAACACTGTTTTTAGCAGACAGGACATAACAGA
+AGGTATGGTTTTTAAATCAGACACGGGAAGGAAAGAACTAAAATCACTAATAGAGGAAAA
+AGGAATGATAGACATTTGGAGAGAAAGAAATGGGAAGAAAAAGGAGTTTTCTAGAAGACA
+AATAGTAGGGAATTTTGTAAACCAATCAAGAATAGACTATGTGTTATGCACAAGAAATAT
+AGAAATTTATATAGAAAAAATAAGGTACGATGAAACTGTTTTAAGTGACCATAAATTTGT
+ATTTTTTAATTTTAATACAGATGAAATACAAAGAGGCCCAGGGGTATGGACATTAAATAG
+TGATATTTTAAATAACGAAGACTATGTTAAAAAAATAACAGAAATAATTGAAAAGGAAAA
+AGTAAACCAGATTTATAATGAAGACAAAAGACTATGGTGGGAAAATGTCAAATTTCTGAT
+TAAAAAATCAACATTAACATTCTGTAGGATAATACAAAAGAATAAAAGACACAAAGAAAA
+AACAATCAAAGAAAACTTAGAAAAAGAACTAGGAAAAAATGAAAAAGACATTCAAAAAAT
+AAAAGAAATGGAGGGAAAACTGAAAGAAATAGAAGAAAAGAAATATGAAGGAGCTAGACT
+AAGAAGCAAAGCAAAATATGTAGCAGAAGGAGAAAAATGCACAAAGTTCTTCTTTGATTT
+AGAAAGACAAAAAGGAAAAGCAGAAACAATAAAGATAATACAAGGAGCAAAAGGAGAAAG
+CATAGAAGGAAATGAAGAAATTTTAAAAGAAATCAAAAAATACTATGAGGAGTTATTTAA
+AACACAGGGAGTTGATGAAGTACAAATGGCAAAATTATTAAAACAGATAAAAACAAAAGT
+AGATGAAGAGGATAAAAAAGAATGCGACCAAGAAATAGGGGAAGAAGAAATAAGAAAAGC
+AATAGAAAGCTTGAACAAAAAGAAAAGTCCAGGAATAGATGGTTTAAATAGTGAATTTTA
+TGTATGTTTTAAAGAAATTTTAATTCCAATTTTAATTGACGTTTTTAAGGAAATACTGCA
+AAAAGAAGAACTAAATGAAAGAATGGGAATGGGATTAATGAAATTAATACACAAAAAAGG
+AGAAAAGACATTGTTAAAAAATTACAGACCAATCACAATGTTAAACACAGATTTGAAGAT
+TTTAACAAAAATTTTAGCAAATAGATTAAAAGAAGTGATGCCAAAAATAATTAAAACAAC
+ACAGGCCTATGCGATAAAAGGAAGAGACATAGCAGACATAACAATGAGCATAAAAGACAT
+CATAGAATATATGAAGGAGAAAAAAGAGGAAGGATATATAATAAGTCTGGATTTTGAAAA
+AGCTTTTGATAGAGTTGAACACCAGTTTTTATTCAAAGTACTCAAAAAGTTTGGTTTTGG
+AGAAGTTTTTAGAAAATGGATAAAGATTTTGTATAAGGGTATTTTAACAAAAGTTAAATG
+TAATGGCTTTTTAACAGAATGTTTTAAAATAACAAGATCGATAAGGCAAGGATGTCCTCT
+GTCAGCACTTTTATATTCACTTGTGGCAGAACCCCTGGGCTTAGCTATCAACGAAGAAGA
+AAAAATAAAAGGAATTGAGATTGAAGAAAATAAAGTAAATAAAAAAATGTTTCAATATGC
+AGATGACACTACATTAATAGTAAAAGGAAAAGAGAGTGTGAAAGAAGCCATGAAAATAGT
+ACAACAATTTTGTAAAGGATCGGGGAGTAAAGTAAATGAAGACAAAACGGTTTATATGAA
+GTTTGGAAAGGAAACAGATTTAGCAGAATGCACCAATTTCAAAGAAGTAGAAGAAATCAA
+GATTTTAGGGGTTTTATTGGGGAAAGATGCCAGAAAAGCGAGAGATAAGATGTGGGAAGG
