Merge pull request #82 from ShawHahnLab/release-0.6.0

Version 0.6.0

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build:
     machine:
-      image: ubuntu-2004:202201-02
+      image: default
     steps:
       - checkout:
           path: igseq

CHANGELOG.md

@@ -1,5 +1,34 @@
 # Changelog
 
+## 0.6.0 - 2024-08-23
+
+### Added
+
+ * `tree` now supports defining seq set groupings via positions in an alignment
+   ([#81])
+ * `tree` now supports writing FigTree settings in NEXUS output files ([#79])
+ * `tree` now writes seq set groupings in NEXUS output files ([#67])
+
+### Changed
+
+ * `tree` defaults to simpler color-coding logic for sets of sequences (for
+   sequences in multiple sets, by default the last set's color is used) ([#77])
+ * `igblast` has its version pinned at 1.21.0 rather than left unspecified
+   ([#70])
+
+### Fixed
+
+ * `igblast` now handles crashes during file input more clearly ([#75])
+ * `phix` can accept a custom path for the read counts CSV file ([#74])
+
+[#81]: https://github.com/ShawHahnLab/igseq/pull/81
+[#79]: https://github.com/ShawHahnLab/igseq/pull/79
+[#77]: https://github.com/ShawHahnLab/igseq/pull/77
+[#75]: https://github.com/ShawHahnLab/igseq/pull/75
+[#74]: https://github.com/ShawHahnLab/igseq/pull/74
+[#70]: https://github.com/ShawHahnLab/igseq/pull/70
+[#67]: https://github.com/ShawHahnLab/igseq/pull/67
+
 ## 0.5.1 - 2023-03-31
 
 ### Changed

README.md

@@ -2,8 +2,6 @@
 
 [![CircleCI Build Status](https://circleci.com/gh/ShawHahnLab/igseq/tree/dev.svg?style=svg)](https://circleci.com/gh/ShawHahnLab/igseq/tree/dev)
 
-**Work in Progress**
-
 A command-line tool for various common Ig-Seq tasks.  These are heavily biased
 toward the peculiarities of our protocol and for rhesus macaque antibody
 sequences.  Your mileage may vary.
@@ -32,15 +30,17 @@ categories: early read processing tasks (demultiplex, trim, merge, etc.), and
 various convenience tools (IgBLAST this against that, what database has the
 closest V gene, etc.).
 
+### Read Processing
+
 Read processing subcommands:
 
- * getreads: Run [bcl2fastq] with an autogenerated sample sheet and some
-   customized settings to write Undetermined I1/R1/R2 fastq.gz files.
- * demux: Demultiplex the I1/R1/R2 files according to per-sample barcodes
+ * getreads: Run [bcl2fastq] with some customized settings to write
+   Undetermined I1/R1/R2 fastq.gz files.
+ * demux: Demultiplex the I1/R1/R2 files according to per-sample barcodes.
  * phix: Map reads left unassigned post-demux to the PhiX genome for
-   troubleshooting
- * trim: Run [cutadapt] to remove adapter/primer/barcode and low-quality
-   sequences on a per-sample basis
+   troubleshooting.
+ * trim: Run [Cutadapt] to remove adapter/primer/barcode and low-quality
+   sequences on a per-sample basis.
  * merge: Merge R1/R2 for each sample with [PEAR].
 
 Each step in the read processing produces a read counts summary CSV table
@@ -103,6 +103,26 @@ The chain type is used to select the appropriate constant region primer:
 See `igseq/data/examples/readproc.sh` for an example read processing workflow
 from start to finish with a small set of reads.
 
+### Convenience Tools
+
+Various convenience subcommands:
+
+ * igblast: Run IgBLAST with a streamlined interface.  This can handle
+   transparent database and auxiliary data file creation from rhesus or human
+   germline V(D)J references.
+ * summarize: Summarize attributes of antibody sequences in a table via
+   IgBLAST.
+ * vdj-gather: Gather VDJ sequences into one directory.
+ * vdj-match: Find closest-matching germline VDJ sequences.
+ * convert: Convert between FASTA/FASTQ/CSV/TSV formats.
+ * identity: Calculate pairwise identities.
+ * msa: Create multiple sequence alignments (using [MUSCLE]).
+ * tree: Create and format phylogenetic trees (using [FastTree]).
+ * list, show: list built-in reference data files, and show file contents with
+   support for pretty-printing some common formats.
+
 [bcl2fastq]: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
-[cutadapt]: https://cutadapt.readthedocs.io
-[PEAR]: https://cme.h-its.org/exelixis/web/software/pear/
+[Cutadapt]: https://cutadapt.readthedocs.io
+[PEAR]: https://cme.h-its.org/exelixis/web/software/pear
+[MUSCLE]: https://drive5.com/muscle5
+[FastTree]: http://www.microbesonline.org/fasttree

conda/meta.yaml

@@ -1,5 +1,5 @@
 # https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
-{% set version = "0.5.1" %}
+{% set version = "0.6.0" %}
 {% set build = "0" %}
 
