diff --git a/docs/packages/airr-R/news.rst b/docs/packages/airr-R/news.rst index 6f619b3dc..96e253f3e 100644 --- a/docs/packages/airr-R/news.rst +++ b/docs/packages/airr-R/news.rst @@ -1,6 +1,11 @@ Release Notes ============= +Version 1.5.0: August 28, 2023 +------------------------------ + +- Updated schema set and examples to v1.5. + Version 1.4.1: August 27, 2022 ------------------------------ diff --git a/docs/packages/airr-R/overview.rst b/docs/packages/airr-R/overview.rst index f0d33e9fd..a952782bf 100644 --- a/docs/packages/airr-R/overview.rst +++ b/docs/packages/airr-R/overview.rst @@ -1,6 +1,6 @@ .. _ROverview: -R Library +AIRR R Reference Library ================================================================================= ``airr`` is an R package for working with data formatted according to diff --git a/docs/packages/airr-R/topics/read_tabular.rst b/docs/packages/airr-R/topics/read_tabular.rst index 5168af399..cf3d3f16a 100644 --- a/docs/packages/airr-R/topics/read_tabular.rst +++ b/docs/packages/airr-R/topics/read_tabular.rst @@ -69,6 +69,7 @@ Examples # Load data file df <- read_rearrangement(file) + See also ~~~~~~~~ diff --git a/docs/packages/airr-R/topics/validate_tabular.rst b/docs/packages/airr-R/topics/validate_tabular.rst index 6ebfc4a8b..bddc42514 100644 --- a/docs/packages/airr-R/topics/validate_tabular.rst +++ b/docs/packages/airr-R/topics/validate_tabular.rst @@ -51,7 +51,6 @@ Examples # Load data file df <- read_rearrangement(file) - .. code:: r diff --git a/docs/packages/airr-R/topics/write_tabular.rst b/docs/packages/airr-R/topics/write_tabular.rst index 5d42d52b9..62c32e302 100644 --- a/docs/packages/airr-R/topics/write_tabular.rst +++ b/docs/packages/airr-R/topics/write_tabular.rst @@ -62,7 +62,7 @@ Examples # Load data file df <- read_rearrangement(file) - + .. code:: r @@ -70,7 +70,7 @@ Examples # Write a Rearrangement data file outfile <- file.path(tempdir(), "output.tsv") write_tabular(df, outfile, schema=RearrangementSchema) - + See also ~~~~~~~~ diff --git a/docs/packages/airr-R/vignettes/Usage-Vignette.rst b/docs/packages/airr-R/vignettes/Usage-Vignette.rst index 4dc25363f..29ec0acc9 100644 --- a/docs/packages/airr-R/vignettes/Usage-Vignette.rst +++ b/docs/packages/airr-R/vignettes/Usage-Vignette.rst @@ -50,7 +50,7 @@ usage is straightforward, as the file format is a typical tabulated file. The argument that needs attention is ``base``, with possible values ``"0"`` and ``"1"``. ``base`` denotes the starting index for positional fields in the input file. Positional fields are those that -contain alignment coordinates and names ending in "_start" and "_end". +contain alignment coordinates and names ending in “\_start” and “\_end”. If the input file is using 1-based closed intervals (R style), as defined by the standard, then positional fields will not be modified under the default setting of ``base="1"``. If the input file is using @@ -76,39 +76,39 @@ Reading Rearrangements ## Rows: 101 ## Columns: 33 - ## $ sequence_id "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7656… - ## $ sequence "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAGCCC… - ## $ rev_comp FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE… - ## $ productive TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE… - ## $ vj_in_frame TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T… - ## $ stop_codon FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, FAL… - ## $ v_call "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-39*0… - ## $ d_call "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "IGH… - ## $ j_call "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IGHJ6… - ## $ c_call "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGHG",… - ## $ sequence_alignment "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT… - ## $ germline_alignment "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCT… - ## $ junction "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTATTTT… - ## $ junction_aa "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTRYSS… - ## $ v_cigar "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X9=1… - ## $ d_cigar "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265S9N… - ## $ j_cigar "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S8N4… - ## $ v_sequence_start 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, 21,… - ## $ v_sequence_end 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 260,… - ## $ v_germline_start 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, … - ## $ v_germline_end 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 316,… - ## $ d_sequence_start 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 265, … - ## $ d_sequence_end 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 270, … - ## $ d_germline_start 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, 4, … - ## $ d_germline_end 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 16, … - ## $ j_sequence_start 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 293,… - ## $ j_sequence_end 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 327,… - ## $ j_germline_start 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, 9, … - ## $ j_germline_end 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, 53,… - ## $ junction_length 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, 45,… - ## $ np1_length 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8, 7… - ## $ np2_length 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1, 11… - ## $ duplicate_count 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3, 2,… + ## $ sequence_id "SRR765688.7787", "SRR765688.35420", "SRR765688.36681", "SRR765688.33811", "SRR765688.44149", "SRR765688.15636", "SRR765688.20304", "SRR765688.13860", "SRR7… + ## $ sequence "NNNNNNNNNNNNNNNNNNNNGCTGACCTGCACCTTCTCTGGATTCTCACTCAGTACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGCCAAATATTACAGCACCAG… + ## $ rev_comp FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA… + ## $ productive TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, T… + ## $ vj_in_frame TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE… + ## $ stop_codon FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, TRUE, FALSE, FALSE, FALSE, FALSE, … + ## $ v_call "IGHV2-5*02", "IGHV5-51*01", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV7-4-1*02", "IGHV2-5*02", "IGHV7-4-1*02", "IGHV6-1*01,IGHV6-1*02", "IGHV7-4-1*02", "IGHV4-3… + ## $ d_call "IGHD5-24*01", "IGHD3-16*02,IGHD3-3*01,IGHD3-3*02", "IGHD3-22*01", "IGHD3-9*01", "IGHD1-26*01", "IGHD2-21*02", "IGHD1-26*01,IGHD2-21*02,IGHD3/OR15-3a*01", "… + ## $ j_call "IGHJ4*02", "IGHJ6*02,IGHJ6*04", "IGHJ4*02", "IGHJ6*02", "IGHJ6*01", "IGHJ4*02", "IGHJ5*02", "IGHJ4*02", "IGHJ4*02", "IGHJ4*02", "IGHJ5*02", "IGHJ6*02", "IG… + ## $ c_call "IGHG", "IGHG", "IGHG", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHA", "IGHG", "IGHA", "IGHG", "IGHA", "IGHG", "IGH… + ## $ sequence_alignment "...........................................................GCTGACCTGCACCTTCTCTGGATTCTCACTCAGT......ACTAGTGCAGTGGGTGTACACTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG… + ## $ germline_alignment "CAGATCACCTTGAAGGAGTCTGGTCCT...ACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGC......ACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTG… + ## $ junction "TGTGCACACAGTGCGGGATGGCTGCCTGATTACTGG", "TGTGCGAGGCATGGATTATACGGTTGTGATCATACCGGCTGTTATACAAGCTTCTACTACTACGGGATGGACGTCTGG", "TGTGCGAGAGAAGAACGTCGAAGTAGTGGTTAT… + ## $ junction_aa "CAHSAGWLPDYW", "CARHGLYGCDHTGCYTSFYYYGMDVW", "CAREERRSSGYFDHW", "CAREGYYFDTTGSPRSHGLDVW", "CARDSGGMDVW", "CVLSRRLGDSGVQKYYFDYW", "CAREGLWDGRVVTDLW", "CARTR… + ## $ v_cigar "20S56N21=1X11=1X7=1X9=3X62=6D2=1X1=2X2=2X50=1X7=1X4=1X22=1X30=", "20S40N15=1X15=1X11=1X2=1X1=1X1=2X3=1X7=1X41=2X2=1X10=1X3=1X1=1X5=2X5=1X4=1X9=1X19=1X24=2X… + ## $ d_cigar "274S5N7=", "305S29N7=", "293S13N12=", "290S9N8=", "283S4N7=", "273S12N8=", "289S6N6=", "267S9N9=", "281S7N5=", "278S7N5=1X7=", "277S8N7=", "297S9N7=", "265… + ## $ j_cigar "288S11N32=1X4=", "318S7N12=1X15=", "305S5N6=1X14=1X21=", "321S15N5=1X23=1X17=", "290S17N19=", "296S26=1X21=", "311S11N4=1X33=", "280S2N17=1X6=1X21=", "299S… + ## $ v_sequence_start 21, 21, 21, 21, 21, 21, 21, 20, 22, 21, 21, 20, 21, 21, 21, 21, 19, 21, 21, 21, 20, 21, 21, 21, 21, 21, 20, 23, 19, 21, 20, 21, 21, 20, 20, 21, 20, 22, 21, … + ## $ v_sequence_end 269, 276, 283, 283, 283, 264, 283, 259, 281, 266, 264, 294, 258, 283, 273, 279, 274, 259, 278, 280, 262, 271, 281, 262, 264, 283, 259, 279, 278, 280, 261, 2… + ## $ v_germline_start 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, … + ## $ v_germline_end 320, 320, 320, 320, 320, 320, 320, 318, 318, 320, 320, 320, 319, 319, 317, 316, 316, 320, 318, 320, 320, 315, 318, 320, 321, 320, 318, 316, 320, 317, 319, 3… + ## $ d_sequence_start 275, 306, 294, 291, 284, 274, 290, 268, 282, 279, 278, 298, 266, 292, 301, 285, 276, NA, 291, 284, 273, 279, 289, 277, 272, 299, 270, 292, 282, 295, 267, 26… + ## $ d_sequence_end 281, 312, 305, 298, 290, 281, 295, 276, 286, 291, 284, 304, 273, 296, 307, 289, 282, NA, 297, 295, 293, 290, 294, 283, 287, 307, 280, 302, 290, 301, 280, 27… + ## $ d_germline_start 6, 30, 14, 10, 5, 13, 7, 10, 8, 8, 9, 10, 10, 7, 22, 14, 4, NA, 24, 4, 2, 5, 8, 9, 6, 3, 1, 3, 7, 7, 4, 6, 11, 14, 12, 8, 2, 11, 8, 10, 5, 24, 4, 17, 5, 5, … + ## $ d_germline_end 12, 36, 25, 17, 11, 20, 12, 18, 12, 20, 15, 16, 17, 11, 28, 18, 10, NA, 30, 15, 22, 16, 13, 15, 21, 11, 11, 13, 15, 13, 17, 11, 17, 18, 19, 13, 8, 16, 20, 1… + ## $ j_sequence_start 289, 319, 306, 322, 291, 297, 312, 281, 300, 301, 289, 319, 276, 300, 317, 299, 296, 271, 336, 321, 303, 304, 300, 297, 293, 322, 289, 311, 315, 320, 283, 2… + ## $ j_sequence_end 325, 346, 348, 368, 309, 344, 349, 326, 339, 347, 335, 361, 326, 334, 350, 333, 346, 320, 370, 338, 332, 338, 339, 333, 340, 368, 332, 345, 342, 362, 327, 3… + ## $ j_germline_start 12, 8, 6, 16, 18, 1, 12, 3, 9, 2, 5, 20, 9, 14, 15, 14, 2, 13, 28, 18, 6, 14, 9, 15, 1, 16, 5, 14, 8, 5, 4, 12, 9, 1, 20, 15, 6, 6, 5, 6, 5, 9, 1, 6, 5, 5, … + ## $ j_germline_end 48, 35, 48, 62, 36, 48, 49, 48, 48, 48, 51, 62, 59, 48, 48, 48, 52, 62, 62, 35, 35, 48, 48, 51, 48, 62, 48, 48, 35, 47, 48, 46, 48, 44, 62, 48, 48, 51, 50, … + ## $ junction_length 36, 78, 45, 66, 33, 60, 48, 45, 36, 61, 51, 48, 51, 30, 54, 30, 48, 42, 71, 66, 78, 42, 36, 51, 57, 66, 51, 42, 72, 60, 45, 45, 45, 42, 36, 36, 57, 48, 51, … + ## $ np1_length 5, 29, 10, 7, 0, 9, 6, 8, 0, 12, 13, 3, 7, 8, 27, 5, 1, 11, 12, 3, 10, 7, 7, 14, 7, 15, 10, 12, 3, 14, 5, 4, 4, 6, 1, 7, 1, 5, 4, 5, 26, 5, 0, 15, 26, 26, 8… + ## $ np2_length 7, 6, 0, 23, 0, 15, 16, 4, 13, 9, 4, 14, 2, 3, 9, 9, 13, NA, 38, 25, 9, 13, 5, 13, 5, 14, 8, 8, 24, 18, 2, 22, 15, 3, 3, 11, 29, 11, 9, 5, 1, 5, 8, 0, 1, 1,… + ## $ duplicate_count 3, 3, 13, 3, 2, 2, 4, 2, 2, 2, 4, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 2, 2, 5, 2, 2, 3, 2, 4, 2, 3, 4, 8, 2, 2, 2, 2, 3, 2, 4, 3, 4, 2, 5, 2, 2, 7, 3,… Reading AIRR Data Models ~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/docs/standards/news.rst b/docs/standards/news.rst index 7b56d2837..43e9df64a 100644 --- a/docs/standards/news.rst +++ b/docs/standards/news.rst @@ -3,12 +3,67 @@ Schema Release Notes ================================================================================ -Version 1.4.2: TBD, 2023 +Version 1.5.0: August 31, 2023 -------------------------------------------------------------------------------- -1. Added "IGI" to all locus enum fields. +**Version 1.5 schema release.** + +General Schema Changes: + +1. Fixed synchronization errors between the OpenAPI v2 and v3 versions of the + AIRR Schema (airr-schema.yaml and airr-schema-openapi3.yaml). +2. Set the default value of ``x-airr.miarr`` attributes to ``defined``. +3. Converted all ``x-airr.format`` attribute values to snake_case, which + specifically impacts any instance of ``controlled vocabulary`` or + ``physical quantity``. +4. Corrected numerous instances of missing `x-airr.miairr` and + `x-airr.identifier` attributes. +5. Replaced ``x-airr.adc-api-optional`` attribute with + ``x-airr.adc-query-support`` in multiple fields. +6. Added "IGI" as a valid value to the ``locus`` enum fields in multiple + schema. +7. Added ``null`` as a valide value to all nullable enum fields. +8. Removed ``discriminator: AIRR`` from all object definitions. + +Germline and Genotype Schema: + +1. Clarified the descriptions of multiple fields in the Germline and + Genotype schema. 2. Modified ``x-airr: nullable`` and ``x-airr: identifier`` values on multiple - Germline schema. + fields in the Germline and Genotype schema. +3. Removed the ``alignment`` field and added the ``unaligned_sequence``, + ``aligned_sequences``, and ``alignment_labels`` fields to the + ``SequenceDelineationV`` object. +4. Converted the enum values in the ``inference_type`` field of + ``AlleleDescription`` to snake_case. +5. Added the ``allele_similarity_cluster_designation`` and + ``allele_similarity_cluster_member_id`` fields to ``AlleleDescription``. +6. Moved the nested objects ``DocumentedAllele``, ``UndocumentedAllele``, and + ``DeletedGenes`` out of ``Genotype`` and defined them as top-level objects + references by the ``documented_alleles``, ``undocumented_alleles``, and + ``deleted_genes`` fields, respectively. +7. Moved the nested object ``MHCAllele`` out of ``MHCGenotype`` and defined + it as a top-level object referenced by the ``mhc_alleles`` field. + +Single-cell Schema: + +1. Added the ``property_type`` field to the ``CellExpression`` object. +2. Moved the nested ``ReceptorReactivity`` object out of ``Receptor`` + and defined it as a top-level object referenced by the + ``reactivity_measurements`` field. + +Subject Schema: + +1. Removed the nested references to ``GenotypeSet`` and ``MHCGenotypeSet`` + in the ``genotype`` field and modified the definition to point to a + top-level ``SubjectGenotype`` object defining these references. + +DataProcessing Schema: + +1. Clarified the description of ``quality_thresholds`` to indicate that + quality filtering is not mandatory. + + Version 1.4.1: August 27, 2022 -------------------------------------------------------------------------------- diff --git a/lang/R/DESCRIPTION b/lang/R/DESCRIPTION index 3af7fa6c2..9963ee423 100644 --- a/lang/R/DESCRIPTION +++ b/lang/R/DESCRIPTION @@ -1,7 +1,7 @@ Package: airr Type: Package -Version: 1.4.1 -Date: 2022-08-27 +Version: 1.5.0 +Date: 2023-08-28 Authors@R: c(person("Jason", "Vander Heiden", role=c("aut", "cre"), email="jason.vanderheiden@gmail.com"), person("Susanna", "Marquez", role=c("aut"), @@ -39,4 +39,4 @@ Suggests: rmarkdown, tibble, testthat -RoxygenNote: 7.2.1 +RoxygenNote: 7.2.3 diff --git a/lang/R/NEWS.md b/lang/R/NEWS.md index 5142830d6..132d36734 100644 --- a/lang/R/NEWS.md +++ b/lang/R/NEWS.md @@ -1,3 +1,9 @@ +Version 1.5.0: August 28, 2023 +------------------------------------------------------------------------------- + ++ Updated schema set and examples to v1.5. + + Version 1.4.1: August 27, 2022 ------------------------------------------------------------------------------- diff --git a/lang/R/docs/build.R b/lang/R/docs/build.R index 1485c7894..e5bbc4e17 100644 --- a/lang/R/docs/build.R +++ b/lang/R/docs/build.R @@ -6,5 +6,5 @@ build_mkdocs(".", doc_path=doc_path, style="sphinx", yaml=F) run_pandoc(doc_path, format="rst", delete=T) # TODO: Post execution we still need to do cleanup: -# Edit the title and about in docs/packages/airr-R/overview.rst +# Edit the title and about in docs/packages/airr-R/overview.rst and about.rst # Remove the progress bar from the example in docs/*_tabular.rst and docs/ExampleData.rst diff --git a/lang/R/inst/extdata/germline-example.json b/lang/R/inst/extdata/germline-example.json index beb9a42db..926b6d428 100644 --- a/lang/R/inst/extdata/germline-example.json +++ b/lang/R/inst/extdata/germline-example.json @@ -1,395 +1,395 @@ { - "GermlineSet": [ - { - "germline_set_id": "OGRDB:G00007", - "author": "William Lees", - "lab_name": "", - "lab_address": "Birkbeck College, University of London, Malet Street, London", - "acknowledgements": [], - "release_version": 1, - "release_description": "", - "release_date": "2021-11-24", - "germline_set_name": "CAST IGH", - "germline_set_ref": "OGRDB:G00007.1", - "pub_ids": "", - "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, - "species_subgroup": "CAST_EiJ", - "species_subgroup_type": "strain", - "locus": "IGH", - "allele_descriptions": [ - { - "allele_description_id": "OGRDB:A00301", - "allele_description_ref": "OGRDB:Mouse_IGH:IGHV-2DBF", - "maintainer": "William Lees", - "acknowledgements": [], - "lab_address": "Birkbeck College, University of London, Malet Street, London", - "release_version": 1, - "release_date": "24-Nov-2021", - "release_description": "First release", - "label": "IGHV-2DBF", - "sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGATGGTAGTGGCACCTACTATCTGGACTCCTTGAAGAGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", - "coding_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", - "aliases": [ - "watson_et_al:CAST_EiJ_IGHV5-3" - ], - "locus": "IGH", - "chromosome": null, - "sequence_type": "V", - "functional": true, - "inference_type": "Rearranged", - "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, - "species_subgroup": "CAST_EiJ", - "species_subgroup_type": "strain", - "status": "active", - "gene_designation": null, - "subgroup_designation": null, - "allele_designation": null, - "gene_start": null, - "gene_end": null, - "utr_5_prime_start": null, - "utr_5_prime_end": null, - "leader_1_start": null, - "leader_1_end": null, - "leader_2_start": null, - "leader_2_end": null, - "v_rs_start": null, - "v_rs_end": null, - "v_gene_delineations": [ - { - "sequence_delineation_id": "1", - "delineation_scheme": "IMGT", - "fwr1_start": 1, - "fwr1_end": 78, - "cdr1_start": 79, - "cdr1_end": 114, - "fwr2_start": 115, - "fwr2_end": 165, - "cdr2_start": 166, - "cdr2_end": 195, - "fwr3_start": 196, - "fwr3_end": 312, - "cdr3_start": 313, - "alignment": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "23", - "24", - "25", - "26", - "27", - "28", - "29", - "30", - "31", - "32", - "33", - "34", - "35", - "36", - "37", - "38", - "39", - "40", - "41", - "42", - "43", - "44", - "45", - "46", - "47", - 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"First release", - "label": "IGHV-2ETO", - "sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC", - "coding_sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCT...GGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGC......ACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGAT.........GATGATAAGTACTATAACCCATCCCTGAAG...AGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC", - "aliases": [ - "watson_et_al:CAST_EiJ_IGHV8-2" - ], - "locus": "IGH", - "chromosome": null, - "sequence_type": "V", - "functional": true, - "inference_type": "Rearranged", - "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, - "species_subgroup": "CAST_EiJ", - "species_subgroup_type": "strain", - "status": "active", - "gene_designation": null, - "subgroup_designation": null, - "allele_designation": null, - "gene_start": null, - "gene_end": null, - "utr_5_prime_start": null, - "utr_5_prime_end": null, - "leader_1_start": null, - "leader_1_end": null, - "leader_2_start": null, - "leader_2_end": null, - "v_rs_start": null, - "v_rs_end": null, - "v_gene_delineations": [ - { - "sequence_delineation_id": "1", - "delineation_scheme": "IMGT", - "fwr1_start": 1, - "fwr1_end": 78, - "cdr1_start": 79, - "cdr1_end": 114, - "fwr2_start": 115, - "fwr2_end": 165, - "cdr2_start": 166, - "cdr2_end": 195, - "fwr3_start": 196, - "fwr3_end": 312, - "cdr3_start": 313, - "alignment": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "23", - "24", - "25", - "26", - "27", - "28", - "29", - "30", - "31", - "32", - "33", - "34", - "35", - "36", - "37", - "38", - "39", - 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"release_version": 1, + "release_description": "", + "release_date": "2021-11-24", + "germline_set_name": "CAST IGH", + "germline_set_ref": "OGRDB:G00007.1", + "pub_ids": "", + "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, + "species_subgroup": "CAST_EiJ", + "species_subgroup_type": "strain", + "locus": "IGH", + "allele_descriptions": [ + { + "allele_description_id": "OGRDB:A00301", + "allele_description_ref": "OGRDB:Mouse_IGH:IGHV-2DBF", + "maintainer": "William Lees", + "acknowledgements": [], + "lab_address": "Birkbeck College, University of London, Malet