+TTTTTTAACAGATATAGAAAGGAGGTTAAATTACTGGAAACTAAGAACACTAACATTAAA
+AGGAAAAGTTTTGATTTTAAATGTTTTAATGGAGTCTAAATTGTGGCATGTTTTATATGT
+TTTAGAAATGCCAATGTGGATAGAAAAGAGGTTGAAAAAATGTTTTACTGATTTTTTATG
+GGGAGGTAAGCCACCAAGGATTGCTTTTAATACAGTCGTAGGGGAAATAGACAAGGGTGG
+TCTGGGTTTAATAGATGTAGAACAAAGAAAAAATAGTTTAAGAGTGAAAAGAATAAAGAA
+GTATCTAGAAAAAGAAAACAAAGCAGAGTGGAAAAAAACAATGAAATATTTTTTAAACAA
+ATGTGGTAATTTTAACATGGGAGATGGGATTTTATGGATGAAAACAAAAGCTTGGATGAC
+AGAAAACTTACCTGAATTTTATAGAGAAATTTTAAGTGCGTGGGGGAATTTTTTAAAACA
+AGTGGAATATAGTCCACATGGAAGGGAAAACATTTTAAACCAACCTCTTTTCTTGAACAA
+TAATATTTTAAGTCAAGGGAAGGTTTTATACTATAAGAAATGGATAGAAGTTGGGATTTT
+AAAAGTGCGGGACATTTTATATGAATTTAAAGAAGGCTTTTTAACTGAACAATATGTTAT
+AGACACAATGGAGGAGGCGAAAGAGGAATACAACAGAAAGGAAATTGAGAAAAATCTTGA
+CATAATTAAACAGGCGATTCCAAAAGAATGGATAAAAAGCATAGAAAATTTTGAAAAAGA
+AAAAGAAACAAAAGAAGTGTATGTGAAAACAGGTGAAAAAATATGCAATTTTAATGAATG
+TACTGTGAAAAATATTTATTGTTTTTTTAGAGAGAATGTTTTTAAAGAACCAACAGCAAA
+CAAATACTGGATAGAGAAATACAAAAATGTAAAAGCAAATGAAATATGGGGAAACATGAA
+AGGAAGGTATGTAGAAACAAAAGTCGAATGTCTAGAATTTTTAATAAGGCACAAAGCAAT
+CTTTTCTGATGTCATTTTAAACAAGATAGGGATGGAACAAAGTGGAATGTGTAAAGTATG
+TCAAAAAGAAGAAGAGGGTTTTTTACACATGTTTTTATATTGTCAAGAATTGGAAGGTTT
+TTTAAAAGATTGTAAAGTTTTAATTAAAGGACTACTTGGAGACTGGGATGAAAATGAAAC
+AGAATGGAACAGAGTAGTGATGTTGGGATGGAATAAGAACAATGAAAATAAGAAAATAGT
+AAACCTATGTATAATGCTGATGAAAAATGCAATGTGGGAAAGGAGAATTGTGGCAAAAAA
+AGAGAAAATGGTGATGGATGTATGGGGAATTTTTAAGAGGAAAATGGAGAGATATGTGGA
+AAAACTGTATATATATCATAAAAATGAGAACATTTTGAGTGAGCTGCACAAAATTCTGAC
+GGACAAAGCATGTCAAGTTTTTAAAGAAATGAACTGGAAACTACCACATTTTTAATGTTT
+TTGAATATGAAATGATTTTTTAATGTCTGTTTTATTATGATTTACTGTAAAAGATTGTAA
+TTGAAATTGGTTCAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAATGCCCGATCTCA
+TCTGAACTCGGAAGTAAAGCAGGGTCGGGCCTGGTAAGTACTTGGATGGGAGACCGCCTG
+GGAATACCAGGTGCTGTAAGCTTTTCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAGAAATGCCCGATCTCATCTGAATTCGGAAGTAAAGCAGGGTCGGGCCTGGTTAGT
+ACT