 package:
@@ -12,7 +12,7 @@ about:
 
 source:
   git_url: https://github.com/shawhahnlab/igseq.git
-  git_rev: master
+  git_rev: release-0.6.0
   git_depth: 1
 
 build:
@@ -44,12 +44,12 @@ requirements:
   run:
     - python>=3.9.7,<4
     - biopython>=1.80,<2
-    - python-newick>=1.3.2,<2
-    - bwa>=0.7.17,<0.8
-    - samtools>=1.16,<2
+    - python-newick>=1.9,<2
+    - bwa>=0.7.18,<0.8
+    - samtools>=1.19,<2
     - cutadapt>=3.7,<4
     - pear>=0.9.6,<1
-    - igblast>=1.19,<2
+    - igblast>=1.21,<1.22
     - muscle>=5.1,<6
     - fasttree>=2.1,<3
 

igseq/__main__.py

@@ -263,6 +263,10 @@ def _main_tree(args):
         pattern=args.set_pattern,
         lists=args.set_list,
         colors=args.set_color,
+        merge_colors=args.merge_colors,
+        figtree_opts=args.figtree_option,
+        set_pos=args.set_pos,
+        set_pos_msa=args.set_pos_msa,
         colmap=colmap,
         dry_run=args.dry_run)
 
@@ -599,6 +603,19 @@ def __setup_arg_parser():
     p_tree.add_argument("--set-color", "-C", action="append",
         help="setname=colorcode, like set1=#ff0000, to override automatic set colors. "
         "This can be given multiple times for multiple set/color pairs.")
+    p_tree.add_argument("--merge-colors", "-M", action="store_true",
+        help="merge the set colors applying to each sequence?  Otherwise (the default) apply "
+        "colors set-by-set with the last set taking precedence")
+    p_tree.add_argument("--figtree-option", "-F", action="append",
+        help="key=value to include in a figtree block for NEXUS output, like "
+        "'nodeLabels.fontSize=8'.  This can be given multiple times.")
+    p_tree.add_argument("--set-pos",
+        help="Position ranges to use to define set membership for sequences.  "
+        "If input is not an alignment, --set-pos-msa is required.")
+    p_tree.add_argument("--set-pos-msa",
+        help="alignment FASTA to use with --set-pos to define set membership.  "
+        "Only required if sets are being defined by alignment position and "
+        "input is not an alignment.")
     p_tree.set_defaults(func=_main_tree)
 
     return parser

igseq/data/environment.yml

@@ -7,11 +7,11 @@ channels:
 dependencies:
   - python>=3.9.7,<4
   - biopython>=1.80,<2
-  - python-newick>=1.3.2,<2
-  - bwa>=0.7.17,<0.8
-  - samtools>=1.16,<2
+  - python-newick>=1.9,<2
+  - bwa>=0.7.18,<0.8
+  - samtools>=1.19,<2
   - cutadapt>=3.7,<4
   - pear>=0.9.6,<1
-  - igblast>=1.19,<2
+  - igblast>=1.21,<1.22
   - muscle>=5.1,<6
   - fasttree>=2.1,<3