Street, London", + "release_version": 1, + "release_date": "24-Nov-2021", + "release_description": "First release", + "label": "IGHV-2DBF", + "sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "coding_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "aliases": [ + "watson_et_al:CAST_EiJ_IGHV5-3" + ], + "locus": "IGH", + "chromosome": null, + "sequence_type": "V", + "functional": true, + "inference_type": "rearranged_only", + "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, + "species_subgroup": "CAST_EiJ", + "species_subgroup_type": "strain", + "status": "active", + "gene_designation": null, + "subgroup_designation": null, + "allele_designation": null, + "gene_start": null, + "gene_end": null, + "utr_5_prime_start": null, + "utr_5_prime_end": null, + "leader_1_start": null, + "leader_1_end": null, + "leader_2_start": null, + "leader_2_end": null, + "v_rs_start": null, + "v_rs_end": null, + "v_gene_delineations": [ + { + "sequence_delineation_id": "1", + "delineation_scheme": "IMGT", + "aligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "unaligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "fwr1_start": 1, + "fwr1_end": 75, + "cdr1_start": 76, + "cdr1_end": 110, + "fwr2_start": 111, + "fwr2_end": 150, + "cdr2_start": 151, + "cdr2_end": 160, + "fwr3_start": 161, + "fwr3_end": 294, + "cdr3_start": 295, + "alignment": [ + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9", + "10", + "11", + "12", + "13", + "14", + "15", + "16", + "17", + "18", + "19", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "29", + "30", + "31", + "32", + "33", + "34", + "35", + "36", + "37", + "38", + "39", + "40", + "41", + "42", + "43", + "44", + "45", + "46", + "47", + "48", + "49", + "50", + "51", + "52", + "53", + "54", + "55", + "56", + "57", + "58", + 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"IGHD3-1*01_S1234", - "sequence": "agtagtagtagt", - "phasing": 1 - } - ], - "deleted_genes": [ - { - "label": "IGHV3-30-3", - "germline_set_ref": "IMGT:Homo sapiens:2022.1.31", - "phasing": 1 - } - ], - "inference_process": "repertoire_sequencing" - } - ] - } - ] + "allele_description_id": "OGRDB:A00314", + "allele_description_ref": "OGRDB:Mouse_IGH:IGHV-2ETO", + "maintainer": "William Lees", + "acknowledgements": [], + "lab_address": "Birkbeck College, University of London, Malet Street, London", + "release_version": 1, + "release_date": "24-Nov-2021", + "release_description": "First release", + "label": "IGHV-2ETO", + "sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC", + "coding_sequence": "CAAGTTACTCTAAAAGAGTCTGGCCCTGGGATATTGAAGCCCTCACAGACCCTCAGTCTGACTTGTTCTTTCTCTGGGTTTTCACTGAGCACTACTAATATGGGTGTAGGCTGGATTCGTCAGCCTTCAGGGAAGGGTCTGGAGTGGCTGGCACACATTTGGTGGGATGATGATAAGTACTATAACCCATCCCTGAAGAGCCGGCTAACAATCTCCAAGGATACCTCCAGAAACCAGGTATTCCTCAAGATCACCAGTGTGGACACTGCAGATACTGCCACTTACTACTGTGCTC", + "aliases": [ + "watson_et_al:CAST_EiJ_IGHV8-2" + ], + "locus": "IGH", + "chromosome": null, + "sequence_type": "V", + "functional": true, + "inference_type": "rearranged_only", + "species": { "id": "NCBITAXON:10090", "label": "Mus musculus" }, + "species_subgroup": "CAST_EiJ", + "species_subgroup_type": "strain", + "status": "active", + "gene_designation": null, + "subgroup_designation": null, + "allele_designation": null, + "gene_start": null, + "gene_end": null, + "utr_5_prime_start": null, + "utr_5_prime_end": null, + "leader_1_start": null, + "leader_1_end": null, + "leader_2_start": null, + "leader_2_end": null, + "v_rs_start": null, + "v_rs_end": null, + "v_gene_delineations": [ + { + "sequence_delineation_id": "1", + "delineation_scheme": "IMGT", + "aligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGA...GGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTC............AGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "unaligned_sequence": "GAAGTGAAGCTGGTGGAGTCTGAGGGAGGCTTAGTGCAGCCTGGAAGTTCCATGAAACTCTCCTGCACAGCCTCTGGATTCACTTTCAGTGACTATTACATGGCTTGGGTCCGCCAGGTTCCAGAAAAGGGTCTAGAATGGGTTGCAAACATTAATTATGAT......GGTAGTGGCACCTACTATCTGGACTCCTTGAAG...AGCCGTTTCATCATCTCGAGAGACAATGCAAAGAACATTCTATACCTGCAAATGAGCAGTCTGAAGTCTGAGGACACAGCCACGTATTACTGTGCAA", + "fwr1_start": 1, + "fwr1_end": 75, + "cdr1_start": 76, + "cdr1_end": 110, + "fwr2_start": 111, + "fwr2_end": 150, + "cdr2_start": 151, + "cdr2_end": 160, + "fwr3_start": 161, + "fwr3_end": 294, + "cdr3_start": 295, + "alignment": [ + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9", + "10", + "11", + "12", + "13", + "14", + "15", + "16", + "17", + "18", + "19", + "20", + "21", + "22", + "23", + "24", + "25", + "26", + "27", + "28", + "29", + "30", + "31", + "32", + "33", + "34", + "35", + "36", + "37", + "38", + "39", + "40", + "41", + "42", + "43", + "44", + "45", + "46", + "47", + "48", + "49", + "50", + "51", + "52", + "53", + "54", + "55", + "56", + "57", + "58", + "59", + "60", + "61", + "62", + "63", + "64", + "65", + "66", + "67", + "68", + "69", + "70", + "71", + "72", + "73", + "74", + "75", + "76", + "77", + "78", + "79", + "80", + "81", + "82", + "83", + "84", + "85", + "86", + "87", + "88", + "89", + "90", + "91", + "92", + "93", + "94", + "95", + "96", + "97", + "98", + "99", + "100", + "101", + "102", + "103", + "104" + ] + } + ], + "unrearranged_support": [], + "rearranged_support": [], + "paralogs": [], + "curation": "Imported to OGRDB with the following notes: watson_et_al: CAST_EiJ_IGHV8-2", + "curational_tags": null + } + ], + "curation": null + }], + + "GenotypeSet": [{ + "receptor_genotype_set_id": "1", + "genotype_class_list": [ + { + "receptor_genotype_id": "1", + "locus": "IGH", + "documented_alleles": [ + { + "label": "IGHV1-69*01", + "germline_set_ref": "IMGT:Homo sapiens:2022.1.31", + "phasing": 1 + }, + { + "label": "IGHV1-69*02", + "germline_set_ref": "IMGT:Homo sapiens:2022.1.31", + "phasing": 2 + } + ], + "undocumented_alleles": [ + { + "allele_name": "IGHD3-1*01_S1234", + "sequence": "agtagtagtagt", + "phasing": 1 + } + ], + "deleted_genes": [ + { + "label": "IGHV3-30-3", + "germline_set_ref": "IMGT:Homo sapiens:2022.1.31", + "phasing": 1 + } + ], + "inference_process": "repertoire_sequencing" + } + ] + }] } diff --git a/lang/python/NEWS.rst b/lang/python/NEWS.rst index 294c36c47..9699e04f5 100644 --- a/lang/python/NEWS.rst +++ b/lang/python/NEWS.rst @@ -1,3 +1,14 @@ +Version 1.5.0: August 31, 2023 +-------------------------------------------------------------------------------- + +1. Updated schema set and examples to v1.5. +2. Officially dropped support for Python 2. +3. Added check for valid enum values to schema validation routines. +4. Set enum values to first defined value during template generation routines. +5. Removed mock dependency installation in ReadTheDocs environments from setup. +6. Improved package import time. + + Version 1.4.1: August 27, 2022 --------------------------------------------------------------------------------