igseq/data/examples/outputs/igblast/igblast.tsv

@@ -1,2 +1,2 @@
-sequence_id	sequence	locus	stop_codon	vj_in_frame	v_frameshift	productive	rev_comp	complete_vdj	v_call	d_call	j_call	sequence_alignment	germline_alignment	sequence_alignment_aa	germline_alignment_aa	v_alignment_start	v_alignment_end	d_alignment_start	d_alignment_end	j_alignment_start	j_alignment_end	v_sequence_alignment	v_sequence_alignment_aa	v_germline_alignment	v_germline_alignment_aa	d_sequence_alignment	d_sequence_alignment_aa	d_germline_alignment	d_germline_alignment_aa	j_sequence_alignment	j_sequence_alignment_aa	j_germline_alignment	j_germline_alignment_aa	fwr1	fwr1_aa	cdr1	cdr1_aa	fwr2	fwr2_aa	cdr2	cdr2_aa	fwr3	fwr3_aa	fwr4	fwr4_aa	cdr3	cdr3_aa	junction	junction_length	junction_aa	junction_aa_length	v_score	d_score	j_score	v_cigar	d_cigar	j_cigar	v_support	d_support	j_support	v_identity	d_identity	j_identity	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	fwr1_start	fwr1_end	cdr1_start	cdr1_end	fwr2_start	fwr2_end	cdr2_start	cdr2_end	fwr3_start	fwr3_end	fwr4_start	fwr4_end	cdr3_start	cdr3_end	np1	np1_length	np2	np2_length
-query	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	IGH	F	T	F	T	F	T	IGHV4-173*01	IGHD4-23*01,IGHD4-41*01	IGHJ4*01	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCACCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGANNNNTACAGTAACNNNNNNNNNNACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSPDYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYCARDTYSNIPPNFDYWGQGVLVTVSS	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYYCARXXYSNXXXXFDYWGQGVLVTVSS	1	296	301	309	320	364	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSPDYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYCAR	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCACCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR	TACAGTAAC	YSN	TACAGTAAC	YSN	ACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	FDYWGQGVLVTVSS	ACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	FDYWGQGVLVTVSS	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCT	QLQLQESGPGLVKPSETLSLTCAVS	GGTGGCTCCATCAGCAGTAACTAC	GGSISSNY	TGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGT	WSWIRQPPGKGLEWIGR	ATCTCTGGTAGTGGTGGGAGCCCC	ISGSGGSP	GACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGT	DYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYC	TGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCA	WGQGVLVTVSS	GCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTAC	ARDTYSNIPPNFDY	TGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGG	48	CARDTYSNIPPNFDYW	16	456.805	17.992	87.208	296M68S	300S4N9M55S3N	319S3N45M	1.262e-130	7.987e-01	1.596e-21	99.324	100.000	100.000	1	296	1	296	301	309	5	13	320	364	4	48	1	75	76	99	100	150	151	174	175	288	331	363	289	330	TACT	4	ATCCCACCCA	10
+sequence_id	sequence	sequence_aa	locus	stop_codon	vj_in_frame	v_frameshift	productive	rev_comp	complete_vdj	d_frame	v_call	d_call	j_call	sequence_alignment	germline_alignment	sequence_alignment_aa	germline_alignment_aa	v_alignment_start	v_alignment_end	d_alignment_start	d_alignment_end	j_alignment_start	j_alignment_end	v_sequence_alignment	v_sequence_alignment_aa	v_germline_alignment	v_germline_alignment_aa	d_sequence_alignment	d_sequence_alignment_aa	d_germline_alignment	d_germline_alignment_aa	j_sequence_alignment	j_sequence_alignment_aa	j_germline_alignment	j_germline_alignment_aa	fwr1	fwr1_aa	cdr1	cdr1_aa	fwr2	fwr2_aa	cdr2	cdr2_aa	fwr3	fwr3_aa	fwr4	fwr4_aa	cdr3	cdr3_aa	junction	junction_length	junction_aa	junction_aa_length	v_score	d_score	j_score	v_cigar	d_cigar	j_cigar	v_support	d_support	j_support	v_identity	d_identity	j_identity	v_sequence_start	v_sequence_end	v_germline_start	v_germline_end	d_sequence_start	d_sequence_end	d_germline_start	d_germline_end	j_sequence_start	j_sequence_end	j_germline_start	j_germline_end	fwr1_start	fwr1_end	cdr1_start	cdr1_end	fwr2_start	fwr2_end	cdr2_start	cdr2_end	fwr3_start	fwr3_end	fwr4_start	fwr4_end	cdr3_start	cdr3_end	np1	np1_length	np2	np2_length
+query	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSPDYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYCARDTYSNIPPNFDYWGQGVLVTVSS	IGH	F	T	F	T	F	T		IGHV4-173*01	IGHD4-23*01,IGHD4-41*01	IGHJ4*01	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCACCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGANNNNTACAGTAACNNNNNNNNNNACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSPDYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYCARDTYSNIPPNFDYWGQGVLVTVSS	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYYCARXXYSNXXXXFDYWGQGVLVTVSS	1	296	301	309	320	364	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCCCCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSPDYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYCAR	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGTATCTCTGGTAGTGGTGGGAGCACCGACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA	QLQLQESGPGLVKPSETLSLTCAVSGGSISSNYWSWIRQPPGKGLEWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFSLKLSSVTAADTAVYYCAR	TACAGTAAC	YSN	TACAGTAAC	YSN	ACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	FDYWGQGVLVTVSS	ACTTTGACTACTGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCAG	FDYWGQGVLVTVSS	CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTCT	QLQLQESGPGLVKPSETLSLTCAVS	GGTGGCTCCATCAGCAGTAACTAC	GGSISSNY	TGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGACGT	WSWIRQPPGKGLEWIGR	ATCTCTGGTAGTGGTGGGAGCCCC	ISGSGGSP	GACTACAACCCCTCCCTCAAGAGTCGAGTCACCATTTCAACAGACACGTCCAAGAGCCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGT	DYNPSLKSRVTISTDTSKSQFSLKLSSVTAADTAVYYC	TGGGGCCAGGGAGTCCTGGTCACCGTCTCCTCA	WGQGVLVTVSS	GCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTAC	ARDTYSNIPPNFDY	TGTGCGAGAGATACTTACAGTAACATCCCACCCAACTTTGACTACTGG	48	CARDTYSNIPPNFDYW	16	456.805	17.992	87.208	296M68S	300S4N9M55S3N	319S3N45M	1.262e-130	7.987e-01	1.596e-21	99.324	100.000	100.000	1	296	1	296	301	309	5	13	320	364	4	48	1	75	76	99	100	150	151	174	175	288	331	363	289	330	TACT	4	ATCCCACCCA	10